60th Annual Maize Genetics Conference
Program and Abstracts
March 22 – March 25, 2018
Palais du Grand Large
Saint-Malo, France
This conference received financial support from:
National Science Foundation
ANR/Amaizing
DuPont Pioneer
Syngenta
Monsanto
National Corn Growers Association
KWS SAAT AG
Bayer Crop Science
AGPM Maiz’Europ BASF Plant Science
Agro Paris Tech Caussade semences
INRA, BAP department Kenfeng Seed Co
Biogemma Euralis
Limagrain Maïsadour
Promaïs Benson Hill
We thank these contributors for their generosity!
Table of Contents
Cover Page ...................................................................................................................
i
Contributors ................................................................................................................. ii
Table of Contents ......................................................................................................... iii
General Information ..................................................................................................... iv
From the MGEC.............................................................................................................. v
Stewardship of Maize Data........................................................................................... vi
Useful Links ............................................................................................................... vii
MaGNET Awards ........................................................................................................ viii
Program ........................................................................................................................
List of Posters ..............................................................................................................
1
7
Abstracts:
Plenary Addresses ...................................................................................................
McClintock Awardee...............................................................................................
Short Talks ..............................................................................................................
Posters .....................................................................................................................
Author Index ...........................................................................................................
19
23
24
57
207
.
Participants .................................................................................................................... 219
History........................................................................................................................... 239
Cover image description
Male inflorescence (tassel) of the maize inbred line B73 at anthesis shedding pollen
grains.
Cover art by
Lele Wang
University of Regensburg,
Germany
General Information
Meeting Registration
Thursday:
12:30 PM to 10:00 PM : M ain Lobby Duguay Trouin
Friday:
8:00AM to 1:00 PM : M ain Lobby Duguay Trouin
Meals
All meals will be served plated in the Grand Large room, level 1; serving hours as listed in the Program. Coffee, tea, soft
drinks and snacks are available at no charge during the breaks that will be held in Poster rooms (levels 2 & 3) and J. Cartier
rotunda, level 1. Please wear your nametag as that will give you entrance into the facility as well as the meals.
Talks and Posters
All Talks will be presented in the Chateaubriand auditorium, level 0.
Posters will be presented in the Lamennais room, level 3 and Surcouf rotunda, level 2. Posters should be hung Thursday
starting at 3 PM and stay up until Sunday morning, but must be removed by 9 AM on Sunday. During poster sessions,
presenters of odd numbered posters are asked to stand by their posters 2:00-3:10 PM on Friday and 3:15-4:30 PM on
Saturday. Presenters of even numbered posters should stand by their posters 3:10-4:15 PM on Friday and 2:00-3:15 PM on
Saturday.
The maize meeting is a forum for presentation and discussion of unpublished material. Photographing or recording of talks
and posters is not allowed. Posting information about talks and posters on social media is allowed only if the author has
explicitly given permission to do so, which is indicated by the
symbol in the abstract book.
Hospitality
After the evening sessions on Thursday, Friday, and Saturday there will be informal socializing and poster gazing in the
Lamennais room, level 3 and Surcouf rotunda, level 2 with refreshments provided until 1 AM (3 free beverages will be
offered each evening among a selection of soft drinks, regional beers and wine). Wine & cheese tasting at no charge will be
organized on Friday evening. Additionally, on Saturday evening there will be music and dancing.
After 1 AM , the Bouvet room, level 1 will be available for continued socializing until 5 AM . This is a “private room” for
socializing and professional networking, and it is permissible for alcoholic beverages to be brought in; however, you must
stay in this room if you are carrying drinks, and please dispose of all trash and bottles in the room.
Steering Committee
Please share your suggestions and comments about the meeting with the 2018 Steering Committee
Alain Charcosset , Chair .... (alain.charcosset@moulon.inra.fr)
Mike Muszynski, co-Chair (mgmuszyn@hawaii.edu)
Erich Grotewold .................(grotewol@mail.msu.edu)
Karen McGinnis ................. (mcginnis@bio.fsu.edu)
Jianbing Yan ..................... (yjianbing@gmail.com)
Natalia de Leon ................ (ndeleongatti@wisc.edu)
Sylvia Sousa...................... (sylvia.sousa@embrapa.br)
Maike Stam ....................... (m.e.stam@uva.nl)
Andrea Eveland ................ (aeveland@danforthcenter.org)
T homas Slewinski ............ (thomas.l.slewinski@monsanto.com)
Andrea Gallavotti ............. (agallavotti@waksman.rutgers.edu)
Stephen Novak ................. (snnovak@dow.com)
Ex officio:
Carson Andorf
David Braun
Marty Sachs
Maud T enaillon, Local Host
.
Acknowledgements
We warmly thank John Portwood and Carson Andorf for their tremendous efforts in organizing, assembling, and advertising
the conference program. We are extremely grateful to Angela Freemyer and her team at the University of M issouri
Conference Office and Rozenn Le Guyader at GQE-Le M oulon for helping to organize the conference, handling registration
and dealing with a multitude of other issues. Special thanks are also extended to Sophie Fontaine, Aurélie Paris and Delphine
Bru and their team at the Palais du Grand Large, for their help in organizing this conference, and to Darwin Campbell and
John Portwood for providing AV and other support. Thanks go to Thomas Slewinski, Stephen Novak and Alain Charcosset
for their efforts in securing funding to support graduate student attendance at this meeting. Finally, many , many thanks go to
M aud Tenaillon for her work as local organizer and M arty Sachs for his wisdom in all things related to the M aize M eeting.
iv
From the Maize Genetics Executive Committee:
Chair: Karen Koch 2020, Paul Chomet 2017, Sherry Flint-Garcia 2017, Shawn Kaeppler 2018, Patrick Schnable 2018,
Kathy Newton 2019, Jianming Yu 2019, Natalia de Leon 2020, Tom Brutnell 2021, David Jackson 2021, and two new
members to be announced.
Awards:
The Early Career Maize Genetics Award will be given to an individual that has been in a permanent
position for less than 8 years. It is expected that the awardee will have made significant research
contributions through genetic studies of maize or related species. (See M aizeGDB)
The 2018 Awardee is James Schnable at the University of Nebraska.
The Mid-Career Maize Genetics Award will be given to an individual that has been in a permanent
position for 9-20 years. The winner will have an outstanding track record of discovery research in maize (or
related species) genetics. (See M aizeGDB)
The 2018 Awardee is M ike Scanlon at Cornell University.
New this year: The R.A. Emerson Award recognizes individuals for their extraordinary lifetime
achievements in maize genetics. Recipients of this award shall be leaders in the maize community who have
made seminal contributions to our understanding of maize genetics. To be eligible for this award, the
nominee should have held a permanent position for over 20 years. (See M aizeGDB)
The 2018 Awardee is Ed Coe at the University of M issouri. The award will be presented at the 2019 M aize
Genetics Conference in Saint Louis, along with a short overview of Ed Coe’s life and work.
The Barbara McClintock Prize for Plant Genetics and Genome S tudies has been created
to memorialize the unequalled contributions of Dr. M cClintock through p roviding
recognition to the most outstanding plant geneticists of the present era. In memory of the
many contributions of Dr. M cClintock, this Prize will be awarded each year to one or more
of the most creative minds and productive scientists in the study of plant genome structure,
function and evolution, including the analysis of gene regulation and epigenetics. The 2018
Awardee is Rob Martienssen who will present the McClintock Prize Address. The 2019 Awardee will be announced
at the meeting and will present the address next year (See M aizeGDB).
Defining the maize genetics community: Who are we?
5,000
4,033
3,063
2,500
0
Cooperators Conference
Attendees*
B. Maize Genetics Conference
composition (%)
Total people ( # )
A. Maize Genetics Cooperators
75
scientist
50
25
56%
student
29% postdoc
15%
0
The Maize Genetics Community:
A. Maize Genetics Cooperators. Total
number is based on the e-mail database
from MaizeGDB.org. The conference
attendees include meetings held in the
US from 2008 to 2017. Each attendee is
counted only once during this time.
B. Maize Genetics Conference attendee
composition. Data are from 2012 and
2015.
Attendee
NSF to fund future meetings and a Research Coordination Network for maize genetics:
The National Science Foundation has just notified the M GEC that support will be provided for a Research
Coordination Network (RCN) entitled, "Broadening and Energizing the M aize Genetics Research Community." In addition
to funding the next 5 years’ M aize Genetics Conferences, the RCN will include separate workshops on 1) Databases and
informatic tools, 2) Genetic resources and technologies, 3) Training, 4) Translating basic discoveries to commercial
products, and 5) Broadening community diversity, expertise, and international interface. The RCN effort was led by former
M GEC Chair, Shawn Kaeppler. Stay tuned for more information.
Planning for the coming year will be based on responses to the recent survey (from M GEC in February of this year).
Some outstanding suggestions and data emerged. These, together with additional information on the RCN will be discussed
at the Community Session of the M aize Genetics Conference this year and posted at M aizeGDB.
For those of you who provided the insightful replies to this year’s survey – Thank you!
v
Let’s Step Up Stewardship of Maize Data
Dear Maize Cooperators,
We are in an exciting time in biology with amazing new technologies and methods that lead to
exponentially more data! We imagine a time in the near future when it will be easy to find all data for a gene,
protein, or process with a few mouse clicks. But this will require changes in how we prepare, describe and
make available our data. We at MaizeGDB have been working closely with representatives from 25
agriculturally related databases to craft standards for data consistency and sharing. The maize community
has a real chance to lead in this effort. Let’s all become excellent stewards of our data, and show others how
good data management is done!
1. Put your sequences and genome assemblies in NCBI Databases.
NCBI (US), EBI (Europe), and DDBJ (Asia) provide stable, long-term databases for DNA, RNA and protein
sequence data and create stable identifiers (accessions) for datasets. These three share sequence data on a
daily basis. If your publication has any sequence data, make sure you submit it to NCBI, EBI, or DDBJ, and
list the accession number in your paper. Note that SNP data will have to be submitted to EBI’s EVA. If you
need help with whole genome assembly submissions, contact MaizeGDB.
2. Don’t rename genes that already have names.
Renaming genes that already have names is becoming a HUGE problem in maize, especially when an
existing name is reused for a different gene. Please look up your gene at MaizeGDB before assigning a
name, and follow the maize nomenclature guidelines. (https://www.maizegdb.org/nomenclature).
3. Attach complete and detailed metadata to your data sets.
When you deposit data, you are asked for information about your data. Please give this the same careful
attention you give to your bench work and analysis. Datasets that are not adequately described are not
reusable or reproducible, and raise questions about the carefulness and accuracy of the researcher.
4. Publish your data with your paper.
Sometimes your data are too large to publish as a table or supplementary material with your paper. These
data can be deposited in data repositories, which provide DOIs (stable identifiers). DOIs should be listed in
your paper.
5. Budget time for Data Management.
Please budget time to do a good job of managing your data.
6. Familiarize yourself with the FAIR data sharing standards.
To support the reuse of scholarly data, a group of data scientists have created a set of recommendations to
make data Findable, Accessible, Interoperable and Reusable.
https://www.force11.org/group/fairgroup/fairprinciples,
The MaizeGDB.org team
Contact us with any questions!
vi
Useful Links
2018 Maize Meeting Website
http://maizegdb.org/maize_meeting/2018
2019 Maize Meeting Website (Available November 2018)
http://maizegdb.org/maize_meeting/2019
Abstract Book (Electronic version)
http://maizegdb.org/maize_meeting/abstracts/2018Program.pdf
Cover Image
http://maizegdb.org/maize_meeting/coverart/
vii
The MaGNET Program and 2018 Awards
MaGNET (Maize Genetics Network Enhancement via Travel) is a program that seeks to recruit and
retain scientists from diverse backgrounds into the maize research community by encouraging their
attendance at the Annual Maize Genetics Conference (MGC). As such, it provides a source of support to
help students and early career scientists from under-represented groups learn about maize genetics and
connect with scientists already in the community. Awardees are not required to have previous maize genetics
research experience, but will hopefully develop an appreciation of the current excitement in the field, and
become an integral part of the community in the future. The program also provides an opportunity for
awardees to explore potential collaborations and develop career contacts.
Each MaGNET Award helps defray the cost of attending the Maize Genetics Conference, including
registration, food, lodging and airfare. In addition, awardees that have never attended the MGC are paired
with an experienced ‘Maize Mentor’, who will help the awardee navigate the conference. Awardees are
identifiable by a special notation on their name tags, and many of them are attending the MGC for the first
time – please congratulate these scientists and welcome them to our famously hospitable conference!
All applicants must show strong potential for a career in the biological sciences, be either citizens or
permanent residents of the USA, and belong to a group traditionally underrepresented in science. T o help
provide a more integrative and effective experience at the Conference for student awardees, faculty mentors
who accompany one or more eligible student applicants are also eligible to apply for a MaGNET award.
2018 MaGNET Awardees
Undergraduate
Estefania Aguilar-Gutierrez, California State University
Felicia Ebot-ojong, University of Georgia
Tiffany Boynton, Florida Agricultural and Mechanical University
Mohammed El-Walid, University of Missouri
Julia Owen, University of California Davis
Husain Agha, University of Missouri
Brieana Hollis, Florida A&M University
Graduate Student
Lamar Burton, Florida International University
Maria-Angelica Sanclemente, University of Florida
Poster #178
Poster #148
Poster #157
Poster #46
Mentor Accompanying Student
Gokhan Hacisalihoglu, Florida A&M University
Rajandeep Sekhon, Clemson University
Lolita Adkins, University of California
Kelly Swarts, Max Planck Institute for Developmental Biology
Arnaud Ronceret, Universidad Nacional Autónoma de México
Alexander Lipka, University of Illinois
Ramesh Katam, Florida A&M University
Katy Guthrie, University of Missouri
Poster #65
Poster #139
Talk #8
Poster #144
Poster #125
Poster #135
The MaGNET program of the Maize Genetics Conference is supported by grant IOS-1748978 from the
National Science Foundation.
viii
Schedule of Events
Talks will be held in the Chateaubriand auditorium.
Posters will be displayed in the Lamennais room and Surcouf rotunda.
Thursday, March 22
1:30 PM – 5:00 PM
OPTIONAL PRE-CONFERENCE WORKSHOPS
1:30 PM – 3:30 PM
1:30 PM – 3:30 PM
3:00 PM – 4:30 PM
3:30 PM – 5:00 PM
“Epigenetics”
“Maize tools & resources”
“Genetic transformation & editing”
“Maize genomes”
Maupertuis
Charcot
Chateaubriand
Maupertuis
Pre-registration recommended for the above sessions.
12:00 PM – 10:00 PM
REGISTRATION (Ground floor)
3:00 PM – 6:00 PM
POSTER HANGING (Lamennais & Surcouf)
6:00 PM – 7:15 PM
DINNER (Grand Large room)
7:30 PM – 9:25 PM
SESSION 1 – WELCOME / THE GENES THAT MAKE MAIZE
Chair: Alain Charcosset / Andrea Gallavotti Talks 1-5. Pages 24-28.
7:30 PM
WELCOME AND ANNOUNCEMENTS
7:45 PM
Thomas Widiez, INRA
[T1]
How to make maize seeds that look “not like dad”: insights in double
fertilization and prospects for novel breeding tools
8:05 PM
Nina Chumak, University of Zürich
Generating clonal progeny in maize
8:25 PM
Thu Tran, University of Missouri - Columbia
[T3]
Maize Carbohydrate partitioning defective33 functions in sucrose
export from leaves
8:45 PM
Phillip Conklin, Cornell University
NARROWSHEATH1 controls cell cycle dynamics to promote
mediolateral outgrowth of leaf primordia
9:05 PM
Keting Chen, Iowa State University
[T5]
Interrogating metabolic and transcriptomic networks to explain
genetic, developmental and environmental variation in the cuticular
lipid landscape on maize silks
9:30 PM – 1:00 AM
INFORMAL POSTER VIEWING & HOSPITALITY
(Lamennais & Surcouf rotunda, Hospitality in Bouvet room until 5 am)
1
(Chateaubriand)
[T2]
[T4]
Friday, March 23
8:00 AM – 1:00 PM
REGISTRATION (Ground floor)
8:30 AM – 10:40 AM
SESSION 2 – GENETIC ARCHITECTURE AND EVOLUTION
Chair: Jianbing Yan
Talks 6-11. Pages 29-34.
8:30 AM
ANNOUNCEMENTS
8:40 AM
Markus Stetter, University of California - Davis
[T6]
How polygenic adaptation during domestication shaped the genetic
architecture of maize
9:00 AM
Christine Dillmann, Université Paris-Saclay
[T7]
Twenty years of divergent selection for flowering time from maize
inbred lines
9:20 AM
Kelly Swarts, Max Planck Institute
Prehistoric selection for temperate climates has far-reaching
implications for global germplasm
9:40 AM
Aaron Kusmec, Iowa State University
[T9]
Distinct genetic architectures for phenotype means and plasticities in
Zea mays
10:00 AM
Jie Liu, Huazhong Agricultural University
[T10]
The conserved and unique genetic architecture of kernel size and
weight in maize and rice
10:20 AM
Jinyu Wang, Iowa State University
[T11]
Genome-wide nucleotide divergence and UV induced mutations
following maize domestication
10:40 AM
BREAK
11:10 AM – 12:55 PM
SESSION 3 – PLENARY TALKS
Chair: Michael Muszynski
(Chateaubriand)
[T8]
Pages 19 & 20.
11:10 AM
Introduction
(Chateaubriand)
11:15 AM
Magnus Nordborg, Gregor Mendel Institute
Epigenetic variation in Arabidopsis
12:05 PM
Francois Tardieu, INRA Montpellier
[PL2]
Drought tolerance: which mechanisms, traits and alleles for which
drought scenarios?
2
[PL1]
Friday, March 23 (continued)
1:00 PM – 2:00 PM
LUNCH (Grand Large room)
2:00 PM – 4:15 PM
POSTER SESSION 1 (Lamennais & Surcouf rotunda)
2:00 PM – 3:10 PM
Presenters should be at odd numbered posters.
3:10 PM – 4:15 PM
Presenters should be at even numbered posters.
Beverages will be available from 3:30 PM in Poster rooms & Jacques Cartier rotunda.
4:15 PM – 5:35 PM
SESSION 4 – EMERGING TOOLS AND CHALLENGES
Chair: Erich Grotewold
Talks 12-15. Pages 35-38.
4:15 PM
Kokulapalan Wimalanathan, Iowa State University
Maize - GO Annotation Methods Evaluation and Review
(Maize-GAMER)
4:35 PM
Mary Galli, Rutgers University
[T13]
Using DAP-seq to map genome-wide ARF transcription factor binding
events in maize
4:55 PM
En Li, China Agricultural University
[T14]
Long-range interactions provide a topological basis for genetic
regulation of complex traits in maize
5:15 PM
Samuel Leiboff, University of California - Berkeley
[T15]
The RNAseq Time Machine: Species-specific shifts in developmental
timing and trajectory underlie morphological differences in maize
tassel and sorghum panicle architecture
5:35 PM – 7:25 PM
SESSION 5 – PLENARY TALKS
Chair: Alain Charcosset
[T12]
Pages 21 & 22.
5:35 PM
Introduction
5:45 PM
Ortrun Mittelsten Scheid, Gregor Mendel Institute
[PL3]
Light control of seed germination: the unusual role of usual suspects
6:35 PM
Jeff Ross-Ibarra, University of UC Davis
A bad genetic history of maize
7:30 PM – 8:45 PM
(Chateaubriand)
[PL4]
DINNER (Grand Large room)
8:50 PM – 1:00 AM
INFORMAL POSTER VIEWING & HOSPITALITY
(Wine & Cheese tasting in Lamennais & Surcouf rotunda, Jacques Cartier rotunda, Hospitality in
Bouvet room until 5 am)
3
Saturday, March 24
8:30 AM – 10:30 AM
SESSION 6 – INTERACTIONS WITH THE ENVIRONMENT
Chair: Natalia de Leon
Talks 16-21. Pages 39-44.
8:30 AM
ANNOUNCEMENTS
(Chateaubriand)
8:40 AM
Sylvia Morais de Sousa, Embrapa Milho e Sorgo
Enhancing phosphorus efficiency in maize and sorghum
9:00 AM
Laurie Maistriaux, Université catholique de Louvain
[T17]
Regulation of aquaporin expression in maize: proximal and distal
eQTLs
9:20 AM
Justin Blancon, BIOGEMMA
[T18]
Innovative and high-throughput field phenotyping method provides leaf
traits for breeding of drought tolerance - From Leaf Area Index
dynamics to its physiological components
9:40 AM
Joerg Degenhardt, Martin Luther University Halle
[T19]
Characterization of biosynthetic pathways and regulatory elements for
the production of the volatile homoterpenes DMNT and TMTT in Zea
mays
[T16]
10:00 AM
Marcel Bucher, University of Cologne
Mycorrhizal phosphate uptake affects maize root-associated
microbiota
10:20 AM
Katherine Murphy, University of California - Davis
[T21]
Discovery of dolabralexins, previously unrecognized terpenoid defense
compounds in maize (Zea mays).
10:40 AM
BREAK
11:15 AM – 12:55 PM
[T20]
SESSION 7 – EXPRESSING THE GENOME
Chair: Andrea Eveland
Talks 22-26. Pages 45-49.
11:15 AM
Jacob Washburn, Cornell University
[T22]
Predicting across the central dogma of molecular biology: DNA to
mRNA abundance
11:35 AM
Bradlee Nelms, Stanford University
[T23]
Mapping the archesporial cell to meiocyte progression using single-cell
RNA-Seq
11:55 AM
Jutta Baldauf, University of Bonn
[T24]
Single parent expression is a general mechanism driving extensive
complementation of non-syntenic genes in maize hybrids
12:15 PM
Edoardo Bertolini, Donald Danforth Plant Science Center
[T25]
The regulatory landscape of developing maize inflorescences: linking
phenotypic variation to the functional non-coding genome
4
Saturday, March 24 (continued)
12:35 PM
Lu Chen, Huazhong Agricultural University
Circular RNAs mediated by transposons are associated with
transcriptomic and phenotypic variation in maize
1:00 PM – 2:00 PM
LUNCH (Grand Large room)
2:00 PM – 4:30 PM
POSTER SESSION 1 (Lamennais & Surcouf rotunda)
2:00 PM – 3:15 PM
Presenters should be at even numbered posters.
3:15 PM – 4:30 PM
Presenters should be at odd numbered posters.
[T26]
Beverages will be available from 3:30 PM in Poster rooms & Jacques Cartier rotunda.
4:30 PM – 5:30 PM
COMMUNITY SESSION - Maize Genetics Executive Committee
MGEC Chair: Karen Koch
(Chateaubriand)
5:30 PM – 7:30 PM
SESSION 8 – AWARDS AND MCCLINTOCK PRIZE
PRESENTATION
Chair: Karen Koch
Page 23.
5:30 PM
Karen Koch, MGEC Chair
Early- and Mid-Career Award, announcement of Emerson Award
5:45 PM
Paul Chomet, NRGene
McClintock Prize Presentation
6:00 PM
Rob Martienssen, Cold Spring Harbor Laboratory
Germline reprogramming, epigenetic inheritance and small RNA: how
to avoid Bad Karma
6:50 PM- 7:50 PM
Musical entertainment by Pao Bran and cocktails (Jacques Cartier
rotunda)
8:00 PM – 9:50 PM
GALA DINNER (Grand Large room)
10:00 PM – 1:00 AM
INFORMAL POSTER VIEWING/DANCE & HOSPITALITY
(Lamennais & Surcouf rotunda, Music by Vincent Gaillard in Jacques Cartier rotunda,
Hospitality in Bouvet room until 5 am)
2:00 AM
Daylight Savings Time begins in EU. Change time to 3:00 AM.
5
Sunday, March 25
Posters should be taken down by 9 am!
TIME CHANGE!! Please remember in the EU daylight-savings time starts today: at 2:00
AM the time changes to 3:00 AM:
9:00 AM – 10:20 AM
SESSION 9 – THE MAIZE (EPI)GENOMES
Chair: Maike Stam
Talks 27-30. Pages 50-53.
9:00 AM
Daniel Grimanelli, Université de Montpellier
[T27]
Dynamics of DNA methylation during maize reproductive development
9:20 AM
Sarah Anderson, University of Minnesota
[T28]
Transposable element contributions to the dynamic maize genome and
transcriptome
9:40 AM
Stephen Moose, University of Illinois
The evolutionary dynamics of maize small RNAs reveals novel
regulatory features in noncoding DNA
[T29]
10:00 AM
Adele Zhou, Cornell University
[T30]
Chromatin as a major determinant in the fate of meiotic double-strand
breaks and positioning of COs along maize chromosomes
10:20 AM
BREAK
10:50 AM – 12:00 PM
SESSION 10 – COMMUNICATING WITHIN AND BETWEEN
CELLS AND PLANTS
Chair: Thomas Slewinski
Talks 31-33. Pages 54-56.
10:50 AM
Michael Muszynski, University of Hawaii
[T31]
Dissecting a new connection between cytokinin and jasmonic acid in
control of leaf growth
11:10 AM
Gerrit Beemster, University of Antwerp
[T32]
How grass keeps growing: a predictive model of leaf growth regulation
based on studies in Zea mays
11:30 AM
Hannes Claeys, Cold Spring Harbor Laboratory
[T33]
TREHALOSE-6-PHOSPHATE PHOSPHATASE4, a paralog of
RAMOSA3, controls inflorescence architecture and shoot apical
meristem activity in maize
11:50 PM
CLOSING REMARKS
12:00 PM
ADJOURNMENT
6
Posters
Computational and Large-Scale Biology
P1
Joseph Gage
<jgage2@wisc.edu>
P2
Anne Lorant
<alorant@ucdavis.edu>
P3
Kokulapalan Wimalanathan
<kokul@iastate.edu>
P4
Kelly Dawe
An expanded diversity panel reveals the magnitude of the maize
pan-genome and limitations of a single-reference genome sequence
for GWAS
Both hard and soft sweeps contribute to local adaptation of natural
populations of teosintes
Bulked Segregant - genotyping-by-sequencing: Cost-effective and
background independent genetic mapping of mutants and QTL
Coming soon: Whole genome assembly of the maize NAM founders
<kdawe@uga.edu>
P5
Jerald Noble
<jnoble333@ufl.edu>
P6
Ian Braun
<irbraun@iastate.edu>
P7
Johann Joets
<johann.joets@inra.fr>
P8
Eva Bauer
<e.bauer@tum.de>
P9
Jiaqiang Dong
Comparing alternative splicing in maize using 4 different reference
genomes
Computational classification of phenologs across biological
diversity
Deciphering molecular origin and functional impact of structural
variation in maize through genome sequences comparison and
integrative analysis of genetic variation, transcriptome and
phenotype data.
Four European Flint reference sequences complement the maize
pan-genome
Functional analysis of maize kernel development
<jd1077@waksman.rutgers.edu>
P10 Jan Freudenthal
Genomic prediction using TensorFlow
<jan.freudenthal@uniwuerzburg.de>
P11 Marcela Karey Tello-Ruiz
Gramene maize pan-genome browser
<mmonaco@cshl.edu>
P12 Tessa Durham Brooks
<tessa.durhambrooks@doane.edu>
P13 John Fernandes
<john.fernandes@stanford.edu>
P14 Jing Wang
Growth and metabolic responses of NAM parent lines to a brief
exposure to cold during early seedling development
High level analysis of W23 and A619 genomes (sequenced by
Novogene) compared to B73 reference
High resolution temporal and spatial transcription atlas of maize.
<1964263754@qq.com>
P15 Jin Cui
<juc326@psu.edu>
P16 Jesse Walsh
Maize Ufo1 mutant plays a role in epigenetic regulation and
alternative splicing
Functional divergence in maize subgenomes
<jesse.walsh@ars.usda.gov>
P17 Ethalinda Cannon
<Ethy.Cannon@ars.usda.gov>
P18 Jack Gardiner
MaizeGDB: stewardship for maize genome assemblies and
annotation
MaizeMine: a data mining warehouse for MaizeGDB
<jack.m.gardiner@gmail.com>
P19 Lisa Harper
<lisaharper@me.com>
P20 John Portwood
Making YOUR data and databases FAIR; Functional gene
annotation and more!
MaizeGDB: new resources for maize researchers
<john.portwood@ars.usda.gov>
P21 Marcela Karey Tello-Ruiz
Mining maize with Gramene
<mmonaco@cshl.edu>
7
P22 Savannah Savadel
<sds14d@my.fsu.edu>
P23 Eve Wurtele
MOA (MNase Open Access) mapping: A new and efficient method
for genome-wide open chromatin profiling in maize, demonstrated
with developing earshoots
New software to identify and explore the orphan genes of maize
<mash@iastate.edu>
P24 Georg Basler
Organ-specific maize metabolic models from ensemble modelling
<basler@mpimp-golm.mpg.de>
P25 Xiang Gao
<caugxiang@163.com>
P26 Urte Schlüter
Parallel transposase tagging (PTT-seq) technology is a costeffective alternative for traditional Sanger sequencing
Predicting crop leaf parameter from leaf reflectance spectra
<u.schlueter@hhu.de>
P27 Jun Zhao
<zhaojun01@caas.cn>
P28 Lifang Zhang
Regulatory networks and kernel length related genes identified by
eQTL analysis in 5 DAP maize kernels
Regulatory Networks Governing Nitrogen Use Efficiencyt in Maize
<zhangl@cshl.edu>
P29 Johann Joets
<johann.joets@inra.fr>
P30 Jianing Liu
<jl03308@uga.edu>
P31 A. Mark Settles
<settles@ufl.edu>
P32 Patrick Monnahan
<pmonnaha@umn.edu>
P33 Hank Bass
<bass@bio.fsu.edu>
P34 Peter Bradbury
<pjb39@cornell.edu>
P35 Junpeng Shi
Sequence analysis of european maize inbred line F2 provides new
insights into molecular and chromosomal characteristics of
presence/absence variants.
Sequence shattering and chromothripsis-like genome
rearrangements following biolistic transformation in rice and
maize
Soil-based machine vision seedling emergence assay for studying
cold tolerance in maize
Structural variation analysis in the Wisconsin Diversity Panel
using multiple de novo genome assemblies
The NUPRIME project: nuclease profiling of four reference tissues
as a resource for maize epigenomics.
The practical haplotype graph: using a simplified pan-genome to
impute genotypes from skim sequence
Tracing the heritability of agronomic traits in maize
<shijunpeng_cau@163.com>
P36 Christine Gault
<cg449@cornell.edu>
P37 Alexandra Asaro
<aasaro@wustl.edu>
Tripsacum de novo transcriptome assemblies reveal parallel gene
evolution in maize and Tripsacum after ancient polyploidy
Using two parent genome mapping to identify expression level
quantitative loci in maize roots
Biochemical and Molecular Genetics
P38 Bertrand Hirel
<bertrand.hirel@inra.fr>
P39 Peng Liu
<mcliup@ufl.edu>
P40 Margaret Bezrutczyk
<Margaret.Bezrutczyk@hhu.de>
P41 Norman Best
<bestn@missouri.edu>
P42 Viviane Cristina Heinzen da
Silva
A system biology approach to identify biochemical markers
representative of high yielding maize lines
An opaque phenotype and altered mitochondrial respiratory chain
are caused by a maize rug3 mutation
Apoplasmic phloem loading in Zea mays L. requires three SWEET
sucrose transporters
barren stalk3 is required for axillary branch development and
maps to the same location as barren stalk2.
Biochemical and structural characterization of a new maize
receptor-like kinase likely involved in drought stress.
<vchsilva@gmail.com>
P43 Zhihong Lang
<langzhihong@caas.cn>
Characterization and functional analysis of maize Terpene
synthetase6 (TPS6) Gene
8
P44 David Braun
Cloning and characterization of a gene which disrupts
carbohydrate partitioning in maize
P45 Nathan Swyers
Development of an amenable system for site-specific addition to a
<ncs89f@mail.missouri.edu>
maize B-Chromosome
P46 Maria-Angelica Sanclemente Effect of sugar levels on the low oxygen response of maize roots
<braundm@missouri.edu>
<sanangelma@gmail.com>
P47 Lei Wang
Effect of water-deficit on phenotypes and transcriptomes of
developing tassel in maize
P48 Nick Ferrigno
Elucidating the transcriptional regulatory network controlling
<nferrigno@mail.smcvt.edu>
SUT and SWEET genes in maize
P49 Borrelli Marocco
Enhancement of maize disease resistance by CRISPR/Cas9 editing
<virginiamaria.borrelli@unicatt.it > of LOX and WRKY genes
P50 Senlin Xiao
Exploration of the molecular mechanism of CMS-S
<wanglei01@caas.cn>
<forestxiao@genetics.ac.cn>
P51 Britney Moss
<mossbl@whitman.edu>
P52 Samuel Hokin
<shokin@carnegiescience.edu>
P53 Isabelle Quilleré
<isabelle.quillere@inra.fr>
P54 Xiaowen Shi
<shix@missouri.edu>
P55 haiyang wang
<wanghaiyang@caas.cn>
P56 Jacob Washburn
<jdw297@cornell.edu>
P57 Michiel Bontinck
<mibon@psb.ugent.be>
P58 Vincenzo Rossi
Functional characterization of maize auxin signaling modules in
yeast
GBS identification of genomic loci associated with embryo twins in
ig1 mutants
Genetic variability for nitrate uptake in a core collection of
European and American maize (Zea mays L.) lines.
Genome imbalance impacts global gene expression and small RNA
expression in maize
Genomic analyses of the genetic basis for shaping maize plant
architecture for adapting to increased planting density
Heritable differences in C4 photosynthetic sub-type across diverse
maize germplasm indicate utility in discover and breeding
High resolution interactomics in the maize leaf growth zone, using
AN3 as a case-study
INDETERMINATE1 direct targets and regulatory mechanisms
<Vincenzo.Rossi@crea.gov.it >
P59 Gibum Yi
<gibumyi@gmail.com>
P60 Heidi Kaeppler
<hfkaeppl@wisc.edu>
P61 Jacob Corll
<jbcorll123@gmail.com>
P62 Claudiu Niculaes
Investigating seed mineral composition of Korean landrace corns
(Zea Mays L.)
Maize genomics, genetic engineering and gene editing research
and services at the Wisconsin Crop Innovation Center
Maize RNA Binding Motif Protein48 (RBM48) is required for
minor intron splicing and promotes endosperm cell differentiation
Maximizing photosynthesis efficiency in maize
<claudiu.niculaes@tum.de>
P63 Bing Liu
<bl472@cornell.edu>
P64 Jing Wang
<1964263754@qq.com>
P65 Gokhan Hacisalihoglu
<gokhan.h@famu.edu>
P66 Rentao Song
<rentaosong@cau.edu.cn>
P67 Jennifer Arp
<jarp@danforthcenter.org>
P68 Giulia Castorina
<giulia.castorina@unimi.it >
Meiotic recombination landscape in maize: impact of chromosome
axis and heat stress
Miniature seed 2109 encodes a nitrate transporter protein
required for maize seed development.
Modulation of cold sensitivity and early seedling performance by
priming in 27 maize NAM parental inbred lines
Opaque11 is a central hub of the regulatory network for maize
endosperm development and nutrient metabolism
Phosphoenolpyruvate carboxykinase mutants reveal interaction of
C4 photosynthesis and nitrogen utilization in maize
Regulation of cuticle deposition during juvenile vegetative phase in
maize
9
P69 Uta Paszkowski
<up220@cam.ac.uk>
P70 Jon Cody
Rhizosphere signaling in arbuscular mycorrhizal symbiosis of
maize.
Site specific recombinases: Tools for genetic engineering in maize
<joncody@mail.missouri.edu>
P71 Changsheng Li
Strigolactone biosynthesis in Zea mays (maize)
<c.li3@uva.nl>
P72 Jun Yang
<yangjun@sibs.ac.cn>
P73 John Gray
<john.gray5@utoledo.edu>
P74 Fadi El Hage
<fadi.el-hage@inra.fr>
P75 Marcel Baer
<Marcel.Baer@uni-bonn.de>
P76 Aleksej Abramov
<aleksej.abramov@tum.de>
P77 Miaoyun Xu
<xumiaoyun@caas.cn>
P78 Chaobin Li
The maize Oxalyl-CoA Decarboxylase1 acting downstream of
Opaque7 is required for oxalate degradation and central
metabolism and affects seed nutritional quality
The maize TFome and the GRASSIUS database: Resources for
regulomics in the grasses
Tissues lignification, cell wall p-coumaroylation and degradability
of maize stems depend on water status
Validation and functional characterization of the maize
lateralrootless 1 (lrt1) gene
Why does maize produce benzoxazinoids and transgenic
Arabidopsis not?
Zma-miR169q/NF-YA14 module is involved in salt stress tolerance
in maize
ZmbZIP22 is a new transcription factor for 27-kD γ-zein gene
<chaobinli@cau.edu.cn>
Cell and Developmental Biology
P79 Francois Tardieu
<francois.tardieu@inra.fr>
P80 Wei Huang
<wilsonhuang23@cau.edu.cn>
P81 Tom Van Hautegem
<tohau@psb.vib-ugent.be>
P82 David Perez
<Dp15g@my.fsu.edu>
P83 Qiujie Liu
<qiujieliu@waksman.rutgers.edu>
P84 Kyle Swentowsky
<kws67291@uga.edu>
P85 Wenjing She
A phenomics-based dynamic model of growth and yield to simulate
hundreds of maize hybrids in the diversity of European
environments
A point mutation in maize hzMS1 gene causes the meiosis defects
in heterozygous mutants
Analysis of leaf growth under mild drought in maize recombinant
inbred lines.
Bioremediation analysis of water pollutants and pathogens within
household water in rural south India
Characterization and cloning of needle1 (ndl1), a temperature
sensitive mutant affecting reproductive organogenesis
Characterization of a novel Kinesin protein required for Ab10
meiotic drive
Characterization of meiotic defects in the maize nrf4 mutant
<wenjing.she@uzh.ch>
P86 Edgar Demesa-Arevalo
<edemesaa@cshl.edu>
P87 Gabriella Consonni
<gabriella.consonni@unimi.it >
P88 Marschal Bellinger
<mbell008@ucr.edu>
P89 Laurens Pauwels
Characterization of RAMOSA3 putative nuclear interactors and
their role in inflorescence development in maize
Characterization of the maize lil1-1 mutant defective in the
Brassinosteroid C-6 oxidase
Characterizing the function of kinectin in plants via Zea mays and
Arabidopsis thaliana
CRISPR/Cas9 gene editing in the maize inbred line B104
<lapau@psb.vib-ugent.be>
P90 Bénédicte Bakan
<benedicte.bakan@inra.fr>
P91 Kamila Kalinowska-Brandt
<kamila.kalinowska@ur.de>
Deposition of lipids in starch granules of maize endosperm is
closely related to zein synthesis and programmed cell death
DiSUMO-LIKE interacts with cell cycle and RNA pathways, and
regulates early embryo development in maize
10
P92 Travis Hattery
<thattery@iastate.edu>
P93 Yongrui Wu
<yrwu@sibs.ac.cn>
P94 Angus Vajk
Diversity in the surface lipid composition of maize silks among
Wisconsin Diversity Panel inbreds in two environments
early delayed kernel 1 (edk1) encodes a microtubule-located
protein essential for early endosperm development in maize
fun is: pleiotropy, unknown genes and double mutants
<vajking@berkeley.edu>
P95 lele wang
<lele.wang@ur.de>
P96 Jara Oppenheimer
Functional analysis of pollen-specific RALFs during reproduction
in maize
Functional analysis of the heterotrimeric Gγ subunits in maize
<jara.oppenheimer@unihamburg.de>
P97 Xingli Li
<xingli.li@ur.de>
P98 Chao Bian
<chao.bian@rutgers.edu>
P99 Beth Thompson
Functional characterization of male gametophyte genes under heat
stress
Functions of PP2A phosphatases in Arabidopsis stomatal
development
Genetic control of maize floral development
<thompsonb@ecu.edu>
P100 Santiago Alvarez Prado
<santiago.alvarez-prado@inra.fr>
P101 Dong Zhaobin
<dongz@berkeley.edu>
P102 Xiaoli Ma
<xiaoli.ma@uni-tuebingen.de>
P103 Claude Welcker
<claude.welcker@inra.fr>
P104 Kevin Begcy
<kevin.begcy@ur.de>
P105 Xiaolong Tian
<cautxl@163.com>
P106 Laurine Gilles
<laurine.gilles@ens-lyon.fr>
P107 Hardeep Gumber
<hardeep@bio.fsu.edu>
P108 Joke De Jaeger-Braet
<joke.jaeger-braet@unihamburg.de>
P109 Yanfang Du
Genetic control of stomatal conductance in maize and conditional
effects to water deficit and evaporative demand as revealed by
phenomics
Genetic mechanisms for bud suppression during maize
domestication
Genome-wide analysis of small RNA-controlled gene networks in
leaf development
Grain abortion under drought in maize: expansive growth and
hydraulics also matter
Heat stress induced male sterility during pollen development in
maize
Hetero-fertilization along with failed egg-sperm cell fusion reveals
single fertilization involved in in vivo haploid induction in maize
How to make maize seeds that look “not like dad”: insights in
double fertilization and prospects for novel breeding tools.
Identification and characterization of LINC complex proteins in
Zea mays L.
Identification of the translational landscape of Arabidopsis and
Maize meiocytes
Integrated analysis of protein abundance, transcript level, and
<yanfangdu@webmail.hzau.edu.cn> tissue diversity to reveal developmental regulation of maize
P110 Annis Richardson
Keeping Separate: mysterious boundaries and the grass leaf
<annisrichardson@berkeley.edu>
P111 Muriel Longstaff
<mtlongstaff@gmail.com>
P112 Madelaine Bartlett
<mbartlett@bio.umass.edu>
P113 Ching-Chih Tseng
<tsengyin@gate.sinica.edu.tw>
P114 Alyssa Anderson
Kinetic and morphological tiller meristem development in
domesticated and wild Setaria
Leveraging next-generation sequencing technology for rapid gene
cloning
MAC1 and AM1 play critical but independent roles to regulate the
mitosis-to-meiosis transition of pollen mother cells in maize
Maize genetics at the intersection of development and immunity
<alyssa.amy@berkeley.edu>
11
P115 Josh Strable
Maize leaf primordia microdomains show genetic signatures of
proximal-distal boundary patterning
P116 Robert Maple
Male-specific argonaute (MAGO) proteins are necessary for
<R.Maple@warwick.ac.uk>
meiosis in maize
P117 Fatma Aydinoglu
MicroRNAs targeting developmental transcription factors control
<faydinoglu@gtu.edu.tr>
maize leaf size by switching cell proliferation to cell expansion
P118 Lei Ding
Modification of the expression of PIP2;5 plasma membrane
<lei.ding@uclouvain.be>
aquaporin affects maize water relations and growth
P119 Mario Arteaga-Vazquez
MOP1 regulates germline specification and gamete development in
<maarteaga@uv.mx>
maize
P120 Yang-Seok Lee
Movement of premiotic phased small-interfering RNAs
<Y.Lee.6@warwick.ac.uk>
(phasiRNAs) is essential for male meiosis in maize
P121 Steffen Knauer
Natural variation in the molecular circuitry underlying cell type
<steffen.knauer@uni-tuebingen.de> specification drives key plant architectural traits in maize
P122 Matthew Warman
nop genes promote pollen tube growth in the maize male
<warmanma@oregonstate.edu>
gametophyte
P123 Karina van der Linde
Pursuing maize (Zea mays) tassel development by small RNA
<karina.van-der-linde@ur.de>
sequencing, transcriptomics, and proteomics
P124 Max Braud
Redundant roles of two paralogous INDETERMINATE DOMAIN
<mbraud@danforthcenter.org>
(IDD) transcription factors in maize development
P125 Ramesh Katam
Relative abundance of Proteins to Multiple stresses suggests
<ramesh.katam@famu.edu>
Cross-Tolerance Mechanism in Soybean
P126 Didier Marion
Responses to hypoxia and endoplasmic reticulum stress:
<didier.marion@inra.fr>
relationships with vitreousness of maize endosperm
P127 Natalie Deans
RMR12 is a CHD3 nucleosome remodeler required for
<deans.11@osu.edu>
maintaining paramutations and normal development
P128 Oscar Sanz Mora
Role of introns in the correct expression of the meiotic cyclin
<osanz.osm@gmail.com>
SOLO DANCERS (SDS) of maize in A. thaliana
P129 Jack Satterlee
Search for genetic modifiers of knotted1
<jjs369@cornell.edu>
<jws429@cornell.edu>
P130 China Lunde
<lundec@berkeley.edu>
P131 Jack Satterlee
<jws429@cornell.edu>
P132 Silvio Salvi
Sex and violence: the classic maize mutant Tasselseed5 is encoded
by a wound-responsive JA-inactivating enzyme
Single Cell Transcriptomic Analysis of the Developing Maize
Embryo
The genetic control of a new tassel seed mutant in maize
<silvio.salvi@unibo.it>
P133 Michaela Matthes
<matthesm@missouri.edu>
P134 Dave Stateczny
The role of boron in vegetative and reproductive development in
maize
The role of CT2 in maize internode development
<dave.stateczny@uni-hamburg.de>
P135 Katherine Guthrie
<klgdn2@mail.missouri.edu>
P136 Thomas Hughes
The role of maize mutant Suppressor of sessile spikelets 2 (Sos2) in
meristem maintenance
The role of ZmSCR1 and ZmSCR1h during maize leaf development
<thomas.hughes@plants.ox.ac.uk>
P137 Janlo Robil
<jmrobil@mail.mizzou.edu>
P138 Peng Yu
<yupeng@uni-bonn.de>
The scarecrow mutation enhances auxin-related leaf and
inflorescence defects in maize
Tissue- and cell-specific multi-omics analyses define a key
molecular pathway of lateral root initiation and its interaction with
arbuscular mycorrhizal fungi in maize
12
P139 Rajandeep Sekhon
<sekhon@clemson.edu>
P140 Martina Balboni
Towards a comprehensive understanding of genetic architecture
underlying senescence
Towards live imaging of meiosis in maize
<martina.balboni@uni-hamburg.de>
P141 Matthew Warman
<warmanma@oregonstate.edu>
P142 Vasco Köhling
<vasco.koehling@gmx.de>
Transcriptomic characterization of male sexual reproduction in
maize
Transient interaction analysis of the Zea mays (L.) CT2 and
PLDα1 proteins in Nicotiana benthamiana (L.)
Cytogenetics
P143 Ding Hua Lee
<dinghua@gate.sinica.edu.tw>
P144 Arnaud Ronceret
AFD1 and DSY2 are both required for chromosomal localization
of ASY1 and meiotic double-strand break formation in maize
Analysis of ten meiotic mutants of maize
<ronceret@ibt.unam.mx>
P145 Natalie Nannas
Dynamics of meiotic spindle assembly in Zea mays
<njnannas@hamilton.edu>
P146 Jodi Weiss
<jdweiss@hamilton.edu>
P147 Olivier Martin
<olivier.c.martin@inra.fr>
P148 Mohamed El-Walid
<mze99d@mail.missouri.edu>
Frequency of abnormal chromosome 10 in tropical landraces of
Zea mays
Meiotic crossovers in maize: the interfering and non-interfering
recombination pathways have different landscapes
Visualizing plastid sequences present on the B Chromosome of
maize
Education & Outreach
P149 Irina Makarevitch
<imakarevitch01@hamline.edu>
P150 Josiane Lorgeou
<j.lorgeou@arvalis.fr>
P151 Francis Denisse McLean
Rodriguez
Doing genetics research in the classroom: CRISPR-Cas9 and cold
stress in plants
Evaluation of genetic progress in grain and silage corn afforded
by the renewal of varieties in France over the past 30 years
Fifty years of mirrored in situ and ex situ conservation of Mexican
maize landraces: socioeconomic dynamics and genomic diversity
<f.mcleanrodriguez@sssup.it >
P152 Denise Costich
<d.costich@cgiar.org>
P153 Denise Costich
<d.costich@cgiar.org>
P154 Hyeyoung Lee
Learning how to rescue a landrace: A study of the giant maize,
Jala, and the community who grows it
The maize collection of CIMMYT’s germplasm bank: promoting
the conservation, use and study of diversity
NSF Plant Transformation Workshop
<leehye@missouri.edu>
P155 Cristina Marco
Maize annotation jamboree on last B73 RefGen_V4 assembly
<marco@cshl.edu>
Quantitative Genetics & Breeding
P156 Lorenzo Stagnati
<lorenzo.stagnati@unicatt.it>
P157 Husain Agha
<hiagha@mail.missouri.edu>
P158 Clement Buet
<clement.buet@biogemma.com>
P159 Matthieu Bogard
<m.bogard@arvalis.fr>
A candidate gene approach to identify markers associated to
Fusarium Kernel Rot resistance in maize
A Novel Mating Design Provides High Power to Detect Epistasis
in Maize
A RNA-Seq atlas on the founder lines of the MAGIC population
“BALANCE”, a supplementary tool for gene discovery
Agronomic trials characterization and clustering using water and
nitrogen stress indices simulated with a crop model
13
P160 Alain Charcosset
<alain.charcosset@inra.fr>
P161 Jorge Nieto-Sotelo
<jorge.nieto@ib.unam.mx>
P162 Clément Buet
<clement.buet@biogemma.com>
P163 Violeta Andjelkovic
<avioleta@mrizp.rs>
P164 Lucio Conti
<lucio.conti@unimi.it >
P165 Randall Wisser
<rjw@udel.edu>
P166 Junjie Zou
<zoujunjie@caas.cn>
P167 Torsten Pook
AMAIZING, a project on Maize Integrative Genomics supported by
the French Investment for the Future Program
Analyses of genetic variation associated to deep planting
resistance in maize revealed genes controlling development,
growth, and adaptation to soil conditions
BALANCE, a powerful MAGIC population for the identification of
genetic determinants involved in the variation of traits of interest
in maize
Changes in carotenoid and tocopherol content in maize grain
during cold storage
Co-regulation of ZCN8 and ZCN12 underlies Maize flowering
variability
Computer-vision into the biology of fungal-leaf interactions in
maize
Construction of maize grain moisture content related near-isogenic
lines for developing SNP molecular marker
Creation of subgroup specific haplotype blocks and libraries
<torsten.pook@uni-goettingen.de>
P168 Arlyn Ackerman
<arlyna@clemson.edu>
P169 Jianming Yu
Deployment of a novel phenotypic platform based on
biomechanical engineering principles provides novel insights into
stalk lodging in maize
Design Thinking and Data Mining in Plant Breeding
<jmyu@iastate.edu>
P170 Clement Mabire
<clement.mabire@inra.fr>
P171 Rahime Cengiz
Development of a new high throughput 105K presence/absence
variation genotyping array for quantitative genetic studies
Development of late temperate maternal haploid inducers
<rahime.cengiz@tarim.gov.tr>
P172 Adrienne Ressayre
<adrienne.ressayre@u-psud.fr>
P173 Christine Dillmann
<christine.dillmann@inra.fr>
P174 Pedro Revilla
Developmental and morphological changes associated to
flowering time shifts produced during divergent selection
experiments in maize : developmental transitions and architecture
Developmental and morphological changes associated to
flowering time shifts produced during divergent selection
experiments in maize : phyllochron
Dissecting the genetics of cold tolerance in maize
<previlla@mbg.csic.es>
P175 Yaoyao Wu
Dissecting the role of lncRNA during maze domestication
<yyw_cau@163.com>
P176 Brigitte Gouesnard
Diversity analysis within a collection of 1191 flint maize inbred
lines using genotyping-by-sequencing
P177 Yacine Diaw
Diversity of maize landraces from south-west of France: origin
<yacine.diaw@supagro.fr>
and morphological differentiation analyzes
P178 Estefania Aguilar-Gutierrez Does subspecific variation correspond to genetic or cytotypic
<Estefania55@mail.fresnostate.edu> variation in the widespread taxon Phlox speciosa
(Polemoniaceae)?
P179 Matteo Dell'Acqua
eQTL mapping and genome wide association study for maize leaf
<m.dellacqua@santannapisa.it >
traits using markers derived by RNA sequencing of two RIL
populations
P180 Marlon Caicedo
Evaluation of functional stay-green in maize inbred lines and their
<mcaicedo@mbg.csic.es>
relationship with agronomic traits
P181 Laetitia Virlouvet
Exploring the genetic basis of cell wall traits upon contrasted
<laetitia.virlouvet@inra.fr>
water regimes in maize
<brigitte.gouesnard@inra.fr>
14
P182 Tes Posekany
Fine mapping of metabolite-QTLs for extracellular surface lipid
accumulation on maize silks
P183 Adam Vanous
Flowering time stability in doubled haploid lines derived from
<adamv@iastate.edu>
exotic maize
P184 Clement Buet
From the sequencing of 16 MAGIC population founders to a 8
<clement.buet@biogemma.com>
million SNP resource on the BALANCE panel
P185 Julie Fievet
Genetic and molecular basis of maize hybrid vigor: genome wide
<julie.fievet@inra.fr>
association studies in factorial hybrid designs
P186 Renyu Zhang
Genetic architecture of complex traits in a maize-teosinte
<zhangrenyu@live.com>
population
P187 Kathryn Michel
Genetic dissection of plant height and flowering using two Stiff
<kathryn.michel@wisc.edu>
Stalk multi-parent advanced generation intercross populations of
maize
P188 Nikola Grcic
Genetic distance in relation with specific combining abilities and
<ngrcic@mrizp.rs>
heterosis for vegetative traits in maize
P189 Eva Bauer
Genetic variation for early development and cold tolerance in DH
<e.bauer@tum.de>
libraries from maize landraces
P190 Jose Varela
Genome wide association studies for kernel starch and protein
<jvarela@wisc.edu>
content in the Wisconsin diversity (WiDiv) maize association panel
P191 Mélisande Blein-Nicolas
Genome wide association study for protein expression under
<melisande.blein-nicolas@inra.fr> normal and water deficit conditions in maize leaves
P192 Jonas Rodriguez
Genome-Wide association of biomass digestibility in the Wisconsin
<jrodriguez36@wisc.edu>
diversity panel
P193 Torbert Rocheford
Genome-wide mapping of kernel color in maize (Zea Mays L.)
<torbert@purdue.edu>
reveals associations with isoprenoid and carotenoid biosynthesis
genes and carotenoid degradation genes
P194 Stéphane Nicolas
Genome-wide SNP genotyping of DNA pools identifies original
<stephane.nicolas@inra.fr>
landraces to enrich maize breeding pools
P195 Albrecht E. Melchinger
Genomic prediction within and among doubled-haploid libraries
<melchinger@uni-hohenheim.de> from maize landraces
P196 Dustin MacLean
Genomic regions associated with Goss’s Wilt resistance in the
<dmacle02@uoguelph.ca>
commercial maize germplasm pool.
P197 Simon Rio
Genomic selection efficiency and a priori estimation of accuracy in
<simon.rio@inra.fr>
a structured dent maize panel
P198 Natalia Martinez-Ainsworth Genomic signatures of local adaptation unveil association with
<natalia.martinez@inra.fr>
present phenotypic variation in teosintes
P199 Brigitte Gouesnard
Genotyping-by-sequencing highlights original diversity patterns
<brigitte.gouesnard@inra.fr>
within a European collection of 1191 maize flint lines, as
compared to the maize USDA genebank
P200 Torbert Rocheford
Germplasm enhancement using former plant variety protected
<torbert@purdue.edu>
inbreds
P201 Milan stevanović
Grain yield and stability parameters of ZP maize hybrids grown in
<mstevanovic@mrizp.rs>
Serbia in the 2014-2017 period
P202 Rosa Ana Malvar
GWAS for resistance to mediterranean corn borer and agronomic
<rmalvar@mbg.csic.es>
traits in a MAGIC population of maize
P203 Torbert Rocheford
GWAS of inflorescence architecture in maize
<posekany@iastate.edu>
<torbert@purdue.edu>
P204 Gladys Cassab
<gladys@ibt.unam.mx>
Hydrotropism: an important root trait for drought and heat
avoidance in maize
15
P205 Yu Zhong
<zhongyu306@cau.edu.cn>
P206 Aimee J. Schulz
<aschulzj@iastate.edu>
P207 Guillaume Ramstein
<gr226@cornell.edu>
P208 Peter Muth
<p.muth@lmu.de>
P209 Valerie Craig
<craigv@uoguelph.ca>
P210 Mike White
<mrwhite4@wisc.edu>
P211 Heather Manching
<hcorn@udel.edu>
P212 Inoussa Sanane
Identification of haploid immature embryos by their morphological
difference in maize
Inbreeding depression in wild maize populations (Zea mays ssp.
parviglumis) subject to habitat degradation in southwest Mexico
Incorporation of functional information into genomic prediction
models in maize
Influence of arbuscular mycorrhiza on stress resilience in a
European maize diversity panel
Inheritance of short-season maize (Zea mays L.) senescence
patterns
Insights into heterotic patterns and allelic diversity of U.S. dent
maize from expired plant variety protection inbreds
Investigating the genetics of selection response for flowering time
in a multi-environment, parallel selection experiment.
Maize resistance to parasitism : life-cycles synchronisation matters
<inoussa.sanane@u-psud.fr>
P213 Merritt Burch
<merritt.b.burch@sdstate.edu>
P214 Silvio Salvi
<silvio.salvi@unibo.it >
P215 Florian Berger
<flo.berger@lmu.de>
P216 Mark Holmes
<holme616@umn.edu>
P217 Laura Manerus
Mapping loci that modify the efficacy of Teosinte crossing barrier
1
Mapping QTLs for Kernel Row Number and Fasciated Ear by
SNP-Based Bulk Segregant Analysis in Maize
MAZE - Accessing arbuscular mycorrhiza-mediated drought stress
resistance in a maize diversity panel
Natural variation for starch composition and processing
characteristics of maize
Navigating the maize of short-season ancestry
<lmanerus@uoguelph.ca>
P218 Felix Seifert
Omics-based prediction of hybrid grain yield in maize
<felix.seifert@cropseq.com>
P219 Calli Anibas
<canibas@wisc.edu>
P220 Antoine Allier
<antoine.allier@inra.fr>
P221 Thomas Altmann
<altmann@ipk-gatersleben.de>
P222 Hyeyoung Lee
Phenotypic and genetic dissection of cold tolerance in maize using
controlled environments and in-field evaluations
Phenotypic and genomic indicators of breeding program
sustainability: application to a north European grain maize
program
Plant phenotyping reveals genetic and physiological factors of
plant performance
Plant Transformation Services
<leehye@missouri.edu>
P223 Snezana Mladenovic Drinic
<msnezana@mrizp.rs>
P224 Anna Giulini
Population structure and genetic diversity of different maize
genotypes
Post breeding
<annapiamaria.giulini@crea.gov.it >
P225 Domagoj Simic
<domagoj,simic@poljinos.hr>
P226 Adama Seye
<adama.seye@inra.fr>
P227 Popi Septiani
<popi.septiani@santannapisa.it >
P228 Kathleen Miller
<kmiller46@wisc.edu>
QTL for photosynthetic and yield performance in IBM population
under two different heat scenarios during flowering time
QTL mapping and genomic predictions for silage quality traits in a
multiparental hybrid design
QTL mapping for fusarium seedling rot resistance in the
recombinant inbred crosses derived from MAGIC maize
population
QTLs affecting sweet corn carbohydrate content and eating quality
in sugary1
16
P229 Slavica Stankovic
<sstojkov@mrizp.rs>
P230 Mihai Miclaus
<mihai.miclaus@icbcluj.ro>
P231 Felix Frey
<ffrey@uni-bonn.de>
P232 Delphine SteinbachH
<delphine.steinbach@inra.fr>
P233 Arnaud Desbiez-Piat
<arnaud.desbiez-piat@u-psud.fr>
P234 Bridget McFarland
<bamcfarland@wisc.edu>
P235 Jason Wallace
Relationships between resistances to Fusarium and Aspergillus ear
rots and mycotoxins contamination in maize kernels
Romania’s 3,000 inbred lines collection as a reservoir of genetic
diversity and the use of its cytolines in linking phenotype to
genotype
Root phenotypic and transcriptomic variation in the European
maize landrace Petkuser in response to cold
ThaliaDB, a tool for data management and genetic diversity data
exploration
The dynamics of adaptive response under strong selection regime
in small populations
The effects of artificial selection on stability and GxE in the Iowa
stiff stalk synthetic maize population
The effects of host and environment on the maize microbiome
<jason.wallace@uga.edu>
P236 Clement Buet
<clement.buet@biogemma.com>
P237 Nicola Bacciu
The phenotypic characterization of the BALANCE maize panel
reveals high potential to discover genetic determinants involved in
drought response
The ProSpect of traditional and molecular breeding.
<nicola.bacciu@keygene.com>
P238 Anne Zanetto
<anne.zanetto@inra.fr>
P239 Catherine Giauffret
<catherine.giauffret@inra.fr>
P240 Karin Ernst
The Zea French Biological Resource Centre: conservation and
utilization of maize genetic resources in France
Three chromosomal segments have a strong effect on
photosynthesis and ability of maize plants to transition to
autotrophy under chilling conditions
Towards cloning of a major chilling tolerance QTL in maize
<karin.ernst@hhu.de>
P241 Bernardo Ordas
<bordas@mbg.csic.es>
P242 Xianran Li
<lixr@iastate.edu>
P243 Elise Tourrette
<elise.tourrette@inra.fr>
P244 Brian Rice
<brice6@illinois.edu>
P245 Tao Zhong
<zhongtaomvp@163.com>
P246 Jinge Tian
Transcriptomic analysis of senescence in maize inbred lines with
different rate of senescence
Turbocharging germplasm banks: genomic prediction goes into
micro-world
Unleashing genetic diversity by increasing meiotic recombination :
an in silico benchmark
Utilizing GWAS Results to Preferentially Treat Genomic Markers
in Prediction Model
ZmAuxRP1, encoding an auxin-regulated protein, coordinates the
balance between growth and defense in maize
ZmCCT9 enhances maize adaptation to higher latitudes
<tianjingelove@126.com>
P247 Yingjia Han
ZmCOPⅡ controls oil content in maize kernel
<hanyingjia325@163.com>
Transposons & Epigenetics
P248 Chunguang Du
<duc@montclair.edu>
P249 Donald McCarty
<drm@ufl.edu>
P250 Michelle Stitzer
<mcstitzer@ucdavis.edu>
A single gene knock-out resource for maize: filling gaps in the
genome with targeted Ds-GFP insertions
Accuracy of the UniformMu resource is improved 15% by mapping
Mu insertions in its native W22 genome
Atypical transposable element copies predict functional
consequence
17
P251 Yubin Li
Buried treasures: the maize transposable elements Dotted and Mrh
<liyubin@caas.cn>
P252 Emily McCormic
<mccormic.11@osu.edu>
P253 Alex Brohammer
<broha006@umn.edu>
P254 Clémentine Vitte
<clementine.vitte@inra.fr>
P255 Cristian Forestan
Characterization and mapping of the required to maintain
repression10 locus affecting paramutation
Characterization of polymorphic transposable element content
between maize inbred lines
Cold induces transcriptional and methylation changes in the
sensitive line B73
Discovering the epigenetic memory of stress response in maize
<cristian.forestan@unipd.it >
P256 Jian Chen
<jianchen@cau.edu.cn>
P257 Jaclyn Noshay
<nosha003@umn.edu>
P258 Maike Stam
<m.e.stam@uva.nl>
P259 Caroline Marcon
Distinct pattern of DNA methylation in different subnucleosomal
domains
Documenting the role of transposable elements in DNA
methylation variation in maize
Identification and characterization of regulatory sequences in Zea
mays
Identification of new maize (root) mutants by Mu-seq
<marcon@uni-bonn.de>
P260 Na Wang
<na.wang25@uga.edu>
P261 Tong Li
<litong@cau.edu.cn>
P262 Susanne Edelmann
<susanne.edelmann@unihamburg.de>
P263 Jay Hollick
Maize centromeres expand in the large genome background of
Oaxaca and Zea. luxurians
Parent-of-origin dependent nucleosome organization and its role
on the regulation of genetic imprinting in maize endosperm
Reduction of DNA methylation during early embryogenesis
enhances growth heterosis of maize plants
RNA polymerase IV contributes to hybrid vigor
<hollick.3@osu.edu>
P264 Benjamin Berube
Single-pollen sequencing for the study of novel meiotic phenotypes
<bberube@cshl.edu>
P265 Surinder Chopra
<sic3@psu.edu>
P266 Thomas Brutnell
The maize Ufo1 mutant results from ectopic over expression of an
endosperm specific gene
The transposon landscape of the inbred W22
<tbrutnell@danforthcenter.org>
P267 William Ricci
<william.ricci@uga.edu>
P268 Allison McClish
<mcclish.23@osu.edu>
Using chromatin features to identify and understand intergenic
transcriptional regulatory elements in maize
Using GRO-Seq as a tool to understand transcriptional regulation
in maize
18
Plenary Talk Abstracts
Plenary 1
Friday, March 23 11:15 AM
Epigenetic variation in Arabidopsis
(presented by Magnus Nordborg <magnus.nordborg@gmi.oeaw.ac.at>)
Full Author List: Nordborg, Magnus 1
1
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. BohrGasse 3, 1030 Vienna, Austria
Epigenetics continues to fascinate, especially the notion that it blurs the line between
“nature and nurture” and could make Lamarckian adaptation via the inheritance of
acquired characteristics possible. That this is in principle possible is clear: in the model
plant Arabidopsis thaliana (thale cress), experimentally induced DNA methylation
variation can be inherited and affect important traits. Less clear is whether this matters in
nature. Recent studies of A. thaliana have revealed a pattern of correlation between levels
of methylation and climate variables that strongly suggests that methylation is important
in adaptation. However, somewhat paradoxically, the experiments also showed that much
of the variation for this epigenetic trait appears to have a genetic rather than an epigenetic
basis. This suggest that epigenetics may indeed be important for adaptation, but as part of
a genetic mechanism that is currently not understood. Genome-wide association studies
revealed a striking genetic architecture of methylation variation, involving major-effect
polymorphisms in many genes involved in silencing, and we are currently utilizing this to
determine whether the global pattern of methylation variation has a genetic or an
epigenetic cause, and to use this information to elucidate the ultimate cause of the global
pattern of variation: natural selection.
19
Plenary 2
Friday, March 23 12:05 PM
Drought tolerance: which mechanisms, traits and alleles for which drought
scenarios?
(presented by Francois Tardieu <francois.tardieu@inra.fr>)
Full Author List: Tardieu, Francois 1 ; Millet, Emilie J 1 ; Alvarez Prado, Santiago1 ; Cabrera
Bosquet, LLorenç1 ; Lacube, Sebastien1 ; Parent, Boris 1 ; Welcker, Claude1
1
INRA LEPSE Montpellier France F34000
Plants are subjected every day to rapid variation of evaporative demand and soil water
availability, resulting in rapid changes in stomatal conductance, expansive growth and
metabolism over minutes. Because yield involves several months, the connection
between physiological mechanisms and response of yield to drought scenarios faces a
massive problem of time scales. Furthermore, yield results from optimization between
traits and alleles that lead to either minimize the risk of crop failure or to increase crop
production. Evolution has tended to favour conservative processes (short crop cycle, low
transpiration and leaf area, large root systems) which are favourable under severe
stresses, whereas yield in milder water deficits is associated with the opposite traits.
Hence, one aims at identifying which traits and alleles are favourable in which drought
scenarios, rather than at a generic ‘drought tolerance’. We deal with these methodological
difficulties by combining phenomics, modelling, genetic analysis and genomic
prediction. A first strategy explores the genetic variability of key processes, which are
translated into parameters of a crop model. This requires detailed analyses in phenotyping
platforms with a capacity of thousands of plants, with the relevant time scales. These
parameters are analysed by GWAS and simulated via genomic prediction. The model can
then simulate yield in hundreds of fields for hundreds of genotypes, from genetic
parameters of each genotype and environmental conditions in each field. A second
strategy directly explores the responses of yield to environmental conditions in
contrasting environmental scenarios, e.g. in 40 fields. This results in a mixed model
whose parameters are analysed genetically and can be estimated by genomic prediction,
thereby allowing one to predict yields in new genotypes and fields. As a whole, the
combination of field and platform data allows identification of combination of traits and
alleles associated with tolerance in specific scenarios of heat and drought.
Funding acknowledgement: INRA, ANR, UE
20
Plenary 3
Friday, March 23 5:45 PM
Light control of seed germination: the unusual role of usual suspects
(presented by: Ortun Mittelsten Scheid
<ortrun.mittelstenscheid@gmi.oeaw.ac.at>)
Full Author List: Zsuzsanna Mérai1 , Kai Graeber 2 , Per Wilhelmsson3 , Kristian K. Ullrich3* ,
Waheed Arshad2 , Christopher Grosche3, Danuše Tarkowská4, Veronika Turečková4 , Miroslav
Strnad4 , Stefan A. Rensing3 , Gerhard Leubner-Metzger2, Ortrun Mittelsten Scheid1
1
Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna
BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
2
School of Biological Sciences, Plant Molecular Science and Centre for Systems and Synthetic
Biology, Royal Holloway University of London, Egham, Surrey, TW20 0EX, United Kingdom
3
Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043
Marburg, Germany
4
Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and
Agricultural Research, Palacký University & Institute of Experimental Botany, Czech Academy
of Sciences, 78371 Olomouc, Czech Republic
*
Current address: Max Planck Institute for Evolutionary Biology, Department of Evolutionary
Genetics, 24306 Plön, Germany
Seed germination is a sensitive period in a plant’s life cycle, and initiation of the process
must be concerted with many internal and external factors. Light is an important
parameter, extensively documented for the model plants Arabidopsis thaliana and
Lactuca sativa, in which light exposure of seeds is required to trigger a well-investigated
signalling cascade resulting in hormonal control of germination. In contrast, seeds of
other plants germinate equally well in light or darkness, and seeds of some species do not
germinate at all as long as they are exposed to light. The mechanism of an inhibiting role
of light on seed germination is not understood.
The talk will present physiological and molecular data generated in experiments with
Aethionema arabicum, a member of the Brassicaceae and related with Arabidopsis.
While gibberellins and abscisic acid are involved in the control of germination in both
species, the light-induced changes of the ratio between the two hormones are antipodal
between Aethionema and Arabidopsis. Genomic information, natural variation, and
differential expression of regulatory genes suggest Aethionema as a suitable model plant
to investigate the molecular mechanism of germination inhibition by light. The data
indicate that similar modular components have been assembled by evolution in different
ways to produce divergent pathways.
21
Plenary 4
Friday, March 23 6:35 PM
A bad genetic history of maize.
(presented by: Jeffrey Ross-Ibarra <rossibarra@ucdavis.edu>)
Full Author List: Ross-Ibarra, Jeffrey1
1
Department of Plant Sciences, University of California - Davis
Deleterious alleles have played an important role in the evolution of maize and teosinte.
Although they vary in their strength and effect across populations or environments, such
mutations have played a role in local adaptation in teosinte, the accumulation of load
during domestication and dispersal of maize, local adaptation of maize landraces, and
ultimately in hybrid vigor for agronomic traits in breeding programs.
22
McClintock Prize
Friday, March 10 7:30 PM
Germline reprogramming, epigenetic inheritance and small RNA: how to
avoid Bad Karma.
(presenter: Rob Martienssen <martiens@cshl.edu>)
Author list: Martienssen, Rob 1;
1
Howard Hughes Medical Institute, Cold Spring Harbor Laboratory Cold Spring Harbor NY 11724
The germlines of animals and plants undergo reprogramming to reset epigenetic marks
acquired during development, and to restore pluripotency to the zygote. When
reprogramming fails, epigenetic inheritance results. Epigenetic inheritance is far more
common in plants than in mammals, as demonstrated by the early work of B. McClintock
and R.A. Brink on transposon cycling and paramutation in maize. We have found that in
Arabidopsis pollen, genome reprogramming in sperm cells results in the loss of RNA
dependent DNA methylation, and the accumulation of a new class of “epigenetically
activated” small RNA (easiRNA). A highly conserved microRNA, miR845, targets the
primer-binding site (PBS) of LTR-retrotransposons and triggers the accumulation of 21
to 22-nucleotide easiRNA in a dose dependent fashion. These easiRNAs mediate
hybridization barriers between diploid seed parents and tetraploid pollen parents (“the
triploid block”). Natural variation for miR845 among Arabidopsis accessions may
account for “endosperm balance” to allow formation of triploid seeds. After fertilization,
DNA methylation is restored in the embryo, guided by small RNA. When
reprogramming fails, for example in Arabidopsis cell culture, easiRNA also accumulate
and RdDM is lost. In a real world example, accumulation of easiRNA and the loss of
RdDM in oil palm tissue culture results in the epigenetic inheritance of the “mantled”
somaclonal abnormality. Mantled is caused by aberrant splicing of the Karma
retrotransposon, found in the intron of the Deficiens gene. A simple DNA methylation
test can predict mantled clones, providing a robust screen to avoid planting infertile
material in environmentally sensitive tropical plantations.
23
Short Talk Abstracts
SESSION 1 – THE GENES THAT MAKE MAIZE
Chair: Andrea Gallavotti
Thursday, March 22. 7:30 PM – 9:25 PM
T1
How to make maize seeds that look “not like dad”: insights in double
fertilization and prospects for novel breeding tools.
(submitted by Thomas Widiez <thomas.widiez@ens-lyon.fr>)
Full Author List: Gilles, Laurine M 1 2; Khaled, Abdelsabour3; Laffaire, Jean-Baptiste2; Chaignon,
Sandrine1; Gendrot, Ghislaine 1; Laplaige, Jérôme 1; Bergès, Hélène 4; Beydon, Genséric 4; Bayle, Vincent 1;
Barret, Pierre5; Comadran, Jordi2; Martinant, Jean-Pierre2; Rogowsky, Peter M 1; Widiez, Thomas1
1
Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA; Lyon; France.
2
Limagrain Europe SAS; Research Centre; Chappes; France.
3
Faculty of Agriculture; Sohag University; Sohag; Egypt.
4
INRA; US1258 Centre National des Ressources Génomiques Végétales; Auzeville; France.
5
INRA; UMR1095 Génétique Diversité Ecophysiologie des Céréales; Clermont-Ferrand; France.
Mixing male and female genetic information during sexual reproduction is considered as key to the
evolutionary success of higher eukaryotes and is the basis of plant breeding. Sexual reproduction in
flowering plants involves double fertilization, characterized by two separate fusion events between the
male and female gametes. A maize line first reported in the 60s deviates from this classic pattern. Crosses
using pollen from this so-called haploid inducer line, trigger the development of the egg cell into a haploid
embryo with only the maternal genome, a process known as in vivo gynogenesis. Derivatives of this maize
haploid inducer line have become the preferred tool of numerous maize breeding companies, because it can
produce perfectly homozygous plants in only 2 generations instead of 5 to 8 in classical breeding schemes.
Our recent results (Gilles et al., EMBO J), together with two other simultaneous independent studies
(Kelliher et al., Nature; and Liu et al., Molecular Plant), identified the major causal gene responsible for
gynogenesis in maize. Our map based cloning restricted the QTL to a zone containing a single gene coding
for a patatin-like phospholipase A, which was named NOT LIKE DAD (NLD) because haploid embryos do
not have paternal contribution. In all surveyed haploid inducer lines NLD carries a 4 pb insertion leading to
a predicted truncated protein. This frameshift mutation is responsible for haploid induction as
complementation with wildtype NLD abolishes the haploid induction capacity. Translational NLD::citrine
fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated
protein is no longer localized to the plasma membrane, contrary to the wildtype NLD protein. In
conclusion, an intact sperm-specific phospholipase is required for successful sexual reproduction and its
targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.
Gene / Gene Models described: not like dad; GRMZM2G471240 or Zm00001d029412
24
T2
Generating clonal progeny in maize
(submitted by Nina Chumak <nina.chumak@botinst.uzh.ch>)
Full Author List: Chumak, Nina 1; Williams, Mark E.2; Brunner, Arco 1; Fox, Tim2; Bernardes de Assis,
Joana1; She, Wenjing1; Pasquer, Frédérique 1; Albertsen, Marc2; Grossniklaus, Ueli1
1
University of Zürich, Department of Plant and Microbial Biology, Zollikerstr. 107, 8008 Zürich,
Switzerland
2
DuPont Pioneer Hi-bred, P.O. Box 1000, Johnston, IA 50131-0184
Apomixis is asexual reproduction through seed. The production of seeds though apomixis, which generates
plants that are genetically identical to the mother plant, has considerable agricultural potential to maintain
desired complex genotypes, e.g. those of F1 hybrids, over many generations.
Gametophytic apomixis deviates from sexual development in three major steps: (1) meiosis is
circumvented or aborted, leading to the formation of unreduced, unrecombined embryo sacs (apomeiosis);
(2) embryogenesis initiates without fertilization of the unreduced egg cell (parthenogenesis); and (3)
developmental adaptations enable the formation of functional endosperm. The aim of our research is to
identify mutations that mimic the major components of apomixis, and to combine them to engineer
apomictically-reproducing maize plants.
In a genetic screen we identified the non-reduction in female 4 (nrf4) mutant, which mimics the first step of
apomixis: apomeiosis. Homozygous nrf4 plants produce up to 95% unreduced embryo sacs. Using SAIFFby sequencing technology, the mutation was mapped to GRMZM2G148133 on the long arm of
chromosome 7, and the identity of Nrf4 was confirmed by two additional mutant alleles. To identify
whether nrf4 leads to first or second division restitution (FDR vs SDR), we analyzed maintenance of
heterozygosity in the progeny of nrf4 mutant plants in comparison to mother plants using a SNP array that
enabled the analysis of 10-20 SNPs on each chromosome. The effect of the nrf4 mutation turned out to be
more complex than expected and leads to both FDR and SDR. Nonetheless, depending on the genetic
background of the mother plant, up to 11% of the unreduced female gametes were genetically identical to
the mother. Indeed, pollination of nrf4 plants by a tetraploid haploid inducer resulted in some clonal
individuals. To our knowledge this is the first evidence that production of clonal ind ividuals through seed is
possible in maize.
Gene / Gene Models described: Nrf4; GRMZM2G148133
Funding acknowledgement: DuPont/Pioneer, SNF
25
T3
Maize Carbohydrate partitioning defective33 functions in sucrose export
from leaves
(submitted by Thu Tran <tmtqk3@mail.missouri.edu>)
Full Author List: Tran, Thu M.1; Bihmidine, Saadia 1; Baker, R. Frank1; Chomet, Paul2; Wagner, Ruth 2;
Grote, Karen 2; Peevers, Jeanette2; Braun, David M.1
1
Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri-Columbia,
Columbia, MO 65211 USA
2
Monsanto, Chesterfield, MO 63017 USA
To sustain plant growth, development, and ultimately crop yield, sucrose must be transported from its site
of synthesis in leaves to distant parts of the plant, such as seeds or roots. Yet we know little about the genes
controlling carbohydrate distribution in plants. Here we discuss our exciting discovery of a gene impacting
sucrose export from maize leaves.
carbohydrate partitioning defective33 (cpd33) is a recessive mutant, which accumulates excess starch and
soluble sugars in the mature leaves. Additionally, cpd33 mutants exhibit chlorosis in the leaf blades, greatly
diminished plant growth, and reduced fertility. Furthermore, application of radioactively labeled F18sucrose to cpd33 mutant and wild-type leaves showed that sucrose export was greatly decreased in cpd33
mutant leaves compared with wild type. The Cpd33 gene has been cloned by genetic fine-mapping and
whole genome sequencing experiments, and its identity confirmed through characterizing multiple mutant
alleles. The Cpd33 gene encodes an evolutionarily conserved plant-specific protein predicted to contain
multiple transmembrane domains. In tobacco leaves, a CPD33-yellow fluorescent protein translational
fusion protein is associated with the plasma membrane; however, the signal appears discontinuously along
the membrane, suggesting that CPD33 is localized at plasmodesmata.
Based on these results, we propose that CPD33 functions to control sucrose export from leaves through
regulating cell-to-cell transport through plasmodesmata. Our ongoing work utilizes molecular approaches
in combination with imaging techniques to test models of CPD33 function. This research reveals a new
gene involved in sucrose export and deepens our understanding of the control of carbohydrate partitioning.
Funding acknowledgement: National Science Foundation (NSF)
26
T4
NARROWSHEATH1 controls cell cycle dynamics to promote mediolateral
outgrowth of leaf primordia
(submitted by Phillip Conklin <pac257@cornell.edu>)
Full Author List: Conklin, Phillip 1; Scanlon, Michael1
1
Cornell University, Ithaca, NY, 14853
The mechanisms whereby lateral organ initial cells are organized from the peripheral zone of the shoot
apical meristem (SAM) are poorly understood in grasses. The maize WUSCHEL-LIKE HOMEOBOX3
(WOX3) gene NARROWSHEATH1 (NS1) is expressed at the marginal boundary of leaf initial cells in the
SAM and in young leaf primordia, where it mediates mediolateral outgrowth. This research teases apart
conserved mechanisms of lateral organ initial cell recruitment versus stem cell organization in the central
zone of shoot meristems and the quiescent center of root meristems. Although several studies have
elucidated the network in the stem cell organizing center in eudicots, these employed overexpression of the
stem cell organizing protein WUS1. We utilize domain-specific analysis of NS1 bound and modulated
targets within the lateral organ initial cells, in maize. In so doing, we investigate whether organization of
lateral organ initials and stem cells in the root (via WOX5) and shoot apical meristems (via WUS and
NS1/WOX3) have the same general functions in distinct developmental domains or in contrast, if they
perform distinct, domain-specific functions. To elucidate the genetic regulation of lateral organ initials, we
compare ChIP-seq targets bound by NS1 and RNA-seq transcripts modulated in laser micro-dissected early
leaf margins. These experiments, combined with microscopic analyses of cell division dynamics, suggest
that NARROWSHEATH1 controls mediolateral outgrowth by direct regulation of cell cycle genes and
growth regulators at the margins of the developing leaf primordia.
Gene / Gene Models described: NS1; GRMZM2G069028
Funding acknowledgement: National Science Foundation (NSF)
27
T5
Interrogating metabolic and transcriptomic networks to explain genetic,
developmental and environmental variation in the cuticular lipid
landscape on maize silks
(submitted by Keting Chen <kchen@iastate.edu>)
Full Author List: Chen, Keting 1 2; Maghoub, Umnia2; Loneman, Derek2; Peddicord, Layton3 4; Lopez,
Miriam4 5; McNinch, Colton 4; Chudalayandi, Siva 4; Dorman, Karin 1 2 6; Lauter, Nick3 4 5; Nikolau, Basil J.1 3
7
; Yandeau-Nelson, Marna D.1 2 3
1
Bioinformatics and Computational Biology Graduate Program; Iowa State University, Ames, IA, 50011
2
Department of Genetics, Development and Cell Biology; Iowa State University, Ames, IA, 50011
3
Genetics and Genomics Graduate Program; Iowa State University, Ames, IA, 50011
4
Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011
5
USDA-ARS Corn Insect and Crop Genetics Research Unit, Ames, IA, 50011
6
Department of Statistics; Iowa State University, Ames, IA, 50011
7
Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology; Iowa State University,
Ames, IA, 50011
The plant cuticle is infused with and coated by non-polar and amphipathic lipids that form a hydrophobic
layer that is protective against environmental stresses. These extracellular surface lipids (SLs) are
comprised primarily of long-chain saturated and unsaturated fatty acids, aldehydes, and hydrocarbons,
which are metabolically linked by enzymatic reactions as the hypothesized precursors, intermediates, and
end products in hydrocarbon biosynthesis. To investigate this biosynthetic pathway, we employed a
systems approach to query the metabolomes and transcriptomes of silks from four genotypes (B73, Mo17
and their reciprocal hybrids) across a spatio-temporal gradient that captures acropetal silk development and
the environmental transition as silks emerge from the husks.
Supervised and un-supervised network analyses were pursued to address key questions: 1) Which
metabolites explain the dynamic variations in SL composition? 2) Which enzymatic processes lead to
variation in these metabolites? and 3) What genes explain the differential metabolome compositions? Our
results show that silk SL composition is dynamic and significantly impacted by encasement status,
genotype, and development. Discriminant analysis revealed that differential utilization of fatty acid
precursors likely contributes to the observed variation in hydrocarbon composition among genotypes.
Product-precursor ratio investigations showed that hydrocarbon abundances are elevated relative to their
associated fatty acid precursors at longer chain-lengths, suggesting increased recruitment of longer-chain
fatty acid precursors into the biosynthetic pathway. Metabolome-transcriptome associations impacting
hydrocarbon production under varied conditions were identified from a partial least squares regression
model built from a set of informative metabolites. Preliminary analysis identified candidate genes
associated with genotype-based variation in the metabolic network, including 3-ketoacyl-CoA synthases
involved in generating fatty acid precursors, and acyl desaturases involved in production of unsaturated
SLs. Analyses are being conducted to interrogate the transcriptome in the context of product -precursor,
product-intermediate and intermediate-precursor relationships to identify candidate genes associated with
specific biochemical reactions in the network.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
28
SESSION 2 – GENETIC ARCHITECTURE AND EVOLUTION
Chair: Jianbing Yan
Friday, March 23. 8:30 AM – 10:40 AM
T6
How polygenic adaptation during domestication shaped the genetic
architecture of maize
(submitted by Markus Stetter <mstetter@ucdavis.edu>)
Full Author List: Stetter, Markus G1; Thornton, Kevin 2; Ross-ibarra, Jeffrey 1
Department of Plant Sciences and Center for Population Biology, University of California; Davis,
California, USA
2
Department of Ecology and Evolutionary Biology, University of California; Irvine, California, USA
1
The domestication of maize has radically changed its morphology and physiology. A number of genes
controlling domestication traits have been identified over the last decades, however, these genes only
explain a fraction of the variation observed for most traits. Genome wide association mapping and genomic
prediction studies show that many traits are controlled by a large number of loci with a variety of effect
sizes. To better understand the genetic architecture of complex traits during domestication, we explicitly
simulated quantitative trait evolution under selection and demographic models specific to maize history. To
explore different traits, we varied the effect size distribution of incoming mutations, the strength of
stabilizing selection and the genomic background, and used machine learning to identify the relative
importance of different parameters. We show that traits exhibiting the greatest phenotypic change and
strongest stabilizing selection in teosinte rely on new beneficial mutations to adapt. Mutations with positive
effects sweep to fixation, resulting in a large number of both soft and hard selective sweeps. Traits under
weaker stabilizing selection and exhibiting less phenotypic change adapt via a subtle shift at many loci
resulting in only few selective sweeps, mostly from genotypic variation that was already present in teosinte.
These subtle shifts in allele frequencies maintain larger genetic variance, but also large effect negative
alleles that are deleterious for further breeding. We show how the effect size of incoming mutations, the
strength of stabilizing selection, the genomic background and population demography influence adaptation,
genetic architecture and the interplay between polygenic adaptation and selective sweeps. Our results
illustrate that polygenic adaptation and selective sweeps are not mutually exclusive but can coexist,
depending on various parameters. We further elucidate the genomic patterns observed in modern maize,
and provide the opportunity to identify new targets for genetic improvement.
Funding acknowledgement: National Science Foundation (NSF), Deutsche Forschungsgemeinschaft (DFG)
29
T7
Twenty years of divergent selection for flowering time from maize inbred
lines
(submitted by Christine Dillmann <christine.dillmann@u-psud.fr>)
Full Author List: Dillmann, Christine 1; Ressayre, Adrienne1; Marchadier, Elodie 1; Charcosset, Alain 1;
Sanane, Inoussa1; Desbiez-Piat, Arnaud1; Tenaillon, Maud I.1
1
Génétique Quantitative et Evolution– Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech,
Université Paris-Saclay ; Gif-sur-Yvette, France, 91190
Two independent Divergent Selection Experiments (DSEs) for flowering time in maize have been
conducted under agronomical conditions in Plateau de Saclay for more than twenty generations. The two
initial populations consisted in two seed lots, each from a single inbred line. At each generation, we
selected and selfed early and late flowering genotypes. By selecting from such a narrow genetic basis, we
expect to have enriched populations for (epi)genetic differences controlling flowering time, while
preserving the original characteristics of the initial inbreds. We used this material to investigate (i)
dynamics of the response to selection by comparing genotypes among generations (ii) genotype-phenotype
map by comparing Early and Late genotypes within DSEs; (iii) patterns of convergence by comparing
Early (Late) genotypes between DSEs.
Altogether, we observed a significant response to selection in both directions (0.5 days/year on average),
with strikingly similar patterns for both DSEs. A revised version of the animal model that explicitly
accounts for the role of new mutations showed that both residual heterozygosity and new mutations
contributed to the selection response.
Early and Late progenitors from generations G13 and G18 were used to perform in -depth characterization
of gene expression, as well as plants growth and development. At the phenotypic level, differences between
Early and Late genotypes concerned primarily the timing of developmental transitions, while organs’
growth rates and phyllochrons were much less variable. RNA-Seq analyses on shoot apical meristems
revealed 2,451 genes that were differentially expressed between Early and Late genotypes during floral
transition (candidate genes), with more common candidates between the two DSEs than expected by
chance (convergence). Finally, using Lepidoptera stem borers as a model, we analysed how plant
phenology shifts interfered with pest life-cycle. We found higher prevalence in one Early population,
synchronized with the arrival of the second generation of adult insects.
Funding acknowledgement: INRA, Labex BASC
30
T8
Prehistoric selection for temperate climates has far-reaching implications
for global germplasm
(submitted by Kelly Swarts <kelly.swarts@tuebingen.mpg.de>)
Full Author List: Swarts, Kelly 1 2; Miller, Zachary 3; Rafal, Gutaker1; Johnson, Lynn 3; Eva, Bauer4;
Glaubitz, Jeffrey 5; Matson, R.G.6; Blake, Michael6; Melissa, Kruse-Peeples8; Sara, Larsson 15; Schünemann,
Verena9; Liu, Xiaolei11; Li, Yu 9; Romay, M. Cinta 5; Ross-Ibarra, Jeffrey 14; Sanchez, Jesus12; Chris,
Schmidt 8; Schön, Chris-Carolin 4; Wang, Tianyu 10; Johannes, Krause 7; Weigel, Detlef1; Zhang, Zhiwu 13;
Buckler, Edward S2 3; Peter, Bradbury 3; Burbano, Hernan1
1
Max Planck Institute for Developmental Biology, Max-Planck-Ring 1, 72076 Tübingen, GERMANY
2
Department of Plant Breeding and Genetics, 175 Biotechnology Building, Cornell University, Ithaca, NY
14853
3
USDA-ARS, Cornell Univ., Ithaca, NY 14853
4
Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, D-85354
Freising, Germany
5
Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853
6
Department of Anthropology, Vancouver Campus, 6303 NW Marine Drive, Vancouver, BC Canada V6T
1Z1
7
Max-Planck-Institut für Menschheitsgeschichte, Kahlaische Strasse 10, 07745 Jena, GERMANY
8
Native Seeds/SEARCH 3584 E. River Rd., Tucson, AZ 85718
9
Eberhard-Karls-Universität Tübingen, Urgeschichte und Naturwissenschaftliche Archäologie, Abt.
Paläogenetik, Rümelinstrasse 23, 72070 Tübingen
10
Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun south Street,
Haidian, Beijing, China, 100081
11
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education &
College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
12
Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan,
Jalisco CP45110, Mexico
13
Department of Crop and Soil Sciences, 105 Johnson Hall, Washington State University, Pullman, WA
99164, USA
14
Dept. of Plant Sciences, 262 Robbins Hall, Mail Stop 4, University of California, One Shields Ave,
Davis, CA 95616
15
DuPont Pioneer, Windfall, IN, 46076
Researchers have long recognized that flowering time in maize is highly correlated with other
agronomically important traits, with implications for trait introgression and breeding. We show that this
association between flowering and modern population structure is at least 2,000 years old and d ates to the
historic temperate adaptation process as maize moved north out of Mexico to the temperate southwest
United States. We then test the impact of this process on agronomically important global germplasm: the
Ames population and US-NAM (American), the EU-NAM Flint and Dent panels (European), and CNNAM (Chinese). We use a random forest classifier to test the prediction accuracy of population
differentiation between American temperate and tropical germplasm on uncorrected GWAS results from
these families. Because these populations derive from geographically restricted germplasm with variance
for flowering, accurate prediction implies a shared selection history. Prediction accuracies (AUC) averaged
across chromosomes are 0.89 for Ames, 0.85 for US-NAM, 0.67 for EU-NAM Flint, 0.59 for EU-NAM
Dent and 0.47 for CN-NAM, suggesting that the North American temperate adaptation process was
important for European temperate adaptation but that the temperate Chinese germplasm derives from an
unrelated selection process.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
31
T9
Distinct Genetic Architectures for Phenotype Means and Plasticities in Zea
mays
(submitted by Aaron Kusmec <amkusmec@iastate.edu>)
Full Author List: Kusmec, Aaron1; Srinivasan, Srikant 2 3; Nettleton, Dan 2 4; Schnable, Patrick S.1 2
1
Department of Agronomy, Iowa State University, Ames, Iowa, USA 50010
2
Plant Sciences Institute, Iowa State University, Ames, Iowa, USA 50010
3
School of Computing and Electrical Engineering, IIT Mandi, Mandi, Himachal Pradesh, India 175005
4
Department of Statistics, Iowa State University, Ames, Iowa, USA 50010
Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different
environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of
paramount importance for maintaining and increasing yields in a world experiencing climate change. Here,
we report the results of genome-wide association analyses of multiple phenotypes and two measures of
phenotypic plasticity in the maize nested association mapping (US-NAM) population grown in multiple
environments and genotyped with ~2.5 million single nucleotide polymorphisms (SNPs). We show that
across all traits the candidate genes for mean phenotype values and plasticity measures form structurally
and functionally distinct groups. Such independent genetic control suggests that breeders will be able t o
select semi-independently for mean phenotype values and plasticity, thereby generating varieties with both
high mean phenotype values and levels of plasticity that are appropriate for the target performance
environments.
Funding acknowledgement: National Institutes of Health (NIH), National Science Foundation (NSF)
32
T10
The conserved and unique genetic architecture of kernel size and weight in
maize and rice
(submitted by Jie Liu <jieliu@mail.hzau.edu.cn>)
Full Author List: Liu, Jie 1; Li, Qing 1; Yan, Jianbing 1
1
National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan,
China, 430070
Maize (Zea mays) is a major staple crop. Maize kernel size and weight are important contributors to its
yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel
test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three
statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified
in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation.
To provide candidate genes for these QTLs, we identified 30 maize gen es that are orthologs of 18 rice
(Oryza sative) genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are
located in the identified QTLs or within 1 Mb region of the significant single nucleotide polymorphisms
(SNPs). We further confirmed the effect of five genes on maize kernel size/weight in an independent
association mapping panel with 540 lines by candidate gene association analysis. Lastly, we mapped a
major QTL (qHKW1) for hundred kernel weight into ~650Kb region harboring 9 genes. Among these 9
genes, only 2 were reported to express during maize kernel development and one of them (qHKW1-9) was
annotated to involve in plant development. Transgenic lines that overexpress qHKW1-9 have significant
increase in hundred kernel weight compared to the negative transgenic lines. Our findings shed light on the
genetic basis of kernel size and weight in maize and provided evidence for a conserved and unique genetic
architecture of kernel traits in maize compared with rice.
Funding acknowledgement: National Science Foundation of China, National Key Research and
Development Programof China, Genetically Modified Organisms Breeding Major Projects, Huazhong
Agricultural University Scientific and Technological Self-Innovation Foundation
33
T11
Genome-wide nucleotide divergence and UV induced mutations following
maize domestication
(submitted by Jinyu Wang <jinyuw@iastate.edu>)
Full Author List: Wang, Jinyu1; Li, Xianran 1; Kim, Kyung Do 2; Scanlon, Michael J.3; Jackson, Scott A.2;
Springer, Nathan M.4; Yu, Jianming 1
1
Department of Agronomy, Iowa State University, Ames, IA 50011, USA
2
Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
3
Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
4
Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
Maize domestication provides an ideal system to understand evolution. The history of maize domestication
has been well documented with tremendous morphological changes, adaptation to diverse environments,
and major demographic shifts. Meanwhile, maize genome also went through profound changes following
domestication bottleneck, i.e., domesticated maize have significantly reduced genetic diversity and
increased mutational load. More recently, a striking pattern, maize building their genomes with more
nucleotide A and T than their wild progenitor teosinte, was discovered. This genome divergence p attern
was consistently observed in multiple other species.
Here, by focusing on the base-composition value summarized from polymorphic sites, we provide novel
insights on maize genome evolution at different regions of the genome: genic versus nongenic,
pericentromeric versus nonpericentromeric, and methylated versus unmethylated. We show that the
divergence in base-composition value between maize and teosinte is larger in nongenic than genic part of
the genome. Interestingly, the divergence is significantly enlarged in pericentromeric regions. Moreover,
motif frequency and sequence context analyses showed the motifs (PyCG) related to solar-UV signature
have higher frequencies in nongenic and pericentromeric regions, particularly when they are methylated,
implicating the role of DNA methylation in promoting solar-UV induced mutations. We also discovered the
enrichment of mutations related to solar-UV signature in maize, which indicates the varied mutation rate
across populations. In addition, a set of genes including ATR and RPA1 involved in UV damage repair
pathways were identified to be associated with the genome divergence between maize and teosinte.
Together, these findings demonstrate that solar-UV radiation and differential mutation repair play a critical
role in the genome divergence between maize and teosinte. Our integrated analysis provides the first
example to establish the important links among UV radiation, mutation, DNA repair, methylation, and
genome evolution.
Funding acknowledgement: National Science Foundation (NSF), Iowa State University Raymond F. Baker
Center for Plant Breeding, Iowa State University Plant Science Institute
34
SESSION 4 – EMERGING TOOLS AND CHALLENGES
Chair: Erich Grotewold
Friday, March 23. 4:15 PM – 5:35 PM
T12
Maize - GO Annotation Methods Evaluation and Review (Maize-GAMER)
(submitted by Kokulapalan Wimalanathan <kokul@iastate.edu>)
Full Author List: Wimalanathan, Kokulapalan1 2; Friedberg, Iddo1 3; Andorf, Carson M 1 4 5; Lawrence-Dill,
Carolyn J1 2 6
1
Bioinformatics and Computational Biology, Iowa State University, Ames , IA 50011, USA
2
Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
3
Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA
50011, USA
4
USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011,
USA
5
Department of Computer Science, Iowa State University, Ames, IA 50011, USA
6
Department of Agronomy, Iowa State University, Ames, IA 50011, USA
We created a new high-coverage, robust, and reproducible functional annotation of maize protein coding
genes based on Gene Ontology (GO) term assignments. Whereas the existing Phytozome and Gramene
maize GO annotation sets only cover 41% and 56% of maize protein coding genes, respectively, this stu dy
provides annotations for 100% of the genes. We also compared the quality of our newly -derived
annotations with the existing Gramene and Phytozome functional annotation sets by comparing all three to
a manually annotated gold standard set of 1,619 genes where annotations were primarily inferred from
direct assay or mutant phenotype. Evaluations based on the gold standard indicate that our new annotation
set is measurably more accurate than those from Phytozome and Gramene. To derive this new high coverage, high-confidence annotation set we used sequence similarity and protein-domain-presence
methods as well as mixed-method pipelines that developed for the Critical Assessment of Function
Annotation (CAFA) challenge. Our project to improve maize annotations is called maize-GAMER (GO
Annotation Method, Evaluation, and Review) and the newly-derived annotations are accessible via
MaizeGDB (http://download.maizegdb.org/maize-GAMER) and CyVerse (B73 RefGen_v3 5b+ at
doi.org/10.7946/P2S62P and B73 RefGen_v4 Zm00001d.2 at doi.org/10.7946/P2M925).
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
35
T13
Using DAP-seq to map genome-wide ARF transcription factor binding
events in maize
(submitted by Mary Galli <marygalli@waksman.rutgers.edu>)
Full Author List: Galli, Mary 1; Khakhar, Arjun2; Chen, Zongliang1; Lu, Zefu 3; Sen, Sidharth4; Joshi,
Trupti4; Nemhauser, Jennifer L.2; Schmitz, Robert J.3; Gallavotti, Andrea 1 5
1
Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA 08854-8020
2
Department of Biology, University of Washington, Seattle, WA, USA 98195
3
Department of Genetics, The University of Georgia, Athens, GA, USA 30602
4
Informatics Institute, University of Missouri, Columbia, MO, USA 65211
5
Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA 08901
AUXIN RESPONSE FACTORS (ARFs) are a family of plant-specific transcription factors (TFs) that
occupy a pivotal position in the signal transduction pathway of the plant hormone auxin. Due to their
ability to directly bind DNA and to interact with components of the auxin receptor, ARFs mediate the large
transcriptional changes and diverse developmental responses regulated by auxin. However, our
understanding of the functional differences among ARF members is severely limited by a lack of genome wide binding data for the numerous family members that are present in higher plant species. Using DAPseq, a genomic DNA-TF binding assay, we obtained comprehensive cis-regulatory maps for fourteen maize
ARFs from the two evolutionarily conserved class A ‘activator’ and class B ‘repressor’ clades. We
identified 124,530 distinct binding sites, generating the largest dataset of ARF targ ets identified in any
plant species to date. We observed minimal genome-wide binding site diversity for ARFs of the same class,
but found substantial differences in motif sequence, spacing, site preference, and association with auxin
induced genes among class A and class B ARFs. Despite these differences, many binding sites and target
loci were occupied by ARFs from both classes, suggesting transcriptional coordination for a large number
of genes related to maize development, domestication and fitness, including putative regulatory targets that
correspond to known QTL regions.
Gene / Gene Models described:
ARF34,ARF16,ARF27,ARF4,ARF29,ARF35,ARF18,ARF25,ARF14,ARF7,ARF10,ARF36,ARF13,ARF39;
GRMZM2G081158,GRMZM2G028980,GRMZM2G160005,GRMZM2G034840,GRMZM2G086949, GR
MZM2G317900,GRMZM2G035405,GRMZM2G116557,GRMZM2G137413,GRMZM2G475263,GRMZ
M2G338259,GRMZM2G702026,GRMZM2G378580,GRMZM2G017187
Funding acknowledgement: National Science Foundation (NSF)
36
T14
Long-range Interactions Provide a Topological Basis for Genetic
Regulation of Complex Traits in Maize
(submitted by En Li <lienen2013@163.com>)
Full Author List: Li, En 1; Liu, Han 1; Huang, Liang liang 1; Li, Yuan 1; Dong, Xiaomei1; Zhang, Xiangbo1;
Zhao, Haiming 1; Song, Weibin 1; Lai, Jinsheng1
1
State Key Lab of Agrobiotechnology and National Maize Improvement Center,Department of Plant
Genetics and Breeding, China Agricultural University;NO.2,The West Street of Yuanmingyuan Park,
Haidian District;Beijing,P.R.China,100193
Higher-order chromosomal organization for transcription regulation is poorly understood in plants. We
performed genome-wide chromatin interaction analysis by paired-end-tag sequencing (ChIA-PET), and
identified more than 20,000 long-range enhancer- and promoter-centered chromatin interaction associated
with H3K4me3 and H3K27ac in maize immature ear and shoot. The P-P, P-E, and E-E interactions
accounted for 65%, 35%, and 5% chromatin interaction between enhancer and promoter, respectively.
Genes which promoters interacted with each other preferred to be co-expressed. The expression levels of
genes with interacting enhancers are higher than that of genes without interacting enhancers. In addition,
compared to genes with intergenic interacting enhancers, genes with enhancers in gene bodies are prone to
be constitutive genes. Comparison of chromatin interactions between tissues revealed that tissue-specific
chromatin organization is associated with the expression of tissue-specific genes. Moreover, the P-E
interactions map also provided a topological basis for the transcription regulation of genes associated with
complex agronomic traits.
Funding acknowledgement: National Science Foundation (NSF)
37
T15
The RNAseq Time Machine: Species-specific shifts in developmental
timing and trajectory underlie morphological differences in maize tassel
and sorghum panicle architecture
(submitted by Samuel Leiboff <sleiboff@berkeley.edu>)
Full Author List: Leiboff, Samuel1; Hake, Sarah C1
1
UC Berkeley / Plant Gene Expression Center; 800 Buchanan Street; Albany, CA, USA 94710
The maize genetics community has identified key regulators of tassel architecture through the study of
mutants and their interactors. By dissecting mutant inflorescence phenotypes, researchers have
characterized a progression of tassel developmental stages. Yet our understanding of the global dynamics
of gene expression and the developmental trajectory of genes outside of classic master regulators is still
fragmented. On the other hand, Sorghum bicolor (L. Moench) is a close maize relative that creates a
complex inflorescence of perfect flowers, or panicle, for which we have little developmental genetic
information.
We took advantage of high-throughput sequencing, dynamic gene expression analysis techniques, and the
rich history of maize genetics to stage and compare maize tassel and sorghum inflorescence development,
independent of morphological features. By conducting tandem RNAseq and image processing on more than
40 individual maize tassel and sorghum panicle primordia across 40 days of development, we generated
dense gene expression matrices that closely track the dynamics and trajectory of inflorescence development
in both species. Using a core set of 1,500 developmentally-responsive transcripts, expression profile
clusters identified about 5 developmental stages for both species. These stages strongly correlate with our
collected inflorescence primordia morphological measurements. Dynamic gene expression patterns
detected putative stage-specific molecular markers for each species and facilitated the comparison of
sorghum and maize panicle development. By constructing gene co-expression networks for maize tassels
and sorghum panicles, we generated large gene expression modules that correlate with developmental
trajectory as well as morphological measurements. Expression modules were enriched for biological
processes such as stem cell regulation and floral development and implicated previously unknown genes
alongside familiar master regulators. Comparing stage-specific molecular markers, co-expression modules,
and maize/sorghum syntenic orthologues of known inflorescence genes, we observed species-specific shifts
in developmental trajectory and timing that may underlie morphological distinctions between these two
essential food crops.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
38
SESSION 6 – INTERACTIONS WITH THE ENVIRONMENT
Chair: Natalia de Leon
Saturday, March 24. 8:30 AM – 10:30 AM
T16
Enhancing phosphorus efficiency in maize and sorghum
(submitted by Sylvia Morais de Sousa <sylvia.sousa@embrapa.br>)
Full Author List: de Sousa, Sylvia M 1; Hufnagel, Barbara2; Azevedo, Gabriel C2; Lopes, Simara M 3; Negri,
Barbara F3; Lana, Ubiraci G P1; Barros, Beatriz A 1; Alves, Meire C1; Carneiro, Andrea A 1; Guimarães,
Claudia T1; Magalhães, Jurandir V1
1
Embrapa Milho e Sorgo, Sete Lagoas, MG, Brasil
2
Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
3
Universidade Federal de São João del-Rei, São João del Rei, MG, Brasil
Phosphorus (P) is an essential nutrient to plants and is acquired as inorganic phosphate from the
rhizosphere solution. P is one of the least available nutrients particularly in highly weathered, tropical soils,
limiting substantially plant growth. Our work aimed to study root traits involved with P acquisition
efficiency and to identify and validate maize and sorghum homologs to Phosphorus Starvation Tolerance 1
(PSTOL1), a gene responsible for enhanced early root growth, P uptake and grain yield in rice. Association
mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system
morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P
conditions. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P
in hydroponics, whereas other alleles increasing root surface area also increase grain yield in low-P soil.
SbPSTOL1 genes colocalized with QTLs for traits underlying root morphology and dry weight
accumulation under low P-soil. For maize, two multiple interval models were used to map QTLs related to
root traits, biomass accumulation and P content in a maize RIL population cultivated in nutrient solution.
Multiple interval mapping models for single and multiple traits were combined and revealed 13 genomic
regions significantly associated with the target traits in a complementary way. Some of these quantitative
trait loci (QTLs) were coincident with QTLs for root morphology traits and grain yield previously mapped,
whereas others harbored ZmPSTOL1 candidate genes. OsPstol1 and its maize and sorghum homologs were
cloned in the pMCG1005 vector and tobacco Petit havana plants were genetically transformed via
Agrobacterium tumefaciens. Several events presented one copy of the transgene and those that also showed
high transgene expression were selected for phenotypic evaluation under low P conditions. The transgenic
plants, T1 and T2 generations, were grown for ~60 days in ½ MS medium with low P under controlled
conditions. When compared with the control, plants transformed with pMCG1005 (empty vector) the
PSTOL1 transgenic plants presented higher vegetative growth and root surface area under low P. Our
results indicated that PSTOL1 homologs have a similar role as osPSTOL1 gene in rice plants and have
potential to enhance P acquisition and yield in different species.
Funding acknowledgement: Embrapa, GCP, Fapemig, CNPq
39
T17
Regulation of aquaporin expression in maize: proximal and distal eQTLs
(submitted by Laurie Maistriaux <laurie.maistriaux@uclouvain.be>)
Full Author List: Maistriaux, Laurie C.1; Jeanguenin, Linda 1; Alvarez Prado, Santiago2; Nicolas, Stéphane3;
Welcker, Claude2; Charcosset, Alain 3; Tardieu, François2; Chaumont, François1
1
Institut des Sciences de la Vie, Université catholique de Louvain, Louvain -la-Neuve, Belgium
2
INRA-LEPSE, Montpellier, France
3
INRA/INA-PG/UPS/CNRS, Station de Génétique Végétale, Gif-sur-Yvette, France
Plasma membrane intrinsic proteins (PIPs) are aquaporins that facilitate the passive movement of water
through biological membranes. These channels are involved in numerous physiological and cellular
processes such as hydraulic conductivity, transpiration, photosynthesis and osmoregulation in plants. In a
context of climatic changes, they could turn out to be key targets for selection of crop varieties optimized
for water use efficiency.
Whereas PIP mRNA levels in maize tissues vary according to the developmental stages and under varying
environmental conditions, the molecular actors and mechanisms regulating the transcription of these genes
remain largely unknown. Relying on the genetic material (254 maize genotypes and ~1000 K SNPs
collection) and expertise of the European DROPS (DROught tolerant yielding PlantS) project, we
performed GWAS (genome-wide association study) analyses in order to identify promising eQTLs
(expression quantitative trait loci) associated with variation in the expression of five PIP genes in the
mature and elongation zones of the leaf. In most cases, highly significant eQTLs were identified close to
the PIP genes themselves suggesting the large impact of cis-regulation, as well as numerous promising
distal eQTLs that appear to be mainly zone-specific. Conditional GWAS, avoiding the cis-eQTLs effects,
allowed the identification of even more proximal and distal eQTLs, highlighting the complex regulation of
the PIP gene expression. Deeper analyses and functional validation of several eQTLs are currently ongoing.
Funding acknowledgement: FNRS (Fonds de la recherche scientifique - Belgique)
40
T18
Innovative and high-throughput field phenotyping method provides leaf
traits for breeding of drought tolerance - From Leaf Area Index dynamics
to its physiological components
(submitted by Justin Blancon <justin.blancon@biogemma.com>)
Full Author List: Blancon, Justin 1; Labrosse, Jérémy 2; Cohen, Dan 2; Comar, Alexis 2; Tixier, MarieHélène1; Lopez, Jérémy 1; Baret, Frédéric3; Praud, Sébastien1
1
BIOGEMMA; Centre de Recherche - Route d'Ennezat; CHAPPES; FRANCE; 63720
2
HIPHEN; Centre INRA PACA - UMR 114 EMMAH - 228, Route de l’Aérodrome; AVIGNON;
FRANCE; 84914
3
INRA; Centre INRA PACA - UMR 114 EMMAH - 228, Route de l’Aérodrome; AVIGNON; FRANCE;
84914
Since last decade genotyping advances, reliable, cheap, and high-throughput phenotyping methods has
become critical to further dissect the genetics of quantitative traits. In maize breeding, substantial efforts
are made to improve drought tolerance. Leaf development and senescence are pivotal in some of the major
physiological strategies for drought tolerance. However, with classical phenotyping methods, monitoring
leaf area in the field across maize whole lifecycle can be laborious, or even unfeasible for a large panel. We
propose an innovative and high-throughput method to phenotype maize Leaf Area Index (LAI) dynamics
and its components from emergence to death. Our approach is based on a simple LAI model, a few ground
measurements and UAV remote sensing. For 15 contrasted genotypes of “BALANCE”, a panel derived
from a MAGIC population, we measured LAI model input parameters (phyllochron, final leaf number,
biggest leaf area, and a senescence factor) in Well-Watered and Water-Deficient conditions. We then
simulated LAI dynamics for these genotypes. All the 380 genotypes of the panel were measured on 9 dates
across the lifecycle, with multispectral sensor mounted on a UAV, in both conditions. We built empirical
relationships between multispectral measurements and simulated LAI of the contrasted genotypes and
applied them to the entire panel. Based on this dataset we were able to inverse the LAI model and retrieve
input parameters leading to these dynamics. Analyses showed that our 15 genotypes training dataset depicts
fairly well the panel diversity when building the empirical relationships. They also indicated that
multispectral data carry enough information to estimate LAI with good precision. Finally, LAI model
inversion led to contrasted results: the senescence factor was retrieved with the higher accuracy, followed
by biggest leaf area, phyllochron and final leaf number. We will discuss these results and draw the
interesting prospects for breeding offered by this method.
Funding acknowledgement: National Association of Research and Technology of France (ANRT)
41
T19
Characterization of biosynthetic pathways and regulatory elements for the
production of the volatile homoterpenes DMNT and TMTT in Zea mays
(submitted by Joerg Degenhardt <joerg.degenhardt@pharmazie.uni-halle.de>)
Full Author List: Schaff, Claudia 1; Richter, Annett2; Zhang, Zhiwu 3; Buckler, Edward 4; Degenhardt, Joerg1
1
Martin Luther University Halle, Institute for Pharmacy, Hoher Weg 8, D- 06120 Halle, Germany
2
Boyce Thompson Institute for Plant Research, Ithaca NY14853-1801, USA
3
Washington State University, Department of Crops and Soil Sciences, Pullman, WA 99163
4
Cornell University Biotechnology Building Ithaca, NY 14853-2901, USA
Plant volatiles have multiple defense functions in the defense of maize against herbivores, fungi, and
bacteria. In addition, these volatiles also have been implicated in signaling within the plant and towards
other organisms. Elucidating the function of individual plant volatiles will require considerably more
knowledge of their biosynthesis and regulation in response to external stimuli. Exploiting the variation of
herbivore-induced volatile blends among 26 maize (Zea mays) inbred lines, we conducted a nested
association mapping (NAM) and genome-wide association study (GWAS) to identify a set of quantitative
trait loci (QTLs) for investigating the pathways of volatile terpene production. The most significant
identified QTL affected the emission of (E)-nerolidol, linalool, and the two homoterpenes, 3,8-dimethyl1,4,7-nonatriene (DMNT), and (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene (TMTT). GWAS associated
this QTL with a single nucleotide polymorphism in the promoter of terpene synthase tps2. Biochemical
characterization of TPS2 verified that this plastid-localized enzyme forms linalool, (E)-nerolidol, and
(E,E)-geranyllinalool. The subsequent conversion of (E)-nerolidol into DMNT maps to a P450
monooxygenase, CYP92C5, which is capable of converting nerolidol into DMNT by oxidative degradation.
A QTL influencing TMTT accumulation corresponds to a similar monooxygenase, CYP92C6, which is
specific for the conversion of (E,E)-geranyllinalool to TMTT. The DMNT biosynthetic pathway and both
monooxygenases are distinct from those previously characterized for DMNT and TMTT synthesis in
Arabidopsis, suggesting independent evolution of these enzymatic activities.
We identified several genomic regions which control the emission of the terpenes DMNT, TMTT, and
nerolidol, and encode potential regulatory elements like transcription factors. Transcriptome analysis
identified several transcription factors that display herbivore-controlled expression patterns. Functional
characterization of one of these transcription factors with maize transposon insertion mutants indicated that
it is specifically involved in the regulation of DMNT and TMTT production after herbivory.
Funding acknowledgement: United States Department of Agriculture (USDA), German Research
Foundation (DFG)
42
T20
Mycorrhizal phosphate uptake affects maize root-associated microbiota
(submitted by Marcel Bucher <m.bucher@uni-koeln.de>)
Full Author List: Gerlach, Nina 1; Fabianska, Izabela 1; Pesch, Lina1; Bucher, Marcel1
Botanical Institute, Cologne Biocenter, Cluster of Excellence on Plant Sciences (CEPLAS), University of
Cologne, Zülpicherstrasse 47b, 50674 Cologne, Germany
1
The crop model maize (Zea mays L.) thrives by interacting with an astounding numb er of microorganisms,
i.e. the so-called microbiota, which comprises mainly bacteria, but also fungi, protozoa and viruses. In most
plants arbuscular mycorrhizal fungi (AMF) are an important functional group of terrestrial microbiota; they
are beneficial for maize growth and health on agricultural soils with low phosphate (Pi) availability. Little
is known about the drivers of microbial community assembly in the mycorrhizal root.
Maize plants colonized by AMF Rhizophagus irregularis exhibited systemic alterations in their leaves,
including anthocyanin and lipid metabolism, changes in metabolic fluxes, but also induction of defense
gene expression and accumulation of secondary metabolites suggesting priming of mycorrhizal maize
leaves (Gerlach et al., 2015). We thus hypothesized that alterations at the root level as a consequence of
AM colonization and symbiotic functions impact the structure of the root-associated microflora.
A transposon insertional maize mutant defective in Pi transporter Pht1;6 was impaired in mycorrhizal Pi
uptake and exhibited strongly reduced colonization by AMF when grown in isolation, and a strong
reduction of shoot growth and cob development. This highlighted the importance of mycorrhizal Pi uptake
for maize performance. Moreover transcriptomic analysis of mycorrhizal wild type relative to pht1;6 via
RNAseq revealed differential regulation of genes involved in signalling, hormone metabolism, and cell
wall biosynthesis. In addition, elemental fingerprinting revealed an altered elemental composition in pht1;6
shoots. When cultivated in community with wild type plants colonization by AMF was restored in pht1;6
(Willmann et al., 2013). Such trans-complementation assays highlighted the impact of neighboring
mycorrhizal plants on the root-associated microbiota of pht1;6. Using methodology to sequence and
explore soil- and root-inhabiting microbial communities by 16S rRNA and ITS surveys, we now show that
Pht1;6 activity is a driver of the taxonomic structure of fungal and bacterial assemblages.
Gene / Gene Models described: ZEAma;PHT1;6; GRMZM5G881088_T01
Funding acknowledgement: German Ministry of Education and Research, International Max Planck
Research School Cologne
43
T21
Discovery of dolabralexins, previously unrecognized terpenoid defense
compounds in maize (Zea mays).
(submitted by Katherine Murphy <kmmurphy@ucdavis.edu>)
Full Author List: Murphy, Katherine M 1; Mafu, Sibongile2; Ding, Yezhang 3; Schmelz, Eric3; Zerbe,
Philipp 1
1
UC Davis; Davis, CA 95616
2
U of Massachusetts-Amherst; Amherst, MA 01002
3
UC San Diego; San Diego, CA 92093
Specialized terpenoids are major components of complex maize (Zea mays) chemical defenses that mediate
responses to herbivores, pathogens and other environmental challenges. Here we describe the discovery,
biosynthesis and elicited production of a new class of maize diterpenoids, named dolabralexins. Metabolite
profiling of common maize cultivars under field conditions supports the widespread biosynthesis of
dolabralexins as predominant metabolites in roots. Oxidative stress and elicitation with fungal Fusarium
pathogens elicit the accumulation of dolabralexins and the transcript expression of corresponding
biosynthetic genes. Consistent with fungal-elicited defenses, select pathway intermediates significantly
inhibit fungal growth in vitro. Furthermore, dolabralexin and previously described kauralexin diterpenoids
are critical for determining the rhizosphere microbiome composition. Together, these findings support
defense-related roles for dolabralexins in maize stress interactions and expand the known chemical space of
diterpenoid defenses as genetic targets for understanding and ultimately improving maize resilience.
Funding acknowledgement: National Science Foundation (NSF), Department of Energy (DOE), University
of California
44
SESSION 7 – EXPRESSING THE GENOME
Chair: Andrea Eveland
Saturday, March 24. 11:15 AM – 12:55 PM
T22
Predicting Across the Central Dogma of Molecular Biology: DNA to
mRNA Abundance
(submitted by Jacob Washburn <jdw297@cornell.edu>)
Full Author List: Washburn, Jacob1; Mejía-Guerra, M. Katherine 1; Kremling, Karl A.1; Buckler, Edward
S.2; Wang, Hai1
1
Cornell University; Ithaca, NY, USA 14853
2
USDA-ARS; Ithaca, NY, USA 14853
The central dogma of molecular biology is a framework for understanding how genetic information results
in organismal level phenotypes. Being able to predict one step along the central dogma from its previous
step would enable greater understanding of basic biology and advances in crop improvement. To do this,
we created a number of machine learning models that take as input genomic regions upstream of coding
sequences. Initially, we used modified natural language processing algorithms (bag-of-words, and
word2vec) to model chromatin domains and transcription factor binding sites in the genome with aROC
values greater than 0.97. Building on those models, we next developed convolutional neural network
(CNN) architectures for the simple problem of predicting if a gene is a pseudo-gene. These models perform
with an aROC above 0.87. We further designed CNN models which predict absolute gene expression
values with an R2 of 0.49. Examination of these models show that they place considerable weight on both
the 5’ and 3’ UTR regions. Some drawbacks of this model however are the potential for gene familyderived contamination in training and testing sets, and dataset imbalance. Additionally, for applied
breeding one actually wants to know relative expression among alleles in a population, not necessarily their
absolute expression values. To overcome these challenges we designed a predictive framework in which
maize genes are compared with their syntenic orthologs in Sorghum and other close relatives. The CNN
model then predicts which ortholog from the group is more strongly expressed. This model performs with
aROC value above 0.90 and represent a first step in promoter strength prediction of maize alleles. These
models have clear applications to cis -regulation, promoter function, gene annotation, and enhancement of
genomic prediction.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
45
T23
Mapping the archesporial cell to meiocyte progression using single-cell
RNA-Seq
(submitted by Bradlee Nelms <bnelms.research@gmail.com>)
Full Author List: Nelms, Bradlee D1; Walbot, Virginia 1
Stanford University; 385 Serra Mall; Stanford, CA 94305; USA
1
Meiosis is one of the most dramatic changes in an organism’s life cycle. In the maize anther, the first cell
type committed to a meiotic lineage forms nearly a week before the onset of meiosis. These meiotic
precursor cells undergo substantial changes during this time: increasing in volume 30 fold, developing a
characteristic morphology with prominent nucleoli, and installing a subset of meiotic proteins onto the
chromosomes. To gain a high resolution view of the developmental pro gram leading up to meiosis, we used
single-cell RNA-sequencing to follow changes in gene expression between the specification of the germinal
lineage through the first few stages of meiotic prophase I. We identified three major phases of gene
expression during this interval, with a particularly rapid rearrangement of the transcriptome shortly before
the onset of meiotic chromosome pairing. Our data suggests substantial coordination between cytoplasmic
remodeling and chromosomal reorganization. We are currently investigating the functional importance of
rapid new transcription during the beginning of meiosis.
Funding acknowledgement: National Science Foundation (NSF)
46
T24
Single parent expression is a general mechanism driving extensive
complementation of non-syntenic genes in maize hybrids
(submitted by Jutta Baldauf <baldauf@uni-bonn.de>)
Full Author List: Baldauf, Jutta A.1; Marcon, Caroline1; Lithio, Andrew2; Vedder, Lucia 3; Altrogge, Lena 3;
Piepho, Hans-Peter4; Schoof, Heiko 3; Nettleton, Dan 2; Hochholdinger, Frank1
1
Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn,
53113 Bonn, Germany
2
Departments of Statistics, Iowa State University, Ames, IA 50011-1210, USA
3
Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115
Bonn, Germany
4
Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany
Distantly related maize (Zea mays L.) inbred lines exhibit an exceptional degree of structural genomic
diversity, which is probably unique among plants. We surveyed how the structural genomic diversity of a
maize inbred line panel (B73, Mo17, A554, H84, H99, Oh43 and W64A) affects the transcriptomic
plasticity of their F1-hybrids during three stages of early primary root development. A RNA -seq experiment
was designed to maximize the number of direct comparisons among the parent-hybrid pairs and to
simultaneously ensure a high degree of precision for indirect comparisons. Genes active in one but inactive
in the second parental inbred line represent an extreme instance of allelic diversity, which was denoted as
single parent expression (SPE). We demonstrated that extreme gene expression complementation in F1hybrids is a general mechanism extensively implemented by genes active in only one parent. In all
genotype-by-stage combinations ~1,000 genes show SPE patterns even in B73-independent hybrid crosses
of the distantly related inbred lines Oh43 and W64A. Along primary root development, a substantial
number of genes displaying SPE patterns were conserved, while only a small proportion were conserved
between the different genotypes. Consequently, the number of expressed genes in all hybrids at all
developmental stages exceeded their parental inbred lines by several hundred. Gene expression
complementation is mainly driven by evolutionary younger non-syntenic genes, which emerged after the
separation of the maize and sorghum lineages. Among those, the highly diversified families of bZIP and
bHLH transcription factors were specifically overrepresented. Based on their attributed functions, these
genes individually provide only minor advantages, but might collectively contribute to the superior
plasticity of hybrids.
Funding acknowledgement: National Institutes of Health (NIH), National Science Foundation (NSF),
Deutsche Forschungsgemeinschaft (DFG),
47
T25
The regulatory landscape of developing maize inflorescences: linking
phenotypic variation to the functional non-coding genome
(submitted by Edoardo Bertolini <ebertolini@danforthcenter.org>)
Full Author List: Bertolini, Edoardo 1; Parvathaneni, Rajiv 1; Shamimuzzaman, Md 1; Lipka, Alexander2;
Vera, Daniel3; Bass, Hank W.4; Eveland, Andrea L.1
1
Donald Danforth Plant Science Center; Saint Louis; MO, U.S.A 63132
2
Department of Crop Sciences, University of Illinois; Urbana; IL, U.S.A 61801
3
The Center for Genomics and Personalized Medicine, Florida State University; Tallahassee; FL, U.S.A.
32306
4
Department of Biological Science, Florida State University; Tallahassee; FL, U.S.A. 32306
Gene regulation has a profound effect on developmental plasticity contributing to plant adaptation and
yield potential. Although many key protein coding genes (PCGs) have been identified that control intricate
aspects of maize development, little is known about how the non-coding space, including long non-coding
RNAs (lncRNAs), cis-regulatory elements and transposable elements, contributes to fine tuning of
developmental processes. To define the functional landscape of early maize inflorescence development, we
generated genome-wide chromatin accessibility maps using micrococcal nuclease sensitivity coupled with
high-throughput sequencing (MNase-seq) in young tassel and ear primordia. We annotated potentially
active regulatory regions in these tissues by applying a segmentation algorithm called ISeg, and by
integrating publicly available datasets.
Depending on the peak-calling stringencies used, our analyses showed that 1.6-4.8% of the maize genome
was accessible during early inflorescence development and approximately 80% of hypersensitive regions
were shared between tassel and ear. Hypersensitive regions were found in various genomic contexts;
enriched within proximal promoters and in the 3’ UTRs and non-coding space immediately downstream of
PCGs. To better understand the role of non-coding functional elements, we annotated 2,760 highconfidence lncRNAs using developmentally staged ear and tassel RNA -seq data. These lncRNAs were
largely within 10 kb of PCGs, overlapped accessible chromatin regions, and were highly expressed in
inflorescence primordia. Approximately 5% of these high-confidence lncRNAs were conserved between
maize and sorghum. In addition, we integrated GWAS analyses for inflorescence architecture traits and
showed enrichment of trait-associated SNPs in accessible regions, which were used to further prioritize
functional elements that contribute to regulation of inflorescence development and variation in phenotype.
Together these data provide genome-scale insight into the coordinated regulation of gene expression during
inflorescence development, and an untapped source of allelic variation that can be leveraged for future
breeding programs.
This work acknowledges funding from NSF-PGRP.
Funding acknowledgement: National Science Foundation (NSF)
48
T26
Circular RNAs mediated by transposons are associated with
transcriptomic and phenotypic variation in maize
(submitted by Lu Chen <luchen@webmail.hzau.edu.cn>)
Full Author List: Chen, Lu 1; Zhang, Pei1; Fan, Yuan 1; Lu, Qiong 1; Li, Qing 1; Yan, Jianbing 1; Muehlbauer,
Gary J2 3; Schnable, Patrick S4; Dai, Mingqiu 1; Li, Lin 1
1
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan
430070, China.
2
Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108 USA.
3
Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108 USA.
4
Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA.
Circular RNAs (circRNAs) are covalently closed RNA molecules. Recent studies showed that circRNAs
can arise from the transcripts of transposons. Given the prevalence of transposons in the maize genome and
dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be
involved in the formation of circRNAs and further modulate phenotypic variation. We performed circRNASeq on B73 seedling leaves and uncovered 2,804 high-confidence maize circRNAs, which show distinct
genomic features.Comprehensive analyses demonstrated that sequences related to LINE1-like elements
(LLE) and their Reverse Complementary Pairs (LLERCPs) are significantly enriched in the flanking
regions of circRNAs. Interestingly, as the number of LLERCPs increase, the accumulation of circRNAs
varies, while that of linear transcripts decreases. Furthermore, genes with LLERCP-mediated circRNAs are
enriched among loci that are associated with phenotypic variation. These results suggest that circRNAs are
likely to be involved in the modulation of phenotypic variation by LLERCPs.Further, we showed that the
presence/absence variation of LLERCPs was associated with expression variation of cicrcRNA -circ1690
and was related to plant ear height potentially through the interplay between circRNAs and functio nal
linear transcripts. Our first study of maize circRNAs uncovers a potential new way for transposons to
modulate transcriptomic and phenotypic variations.
Funding acknowledgement: National Key Research and Development Program of China to Mingqiu Dai
and Lin Li (2016YFD0100600; 2016YFD0100802),Huazhong Agricultural University Scientific &
Technological Self-innovation Foundation to Lin Li(Program No. 2015RC016)
49
SESSION 9 – THE MAIZE (EPI)GENOMES
Chair: Maike Stam
Sunday, March 25. 9:00 AM – 10:20 AM
T27
Dynamics of DNA methylation during maize reproductive development
(submitted by Daniel Grimanelli <daniel.grimanelli@ird.fr>)
Full Author List: Grimanelli, Daniel1; Regulsky, Michael2; Schnittger, Arp3; Dombey, Rodolphe 1;
Martienssen, Rob 2
1
Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France
2
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
3
Biozentrum Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
Maize is blessed with relatively large reproductive cells, and an exceptional cytology. It is thus a powerful
experimental model to analyze chromatin dynamics during reproduction at high resolution, in a stagespecific manner, using a combination of methylome analysis, and hyper-resolution microscopy. We have
developed efficient protocols to study DNA methylation using bisulfite sequencing in isolated reproductive
cells, in both wild type plants and mutants affected in DNA methyl-transferase activity. We have generated
a temporal series of methylomes covering individual stages of male meiosis, including prophase I
(leptotene, pachytene, dyakinesis), metaphase I, dyades, prophase II, tetrads and young spores. The data
shows that DNA methylation during meiosis is dynamic, and significantly different from the patterns
observed in somatic cells. We further looked at the dynamic of methylation in developing embryos. We
uncovered a rapid process of hyper-methylation specifically in the CHH context, which is strictly
dependent on RNA-directed DNA methylation. DNA methyl-tranferase mutants in maize display a number
of developmental effects, including strict embryo lethality for CG methyltransferases, but also distinctive
effects on meiosis, gametogenesis and embryogenesis for mutants affecting CHG and CHH methylation.
We are currently analyzing the functional bases of these phenotypes using both classical cytology, bisulfite
sequencing and hyper-resolution microscopy. The data shows that Zmet5, a maize homologue of
Arabidopsis CMTs, is a key player of meiocyte methylation at non-CG sites. The mutant shows high
degrees of sterility, linked to clear meiotic abnormalities. Altogether, the data indicates t hat maize
represents a remarkable model to establish causal relationships between DNA methylation patterns and
reproductive functions.
Funding acknowledgement: ANR, DFG, HHMI
50
T28
Transposable element contributions to the dynamic maize genome and
transcriptome
(submitted by Sarah N. Anderson <sna@umn.edu>)
Full Author List: Anderson, Sarah N.1; Stitzer, Michelle C.2; Noshay, Jaclyn M.1; Brohammer, Alex1;
Zhou, Peng 1; Hirsch, Candice N.1; Ross-Ibarra, Jeffrey 2; Hirsch, Cory D.1; Springer, Nathan M.1
1
University of Minnesota Twin Cities, St. Paul MN 55108
2
University of California Davis, Davis CA 95616
Transposable elements (TEs) comprise the majority of the maize genome and have the potential to
contribute substantially to structural and expression variation among genotypes. Our understanding of the
consequences of variable TE insertions has been limited by challenges associated with assembling and
analyzing repetitive sequences genome-wide. The recent availability of high-quality de novo genome
assemblies for W22 and PH207, along with a structural annotation of TEs, provides the opportunity for
genome-wide analysis of the contribution of TEs to genome structural variation in maize. For over 150,000
TEs present in the B73 genome, we used flanking sequences to classify elements as conserved or
polymorphic in PH207 and W22. Over 700 Mb of the B73 genome assembly co nsists of TE insertions that
are absent from the W22 assembly. We also find differences in DNA methylation among lines at
polymorphic sites, demonstrating a genetic contribution to epigenetic variation. In addition to creating
structural variation, TEs also affect the transcriptome through their own expression or through effects on
nearby genes. Using a novel approach to monitor the expression of TE families using unique and multiply mapping RNAseq reads, we show that ~5% of the transcriptome is derived fro m TEs in most tissues. A
targeted analysis of RNAseq data from maize seedlings subjected to abiotic stresses such as heat, cold,
salinity or drought revealed hundreds of TE families and thousands of genes that were up - or downregulated. Many genes with altered expression are located near up-regulated TEs suggesting a possible
regulatory influence of TEs on nearby genes, a model that we are testing in genotypes with variable TE
insertions. The analysis of shared and polymorphic TE insertions in multiple maize genomes will be critical
for defining the role of TEs in creating genetic, epigenetic and gene expression variation in maize.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
51
T29
The evolutionary dynamics of maize small RNAs reveals novel regulatory
features in noncoding DNA.
(submitted by Stephen Moose <smoose@illinois.edu>)
Full Author List: Moose, Stephen1; Zhang, Bosen1; Barber, Wesley1; Li, Qing 1 2; Bubert, Jessica 1
1
University of Illinois; Urbana, Illinois, USA 61801
2
Huazhong Agricultural University, Wuhan, Hubei, China, 430070
The majority of the maize genome is composed of transposon-derived repeats. The contribution of these
noncoding sequences to regulatory variation and phenotypic traits is difficult to assess because they are not
effectively captured by SNPs and are subject to epigenetic control. Small RNAs (sRNAs) modulate
chromatin and transposon silencing via both RNA-directed DNA methylation (RdDM) and RNA
interference. To gain insights into the activities of noncoding DNA, we sequenced sRNAs from diverse
populations of maize inbreds, their corresponding hybrids, and pedigrees derived from crosses of divergent
inbred parents. Multiple modes of sRNA variation were observed that exhibit distinct population structures
compared to SNPs, and suggest genome-scale regulatory function. Short (21-22nt) sRNAs active in RNAinterference of transcribed transposons show rapid and dynamic evolution compared to long (24nt) sRNAs
associated with heterochromatic silencing. We find wide variation for the abundance of 24nt sRNAs
clustered within 200-bp of the boundaries of some maize genes, which coincide with islands of CHHmethylation, open chromatin, and stronger mRNA expression. We discovered these “gene boundary
sRNAs” are always highly abundant among inbreds from the Stiff Stalk heterotic gro up, but are variable
and less abundant in Non-Stiff Stalk inbreds. Integration of sRNA variation with RNASeq expression
profiles and phenotypic data using WGCNA regulatory network approaches identifies functional modules
associated with grain yield. One such module contains the RLG00010 transposon recently discovered to be
enriched in transcriptional enhancers. Another reveals that phasiRNAs, which are required for male fertility
in cereals, are also present in the developing ear and are negatively correlated with grain yield. We
conclude that sequencing sRNAs reveals novel genome-scale regulatory properties that are not evident
from DNA-trait associations, yet can be associated with important productivity traits.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
52
T30
Chromatin as a major determinant in the fate of meiotic double-strand
breaks and positioning of COs along maize chromosomes
(submitted by Adele Zhou <az266@cornell.edu>)
Full Author List: Zhou, Adele 1; Wang, Minghui1; Sidhu, Gaganpreet 1; Dukowic-Schulze, Stefanie2;
Avoles-Kianian, Penny 2; Springer, Nathan 2; Sun, Qi1; Chen, Changbin2; Kianian, Shahryar2; Pawlowski,
Wojtek1
1
Cornell University; Ithaca, NY, 14850
2
University of Minnesota, Minneapolis, MN, 55455
Most crossing-overs (COs) in maize, and other large-genome plants, are located near chromosome ends,
while few are in pericentromeric or centromeric chromosome regions. As ~20% of maize genes are in the
recombination-suppressed regions, this pattern presents a serious challenge to plant breeding. To solve this
problem, we study recombination pathway dynamics. COs are products of the meiotic recombination
pathway that is initiated by programed double-strand breaks (DSBs) in chromosomal DNA. Although the
CO distribution is biased, DSBs, which are much more numerous than COs, are present in maize in all
chromosome locations, including pericentromeric and centromeric regions. Previous studies have linked
meiotic recombination landscape to chromatin features, but it is not well understood how this interaction is
regulated and how it affects which of the many DSBs become COs. To address this question, we elucidated
the genome-wide relationship between DSBs, COs, chromatin marks H3K4me3, H3K9me2, and DNA
methylation. We found that DNA methylation is a major contributor to the decision of which DSBs become
COs and this decision is progressively enforced when meiotic DSBs are repaired. Interestingly, this process
proceeds differently in B73 and CML228, two maize inbreds with dramatically differing numbers of
recombination events. The relationship between DSBs, COs, and chromatin state is altered when DNA
methylation levels are reduced in the zmet2 mutant. In zmet2, CO numbers are increased overall and CO
distribution is dramatically shifted, with the CO number increasing in pericentromeric regions, at the
expense of chromosome ends. Thus, the zmet2 mutant can be used to facilitate recombination in
pericentromeric regions of maize chromosomes. We propose that a reduction in DNA methylation opens up
CO formation to regions of the genome that were previous blocked by DNA methylation.
Funding acknowledgement: National Science Foundation (NSF)
53
SESSION 10 – COMMUNICATING WITHIN AND BETWEEN CELLS AND PLANTS
Chair: Thomas Slewinski
Sunday, March 25. 10:50 AM – 12:00 PM
T31
Dissecting a new connection between cytokinin and jasmonic acid in
control of leaf growth
(submitted by Michael Muszynski <mgmuszyn@hawaii.edu>)
Full Author List: Del Valle-Echevarria, Angel R.1; Uyehara, Aimee N1; Cahill, James F.1 2; Nelissen,
Hilde3; Hunter, Charles 4; Jander, Georg 5; Muszynski, Michael G.1 2
1
Dept. of Tropical Plant and Soil Sciences, University of Hawaii at Mānoa, Honolulu, HI
2
Dept. of Genetics, Development and Cell Biology, Iowa State University, Ames, IA
3
VIB-UGhent Center for Plant Systems Biology, Ghent, Belgium
4
Chemistry Research Unit, CMAVE-USDA, Gainesville, FL
5
Boyce Thompson Institute, Ithaca, NY
Growth is critical for multicellular plant development and underlies many important agronomic traits. A
comprehensive understanding of the interacting signals that fine-tune plant growth, such that it is balanced
with other physiological responses, has yet to be fully realized. We are using the maize leaf as a model to
better understand the signals regulating plant growth, since the two cellular processes driving growth –
division and elongation – are spatially separated into distinct zones at the leaf base. Our analysis of the
semi-dominant Hairy Sheath Frayed1 (Hsf1) mutant indicated it had a smaller cell division zone and
reduced leaf growth caused by hypersignaling of the phytohormone cytokinin. Cytokinin (CK) typically
functions to promote cell proliferation but can also repress growth in certain contexts. How CK mediat es
repression is not well-defined. Our analysis of Hsf1 revealed that the mutant over accumulates jasmonic
acid (JA) in growing leaves, a hormone previously shown to both repress cell division and activate defense
pathways. This result suggested CK may crosstalk with JA in the control of leaf growth. Such a connection
was previously unrecognized and may explain one route by which CK can repress growth. To investigate
this connection, we determined that exogenous JA application repressed leaf growth while JA -deficiency
increased leaf growth in maize. We also assessed JA pathway gene expression levels in the division and
elongation zones of emerging leaves of Hsf1/+ and wild type (WT) seedlings. Several JA biosynthesis and
responsive genes were significantly upregulated in the growth zone of Hsf1 mutants compared to WT sibs.
JA-pathway gene expression was also induced in B73 inbred seedlings transiently treated with CK. Overall,
our results suggest CK signaling promotes JA accumulation through up-regulation of JA biosynthesis.
Further analysis of this new connection may provide insights into the mechanisms by which plants balance
growth with other processes, such as defense response.
Funding acknowledgement: National Science Foundation (NSF)
54
T32
How grass keeps growing: a predictive model of leaf growth regulation
based on studies in Zea mays
(submitted by Gerrit Beemster <gerrit.beemster@uantwerpen.be>)
Full Author List: De Vos, Dirk1 2; Nelissen, Hilde3 4; AbdElgawad, Hamada 1; Prinsen, Els 1; Broeckhove,
Jan 2; Inzé, Dirk3 4; Beemster, Gerrit 1
1
Laboratory for Integrated Plant Physiology Research (IMPRES), Department of Biology, University of
Antwerp, Antwerp, Belgium
2
Modeling Of Systems And Internet Communication (MOSAIC), Department of Mathematics and
Informatics, University of Antwerp, Antwerp, Belgium
3
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
4
VIB Center for Plant Systems Biology, Ghent, Belgium
Due to its size maize is an excellent model system to investigate the regulation of leaf growth in grass
species. Here we propose a mathematical model based on hormone cross-talk with auxin and cytokinin as
the primary signals determining basal rate and duration of growth. On top of that platform active
gibberellins provide an additional layer largely controlling growth rate, in a DELLA dependent way, which
may be vital for developmental plasticity and stress response. The model implemented with the modelling
software VPTissue can reproduce steady maize leaf growth characteristics as well as spatial patterns of
hormones and pathway enzymes in wild type, overexpression and dwarf lines. Importantly, the model
predicts temporal changes in hormone regulation such as a standing and then retreating GA1/8 wave and
how this affects leaf growth. Deviation between model and experimental data suggest the existence of a a
growth-driven negative feedback on growth termination, which could be experimentally validated by
excision and shading of the emerged part of the growing leaf.
Funding acknowledgement: Flanders Science Fund (FWO), Belgian Science Policy Office (BELSPO)
55
T33
TREHALOSE-6-PHOSPHATE PHOSPHATASE4, a paralog of
RAMOSA3, controls inflorescence architecture and shoot apical meristem
activity in maize
(submitted by Hannes Claeys <hclaeys@cshl.edu>)
Full Author List: Claeys, Hannes1; Vi, Son Lang 1; Goldshmidt, Alexander1; Feil, Regina2; Eveland,
Andrea3; Lunn, John 2; Jackson, David 1
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
2
Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
3
Donald Danforth Plant Science Center, St. Louis, MO, USA
In recent years, the disaccharide trehalose-6-phosphate (T6P) has emerged as an important regulator of
meristem function. A prime example of this is the classical maize mutant ramosa3 (ra3), which has
branched ears and more highly branched tassels due to a reduction in meristem determinacy. The causal
gene encodes a trehalose-6-phosphate phosphatase (TPP) that degrades T6P by converting it to trehalose.
However, how RA3 regulates meristem function remains enigmatic.
In order to find additional factors involved in RA3 function, ra3 was mutagenized to identify additional
mutations that enhance its ear branching phenotype. This screen revealed four alleles of tpp4, mutated in a
paralog of RA3. TPP4 is expressed in the same domain as RA3, and its expression is upregulated in ra3
mutants, indicating functional redundancy where TPP4 partially compensates for loss of RA3. All mutant
alleles have amino acid substitutions in conserved residues, resulting in a range of residual enzymatic
activities. Nonetheless, all alleles have similar phenotypic strength and behave semidominantly, suggesting
that there is no straightforward relation between TPP activity and phenotype. In agreement with this, no
change in T6P levels could be detected in these mutants, adding to a growing body of evidence for
regulatory functions for TPPs.
In the presence of functional RA3, tpp4 mutants have no inflorescence architecture phenotypes, but show
enlarged shoot apical meristems (SAMs). While the SAM is wider throughout development in tpp4
mutants, SAM height is only significantly increased around the floral transition, suggestive of earlier
flowering. Accordingly, floral transition markers are expressed earlier in tpp4 SAMs, and there is a
tendency towards earlier anthesis and silking in the field. These results suggest that the function of T6P in
flowering time regulation, first reported in Arabidopsis, is conserved in maize, and further establish the
importance of TPPs in the regulation of meristem activity.
Gene / Gene Models described: TPP4; Zm00001d052227
Funding acknowledgement: National Science Foundation (NSF), EMBO, DuPont-Pioneer
56
Poster Abstracts
P1
An expanded diversity panel reveals the magnitude of the maize pan-genome and
limitations of a single -reference genome sequence for GWAS
(submitted by Joseph Gage <jgage2@wisc.edu>)
Full Author List: Gage, Joseph L. 1 ; Vaillancourt, Brieanne2 3 ; Gustafson, Timothy J. 1 ; Hamilton, John2 3 ; Tracy, William F. 1 ;
Buell, C. Robin 2 3 ; Kaeppler, Shawn M. 1 4; de Leon, Natalia1 4
1
Department of Agronomy, University of Wisconsin - Madison, Madison, WI, USA 53706
2
Department of Plant Biology, Michigan State University, East Lansing, MI, USA 48824
3
DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA 48824
4
DOE Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI, USA 53706
Recent work in plants, including maize, has illustrated the relative prevalence of core and dispensable genes
within a given species. The goal of this work is to assess the impact of utilizing different maize genome
references to identify sequence variation and the relative contribution of different components of the pan-genome
to phenotypic expression. Previous work with a 503-member North American diversity panel of maize identified
nearly 9,000 novel transcripts not present in the reference B73 RefGen_v2. To better capture the diversity
available within temperate North American maize germplasm, we enlarged t hat diversity panel to include whole
seedling RNA-seq from a total of 942 inbreds and generated pan-genomes in parallel using both the Zm-B73REFERENCE-GRAM ENE- 4.0 and the Zm-PH207- REFERENCE_NS-UIUC_UMN- 1.0 genomes as
references for read alignment and subsequent SNP calling and expression profiling. A total of 34,447 and 39,672
novel transcripts were identified using the B73 and the PH207 reference genomes, respectively, comprising a
fourfold increase in the number of novel transcripts compared to previous estimates. This suggests that the
number of dispensable genes and the overall size of the maize pan-genome are much larger than previously
thought. Genome-wide association studies of reproductive and disease resistance traits reveal associations
between phenotypes and both core and dispensable genes. This finding highlights the importance of considering
novel transcripts and multiple references for the detection of phenotype-associated variants that would otherwise
be difficult or impossible to identify due to presence/absence variation in a traditional single-reference
framework.
Funding acknowledgement: United States Department of Agriculture (USDA), Department of Energy (DOE)
P2
Both hard and soft sweeps contribute to local adaptation of natural populations of
teosintes
(submitted by Anne Lorant <alorant@ucdavis.edu>)
Full Author List: Lorant, Anne1 3 ; Doebley, John2; Tenaillon, Maud3 ; Ross-Ibarra, Jeffrey1
Dept. of Plant Sciences, University of California, Davis, CA 95616, USA.
2
Laboratory of Genetics, University of Wisconsin, 425 Henry Mall, Madison, WI 53706. USA.
3
Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud,
Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France.
1
M aize was domesticated from the wild grass teosinte, Zea mays ssp. parviglumis . While much is known about
the genetics of maize domestication and differences between maize and teosinte, we know relatively little about
the evolution of teosinte in natural populations. To begin to understand the evolutionary forces shaping genetic
diversity in teosinte, we sequenced the genomes of multiple wild-collected individuals from each of six natural
populations spanning much of the geographic range of teosinte in southern M exico. Here we present preliminary
population genetic analyses of these samples. We find evidence of hard and soft selective sweeps mostly private
to individual populations, suggesting considerable local adaptation. We also show variable differentiation and
inbreeding among populations, consistent with hierarchical population structure and metapopulation dynamics.
Overall, our results on the evolution of teosinte in its natural habitats will likely provide insight into the genomewide patterns of diversity in locally adapting plants as well identify loci relevant for adapting maize to new and
changing environments.
Funding acknowledgement: National Science Foundation (NSF)
57
P3
Bulked Segregant - genotyping-by-sequencing: Cost-effective and background
independent genetic mapping of mutants and QTL
(submitted by Kokulapalan Wimalanathan <kokul@iastate.edu>)
Full Author List: Wimalanathan, Kokulapalan 1 2; Weeks, Rebecca2 3; Unger-Wallace, Erica2; Vollbrecht, Erik 1 2 3
Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011
2
Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011
3
Interdepartmental Genetics, Iowa State University, Ames, IA 50011
1
Genetic mapping of new mutants, which allows us to map a mutant phenotype to a causal locus or loci in the
genome, is a crucial step in forward genetics. Construction of a mapping population that consists of mutant and
normal individuals is essential for genetic mapping. The mapping population can be used by different highthroughput methods for genetic mapping. Single Nucleotide Polymorphism (SNP) arrays and Sequenome-based
methods detect presence and absence of pre-discovered SNPs, and therefore are not background independent. In
contrast, high-throughput sequencing (HTS) based methods used for genetic mapping are generally background
independent. Some HTS methods such as Genotyping-by-sequencing (GBS) and RAD-seq use DNA for
mapping, while other methods such as BSR-seq and M M APPR use RNA. Current DNA-based methods barcode
DNA extracted from each individual in the mapping population to construct the sequencing library, and RNAbased methods construct a separate library from each of two pools, namely mutant and normal. Both approaches
provide high resolution maps to identify causal loci, but are not cost-effective for screening a large number of
mutant families such as may be recovered from an enhancer/suppressor screen. Here we present a low-resolution,
but cost-effective, HTS-based method for genetic mapping. For each new mutant we pooled tissue from
phenotyped individuals to create a mutant pool and a normal pool. We adapted the original GBS method to
construct sequencing libraries, prepared libraries for several pairs of pools and determined rough map positions.
Our method is cheaper than the current GBS protocol, easier than using RNA for library construction, and
without sampling biases inherent in using RNA expressed in a certain tissue type(s). We are currently fine
mapping the intervals identified by BS-GBS, and extending the method to map natural modifiers. Here we
present the pipeline and results from these genetic mapping efforts in maize.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
P4
Coming soon: Whole genome assembly of the maize NAM founders
(submitted by Kelly Dawe <kdawe@uga.edu>)
Full Author List: Dawe, R. Kelly 1; Ware, Doreen 2; Hufford, Matthew B. 3
Department of Genetics, University of Georgia, Athens, GA
2
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
3
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
1
M aize is an important crop and model organism for plant genetics. However, currently, nearly all forms of
sequence analysis are referenced to the single B73 inbred. Beyond B73, the most extensively researched maize
lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross section of
modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as
much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To
capture and utilize this variation, the NAM founder inbreds and a twenty-sixth line containing abnormal
chromosome 10 will be sequenced and assembled using a high-throughput strategy. Scaffolds will be validated
by BioNano optical mapping, and ordered and oriented using linkage data. RNA-seq data from multiple tissues
will be used to annotate each genome, and assemblies and annotations will be released with genome browser
support through M aizeGDB, NCBI, and Cyverse. Comparative genomic tools will be used to identify and catalog
the maize pangenome, and assess the role of structural variation such as presence-absence variation and copy
number variation in the determination of agronomic traits. Timeline and results will be disseminated through a
project web site. This work will be supported by NSF award #1744001.
Funding acknowledgement: National Science Foundation (NSF)
58
P5
Comparing alternative splicing in maize using 4 different reference genomes
(submitted by Jerald Noble <jnoble333@ufl.edu>)
Full Author List: Noble, JD1; Ling, Qinyin 1; Barbazuk, W. Brad1
University of Florida. 420 Cancer and Genomics Research Complex. Gainesville, FL. USA. 32608
1
M aize is a highly polymorphic species with extensive genetic diversity, gene copy number variation, and gene
presence-absence variation between genotypes of inbred lines. The current reference genome used for maize
bioinformatics studies is the genome of the B73 inbred line. Previous work has been conducted investigating
alternative splicing (AS) dynamics in maize between tissues, as a result of stress responses, and between
genotypes.
AS is a process enabling multiple transcript isoforms to be coded from a single gene thereby expanding an
organism’s proteome without increasing the size of the genome. Given the genetic diversity of maize, this study
profiles the diversity and conservation of AS between 27 maize genotypes. However, instead of comparing these
AS events between genotypes using only the B73 v4 reference genome, this study integrates the AS events
discovered in these genotypes relative to the W22, PH207, and CM L247 reference genomes. Currently all AS
events occurring in these genotypes relative to these reference genomes have been discovered and validated.
Preliminary results generated by comparing the AS events between genotypes relative to each reference genome
and by comparing the AS events discovered within genotypes using different reference genomes.
Funding acknowledgement: National Science Foundation (NSF)
P6
Computational classification of phenologs across biological diversity
(submitted by Ian Braun <irbraun@iastate.edu>)
Full Author List: Braun, Ian R1; Lawrence-Dill, Carolyn J1
1
Iowa State University; Ames, Iowa, 50011
Phenotypic diversity analyses are the basis for research discoveries that sp an the spectrum from basic biology
(e.g., gene function and pathway membership) to applied research (e.g., plant breeding). Phenotypic analyses
often benefit from the availability of large quantities of high-quality data in a standardized format. Image and
spectral analyses have been shown to enable high-throughput, computational classification of a variety of traits
across a wide range of phenotypes. However, equivalent phenotypes expressed across individuals or groups that
are not anatomically similar can pose a problem for such classification methods. In these cases, high-throughput,
computational classification is still possible if the traits and phenotypes are documented using standardized,
language-based descriptions. In the case of text phenotype data, conversion to computer-readable “EQ”
statements enables such large-scale analyses. EQ statements are composed of entities (e.g., leaf) and qualities
(e.g., length) drawn from terms in ontologies. In this work, we present a method for automatically converting
free-text descriptions of plant phenotypes to EQ statements using a machine learning approach. A random forest
classifier identifies potential matches between phenotype descriptions and terms from a set of ontologies
including GO (gene ontology), PO (plant ontology), and PATO (phenotype and trait ontology), among others.
The features used by this classifier include semantic, syntactic, and context similarity metrics between words and
ontology terms. This classifier is trained and tested using a dataset of manually converted plant descriptions and
EQ statements from the Plant PhenomeNET project (Oellrich, Walls et al., 2015). The most likely matching
terms identified by the classifier are used to compose final EQ statements with confidence scores. Result s of
evaluating the accuracy of this approach are presented, and potential use across datasets to enable automated
phenolog discovery are discussed.
Funding acknowledgement: National Science Foundation (NSF)
59
P7
Deciphering molecular origin and functional impact of structural variation in
maize through genome sequences comparison and integrative analysis of genetic
variation, transcriptome and phenotype data.
(submitted by Johann Joets <johann.joets@inra.fr>)
Full Author List: Joets, Johann 1; Coursol, Sylvie2; T urc, Olivier 3; Cabrera-Bosquet, Llorenc3; Martin-Magnette, MarieLaure4 5 6; Salvi, Silvio 7; Venon, Anthony 1; Chaignon, Sandrine 2; Laplaige, Jérôme8; Gendrot, Ghislaine 8; Palaffre,
Carine9; Castel, Stéphanie9; Pateyron, Stéphanie 4 5; Brunaud, Véronique4 5; T aconnat -Soubigou, Ludivine4 5; Dumas,
Fabrice1; Marande, William 10; Rousselet, Agnès1; Belcram, Harry 1; Charcosset, Alain 1; T ardieu, François3; Welcker,
Claude3; Rogowsky, Peter 8; Vitte, Clémentine1
1
GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisT ech, Univ. Paris-Saclay, Gif-sur-Yvette, France.
2
Institut Jean-Pierre Bourgin, INRA, AgroParisT ech, CNRS, Université Paris-Saclay, RD10, F-78026 Versailles
Cedex, France.
3
LEPSE, INRA, Univ. Montpellier, 34060 Montpellier, France.
4
Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Saclay,
Batiment 630, 91405 Orsay, France.
5
Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay,
France.
6
UMR MIA-Paris, AgroParisT ech, INRA, Université Paris-Saclay, 75005, Paris, France .
7
Department of Agricultural and Food Sciences - DIST AL, University of Bologna, Viale Fanin, 44, 40127 Bologna,
Italy.
8
Laboratoire Reproduction et Développement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon 1 CNRS, INRA,
69000 Lyon, France.
9
UE0394 SMH Maïs, INRA, France.
10
Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet -Tolosan, France.
Structural variation (SV) is a major driver of plant adaptation and genome evolution. It originates from
transposable element insertion, as well as gene Copy Number (CNV) and Presence/Absence Variation (PAV).
M aize is a crop species with a complex genome, and exhibits extensive SV among lines, as well as strong
phenotypic differences. It is therefore a good model to explore the diverse molecular mechanisms leading to SV,
and to investigate to what extent SV impacts phenotypic variation. Finally, the geographical origin of the
different maize inbred lines is well described, allowing for linking SV to environmental adaptation.
Here, we present whole genome assemblies from seven European and American maize lines of various
geographical origins and phenotypes, and with contrasted genome size. This dataset allows unprecedented
genome-wide comparisons and characterization of maize SV with high sequence accuracy, thus offering the
opportunity to evaluate the prevalence of the molecular mechanisms underlying these variations and to
characterize the features responsible for genome size variation.
These seven maize lines together with B73 were cultivated under contrasted water conditions in the
PHENOARCH phenotyping platform allowing precise characterization of growth and development together with
precise measurements of environmental conditions. Thirteen different organs harvested at various developmental
stages have been used for RNA-seq-based transcriptome analysis. This massive dataset will be used to evidence
the possible role of SVs in quantitative responses to water deficit as well as the impact of SVs in gene regulation
networks. Overall, this work will provide insights on the molecular origins and functional consequences of SV.
Funding acknowledgement: French National Research Agency (Amaizing, ANR-10-BTBR-03), France Agrimer,
LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS)
60
P8
Four European Flint reference sequences complement the maize pan-genome
(submitted by Eva Bauer <e.bauer@tum.de>)
Full Author List: Bauer, Eva 1; Haberer, Georg2; Seidel, Michael A. 2; Gundlach, Heidrun 2; Hochholdinger, Frank 3;
Marcon, Caroline3; Baruch, Kobi4; Spannagl, Manuel2; Mayer, Klaus F.X. 2; Schön, Chris-Carolin 1
1
Plant Breeding, T UM School of Life Sciences Weihenstephan, T echnical University of Munich, 85354 Freising,
Germany
2
Plant Genome and System Biology, Helmholtz Zentrum München GmbH; 85764Neuherberg, Germany
3
Crop Functional Genomics, Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany
4
Energin .R T echnologies 2009 Ltd (NRGENE), Ness Ziona, 7403648, Israel
Compared to US Dent material, the European Flint germplasm represents a distinct group which is not well
represented by Dent genomic resources. To gain insight in structural and functional differences between Flint
and Dent genomes, we generated four de novo Flint reference sequences. We sequenced the inbred lines EP1
originating from the Spanish landrace –‘Lizargarate’, F7 from the French landrace ‘Lacaune’, DK105 from the
German landrace ‘Gelber Badischer Landmais’, and doubled-haploid line PE0075 from the German landrace
‘Petkuser Ferdinand Rot‘ at 214x to 320x coverage. Pseudochromosomes were assembled with NRGene’s
DeNovoM AGIC 2.0 or 3.0 technology, respectively, and total assembly sizes ranged from 2.2 to 2.5 Gb. For EP1
and F7 comprehensive RNAseq data are available to assist gene annotation. We made use of the PGSB maize
repeat database (Spannagl et al. 2016, Nucl Acid Res) for repeat annotation). To investigate structural genomic
variation, we performed pairwise whole genome alignments (WGAs) using the M UM mer software (Kurtz et al.
2004, Genome Biol) between EP1, F7, B73_v4 (Zm00001d) and PH207 (Zm00008a). Numerous
insertions/deletions, inversions, and transclocations, were detected, ranging from several kb to M b. Results of the
WGAs and comparison with high-density genetic mapping data will be presented.
Beta-versions of the de novo assembled genomes, Zm-EP1-REFERENCE-TUM -1.0 (Zm00010a) and Zm-F7REFERENCE-TUM -1.0 (Zm00011a), have been released in collaboration with NCBI and M aizeGDB under the
Toronto Agreement for prepublication data sharing. The assemblies of DK105 and PE0075 will be released when
annotation has been completed.
Funding acknowledgement: Bavarian State M inistry of the Environment and Consumer Protection (BayKlimaFit;
http://www.bayklimafit.de/), German Federal M inistry of Education and Research (BM BF; M AZE;
http://www.europeanmaize.net/)
P9
Functional analysis of maize kernel development
(submitted by Jiaqiang Dong <jd1077@waksman.rutgers.edu>)
Full Author List: Dong, Jiaqiang1; Kumar, Dibyendu1; Feng, Yaping1; Ge, Fei1; Messing, Joachim 1
Waksman Institute of Microbiology, Rutgers, T he State University of New Jersey, 190 Frelinghuysen Road,
Piscataway, New Jersey, USA 08854-8020
1
High-throughput, long-read sequencing methods provide whole genome assemblies for molecular genetic
analysis, including the analysis of EM S mutants by bulked segregants analysis (BSA). Although BSA is widely
used to identify SNPs that are linked to phenotypes, it is more challenging for maize because of the proportion of
transposable elements in its genome. Still, key mechanisms of maize kernel development could be derived from a
classical defective kernel (dek) mutant collection, generated by Neuffer and Sheridan in the 1980s, if the
sequences of these EM S mutations could be identified. However, these dek mutations were generated in
genotypes, whose genome had not been sequenced. To locate these mutations in the genome, we introgressed the
dek phenotypes into two inbred lines, by backcrossing all 30 dek mutants available from the maize stock center to
both B73 and W22 four times. These inbreds have been selected because their genomes have been sequenced by
single molecule, long-read sequencing platforms, which provide a better resource for such an approach than
highly fragmented short-read whole-genome assemblies. We have selfed and collected bulked samples for each
introgression and can now identify the molecular nature of each dek phenotype by either exome or RNA
sequencing because of the divergence of B73 and W22 genome.
Funding acknowledgement: Waksman Institute of M icrobiology
61
P10
Genomic prediction using TensorFlow
(submitted by Jan Freudenthal <jan.freudenthal@uni-wuerzburg.de>)
Full Author List: Freudenthal, Jan 1; Hölker, Armin 2; Mayer, Manfred2; Schön, Chris-Carolin 2; Korte, Arthur 1
Center for Computational and T heoretical Biology; JMU Würzburg; Emil-Fischer Straße 32, D-97074 Würzburg
2
Lehrstuhl für Pflanzenzüchtung; T echnische Universität München; Liesel-Beckmann-Str. 2, D-85354 Freising
1
Genomic prediction has proven to be a powerful tool to increase the gain of selection in plant and animal
breeding programs. A variety of statistical procedures are commonly applied to predict performance of untested
genotypes, including GBLUP and a set of related algorithms known as the bayesian alphabet. In recent years
machine learning algorithms were used interdisciplinary for prediction and classification. This was accelerated
after Google published their own machine learning library Tensor Flow.
We used Tensor Flow, implemented in Python 3, to use probabilistic neural networks to predict performance of
simulated data, maize landraces and A. thaliana phenotypes and compared the results to the performance of
GBLUP and were able to show that our machine learning architecture was capable to outperform GBLUP in
some cases. Furthermore we assessed the capability to predict within and across two landrace doubled-haploid
populations derived from Petkuser and Kemater maize landraces. In the future it is planned to include
environmental "markers" in those models to predict traits of interest of unknown genotypes in untested locations
and to account for GxE
P11
Gramene maize pan-genome browser
(submitted by Marcela Karey Tello-Ruiz <mmonaco@cshl.edu>)
Full Author List: Wei, Sharon 1; Stein, Joshua C. 1; Olson, Andrew1; Jiao, Yinping1; Wang, Bo 1; Campbell, Michael1;
T ello-Ruiz, Marela K. 1; Ware, Doreen 1 2
1
Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA 11724
2
USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit; Ithaca, NY, USA 14853
M aize is the most genetically diverse crop in the world, with differences in gene content estimated between 520% among lines. Capturing the pan-Zea gene space and structural variation requires additional reference
genomes, and the infrastructure to store, analyze and make accessible. To support this effort, Gramene has
developed a dedicated genus-level browser resource: maize-pangenome.gramene.org, built upon the Ensembl
infrastructure and guided by FAIR practices. Our first pass of this resource includes B73, W22, and PH207
complete reference genomes, along with 7 monocot and dicot outgroup species. These served as input to generate
phylogenetic resources based on protein and whole-genome DNA alignments. Insights into ancestrally conserved
regions and structural rearrangements are defined by pairwise whole-genome alignments and displayed in a
number of informative ways, including a multi-species view that allows graphical stacking of browsers and
interspecies navigation. The gene trees can be used to programmatically identify gene expansions and losses
between different maize accessions, which may explain evolutionary adaptations, inaccuracies in the gene
models, or errors in the underlying reference genome assemblies. We anticipate maize accessions like the NAM
populations being added to this resource. To test the utility of these resource and to assess quality of the gene
structure predictions, Gramene outreach efforts include the first maize annotation jamboree co-organized with
the M aizeCODE project. This work constitutes an initial prototype to support the infrastructure to identify
misannotated gene structures and a process to correct these guided by the gene trees. In addition to providing
resources to support quality assessment, as well as insights into many outstanding questions in the evolutionary
history of the Zea genus, this resource will provide a basis for functional characterization of genes and the
identification of targets for agronomic improvement of maize. This project is funded by NSF (IOS-1127112) and
partially from USDA-ARS (1907-21000-030-00D).
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
62
P12
Growth and metabolic responses of NAM parent lines to a brief exposure to cold
during early seedling development
(submitted by Tessa Durham Brooks <tessa.durhambrooks@doane.edu>)
Full Author List: Long, Connor 1; Meier, Nate1; Bell, Bryan 1; Zwiener, Benjamin 2; Lucas, Lance1; Crow, Chayton 1;
Doan, T u1; Durham Brooks, T essa 1
1
Biology Department, Doane University, Crete, NE 68333
2
Information Science and T echnology Department, Doane University, Cr ete, NE 68333
Early planting can help prolong the growing season, thereby increasing yields, but this practice also makes it
more likely that seedlings will be exposed to cold stress. Depending on the underlying genetics, early cold stress,
even in short bouts, can impact adult phenotypes. Therefore, the processes underlying cold tolerance in early
development are useful targets for crop improvement. Identification of seedling biomarkers associated with the
effects of early cold stress on adult growth would make it possible to more efficiently identify genetic factors that
contribute to cold resistance. Beneficial microbes aid in protecting plants against abiotic stresses including
temperature stress and chemical exudates are key signals facilitating this relationship. An objective of this study
was to explore how root exudate composition varies by genotype before and after a short bout of cold stress
delivered at the seedling stage in twelve NAM parent lines. Seedlings were germinated on paper and grown in
agar tubes. After three days, a 24 hour cold stress treatment at 10°C was given to half of the seedlings. After two
additional days of incubation at the control temperature, seedlings were removed from the agar tubes and were
transferred to peat pots where they hardened for a week before transplanting to the field. Water soluble
compounds were extracted from the agar remaining in each tube and metabolic fingerprints have begun to be
collected from each sample using NM R spectrometry. Shoot growth, plant biomass and root morphology
measurements were collected from each individual. Genotypes were found to vary in their adult growth in
response to the seedling cold stress treatment. Seedling root digital biomass and growth rate are being used to
normalize NM R spectra. Spectral regions differing by genotype and cold treatment are under investigation.
Funding acknowledgement: National Science Foundation (NSF)
P13
High level analysis of W23 and A619 genomes (sequenced by Novogene)
compared to B73 reference
(submitted by John Fernandes <john.fernandes@stanford.edu>)
Full Author List: Harness, Alex 1; Fernandes, John F2; Walbot, Virginia2
Donald Danforth Plant Science Center, St. Louis, Missouri, USA
2
Department of Biology, Stanford University, Stanford, California, USA
1
Novogene generated paired-end 150-nt reads for W23 and A619 inbred lines on an Illumina HiSeq machine.
Sequences were evaluated for quality, deduped, aligned to B73 using BWA mem (Li et al; v0.7.8), and processed
for SNPs using Samtools (v 0.1.19) mdup. Based on the resequencing data variant calls, pseudo-reference
genomes were generated using GATK (v3.6) FastaAlternateReferenceM aker. We compared the genomes and
provide a high level analysis of the results. We show an overview of the process and are working with Novogene
to streamline and improve a few of the data analysis and presentation steps. Variant Call Format (VCF) files for
each inbred will be made available on Gramene’s genome browser.
Funding acknowledgement: National Science Foundation (NSF)
63
P14
High resolution temporal and spatial transcription atlas of maize.
(submitted by Jing Wang <1964263754@qq.com>)
Full Author List: Wang, Jing1; Chen, Jian 1; Zhao, Haiming1; Song, Weibin 1; Lai, Jinsheng1
1
State Key Lab of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and
Breeding, China Agricultural University Beijing 100193, P.R.China
M aize is an important model species and a major constituent of human and animal diets. To understand how the
underlying genome sequence results in specific plant phenotypes, information on the temporal and spatial
transcription patterns of genes is crucial. Here we present a comprehensive atlas of global transcription profiles
across developmental stages and plant organs. We profiled transcript levels using RNA samples from 950 diverse
tissues representing 5 major organ systems and varying developmental stages of the maize plant. The organ
systems included root, stem, leaves, tassel, ear and seed. Each tissue was represented by three biological
replicates. The developmental stages included day after sowing1, 2, 3, 4, 5, 6, seedling, trefoil stage, four leaf
stage, elongation stage, panicle differentiation stage, flare opening, tasseling stage, days to silking, grain filling,
milk repeness stage and dough stage.
Funding acknowledgement: Natural Science Foundation of China
P15
Maize Ufo1 mutant plays a role in epigenetic regulation and alternative splicing
(submitted by Jin Cui <juc326@psu.edu>)
Full Author List: Cui, Jin 1 2; Wittmeyer, Kameron 1 2; Lee, T zuu-fen 3 5; Meyers, Blake3 4; Chang, Pearl6; Rita Lu, JuiHsien 6; Yen, Ming-Ren 6; Chen, Pao-Yang6; Chopra, Surinder 1 2
1
Intercollege Graduate Program in Plant Biology, T he Pennsylvania State University, University Park, PA 16802, USA
2
Department of Plant Science, Pennsylvania State University, University Park, PA 16802, USA
3
T he Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
4
Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
5
Dupont Pioneer, Des Moines, IA 50131, USA
6
Institute of Plant and Microbial Biology, Academia Sinica, T aipei 11529, T aiwan
The maize Unstable for orange1 (Ufo1) is a dominant mutation that gives rise to ectopic phlobaphenes
accumulation in various tissues and shows pleiotropic growth defects. The Ufo1 presence is accompanied by
overexpression and hypomethylation of the reporter gene pericarp color1 (p1), an R2R3 M yb transcription factor
involved in the regulation of phlobaphenes biosynthesis. The Ufo1 mutant also exhibits poor penetrance and low
expressivity, and in order to better understand Ufo1’s role in epigenetic gene silencing, growth development and
various stress response, we have performed RNA sequencing, small RNA sequencing and whole genome
bisulfite sequencing from pericarp tissue.. Around 3000 (14%) genes were found to be differentially expressed
(DE) (FDR < 0.05) in the mutant whereas around 800 genes were differentially methylated either in the promoter
or gene body region and around 6% of the de novo identified small RNA loci were DE. A strong association was
discovered between 24-nt small RNA expression and DNA methylation. Furthermore, we discovered that Ufo1
mutation inhibits RNA splicing (intron retention in particular). Gene ontology analysis showed that the
differentially spliced genes are enriched in GO terms for nucleotide binding/ATPase activity. Interestingly, we
also found that a subset of alternative splicing events is affected by changes in DNA methylation at the splice
sites. Overall, our analysis indicates that Ufo1 mutation perturbs a subset of small RNAs and that DNA
methylation is affected in gene bodies, which in turn may alter alternative splicing.
Funding acknowledgement: National Science Foundation (NSF)
64
P16
Functional divergence in maize subgenomes
(submitted by Jesse Walsh <jesse.walsh@ars.usda.gov>)
Full Author List: Walsh, Jesse R. 1; Woodhouse, Margaret R.2; Andorf, Carson M. 1 2; Sen, T aner Z.1 2;
U.S. Department of Agriculture, Agricultural Research Service
2
Iowa State University
1
The maize organism experienced a whole genome duplication event approximately 5-12 million years ago. Since
this event occurred after speciation from sorghum, the original genomes can be reconstructed by mapping
syntenic regions to the sorghum chromosomes. Evolution in maize has been shown to result in uneven gene loss
between each of the ancient genomes. This fractionation and divergence between these genomes continue today,
influencing agronomic traits. Loss of one gene of a pair of homeologs can be explained as selective pressure
favoring one copy of the gene and rendering the other unnecessary. Among those genes where both homeologs
remain is the possibility for not only functional loss of one of the gene pairs, but generation of novel functions.
Here we regenerate the subgenome reconstructions for the current B73 RefGen v4 genome assembly that were
originally described for B73 RefGen v2. We find that the primary subgenome has a greater range of GO
assignments, and that there is a relative lack of overlap between the subgenomes in terms of GO than would be
suggested by expression and abundance data. By comparing both expression and abundance measures for these
gene pairs across multiple tissues, we observe functional divergence of these homeologs. Although the primary
maize subgenome is often expressing more highly than the secondary homeologs, we observed tissue-specific
cases where the higher expressing homeolog belongs to the secondary subgenome.
Funding acknowledgement: National Science Foundation (NSF), USDA-ARS
P17
MaizeGDB: stewardship for maize genome assemblies and annotation
(submitted by Ethalinda Cannon <Ethy.Cannon@ars.usda.gov>)
Full Author List: Cannon, Ethalinda KS1 2; Woodhouse, Margaret H2; Harper, Lisa1; Gardiner, Jack 3; Portwood II,
John 1; Schaeffer, Mary 3; Walsh, Jesse1; Andorf, Carson 1
1
USDA-ARS Corn Insect and Crop Genectis Research, Ames, IA
2
Iowa State University, Ames, IA
3
University of Missouri, Columbia, MO
M aizeGDB is the genetics and genomics database for the model organism and agriculturally important crop Zea
mays. One of the main priorities at M aizeGDB is to provide genome assembly and annotation stewardship for
the maize research community. With falling sequencing costs and improved genome assembly methods, it has
become feasible to generate dozens of reference-quality genome assemblies for maize accessions of importance
to maize breeders and researchers. M aizeGDB currently hosts information for 10 high-quality genome
assemblies (Zea mays ssp. mexicana, B104, B73, CM L247, EP1, F7, Ki11, M o17, NC350, PH207, W22, and
others) and has integrated them with data held by M aizeGDB. This enables both exploring individual genomes,
and comparing them in sets. In anticipation of more genomes expected in the near future, M aizeGDB developed
a set of minimum standards for adopting a new genome assembly, designed templates for collecting essential
metadata related to the genome and assembly, enforced naming conventions set out by the maize nomenclature
committee, created documentation to help submit genome assemblies to GenBank, and developed a pipeline for
loading new assemblies. All of this enables comparative analysis. In addition to bringing in new genome
assemblies and providing the research community with means of improvement , M aizeGDB will continue
stewardship of the B73 genome assembly and annotation, which is expected to remain the representative
reference maize genome assembly for the foreseeable future. M ultiple, high-quality genome assemblies and
annotations integrated with trait, phenotype, and germplasm data, will improve researchers' ability to conduct
trait and germplasm analyses and to choose appropriate germplasm for breeding programs.
Funding acknowledgement: United States Department of Agriculture (USDA)
65
P18
MaizeMine: a data mining warehouse for MaizeGDB
(submitted by Jack Gardiner <jack.m.gardiner@gmail.com>)
Full Author List: Gardiner, Jack M. 1; T ayal, Aditi1; Unni, Deepak R. 1; T riant, Deborah R1; Nguyen, Hung N. 1; Le
T ourneau, Justin 1; Andorf, Carson M. 2; Elsik, Christine G. 1 3
1
Division of Animal Sciences, University of Missouri, Columbia, MO, USA 6 5211
2
USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, USA 50011
3
Division of Plant Sciences, University of Missouri, Columbia, MO, USA 65211
M aizeM ine (http://maizemine.maizegdb.org), the new data mining warehouse for M aizeGDB, accelerates
genomic analysis by enabling researchers without scripting skills to create and export customized annotation
datasets merged with their own research data for use in downstream analyses. M aizeM ine uses the InterM ine
data warehousing system to integrate genomic sequences from the B73_RefGen_v3 and B73_RefGen_v4
genome assemblies, three sets of gene annotations (AGPv3, AGPv4, RefSeq), Gene Ontology (GO), protein
annotations (UniProt), protein families and domains (InterPro), homologs (Ensembl Compara), pathways
(CornCyc, KEGG, Plant Reactome), and single nucleotide variants (dbSNP). M aizeM ine also provides precomputed variant effects and expression levels based on RNA-seq data from the Zea mays Gene Expression
Atlas (NCBI BioProject PRJNA171684). Database cross references facilitate easy gene identifier conversion
between AGPv3, AGPv4 and RefSeq. M aizeM ine provides simple and sophisticated search tools, including a
keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating
custom queries. The Genomic Region search tool executes queries based on lists of genome coordinates, and
supports both B73_RefGen_v3 and B73_RefGen_v4. The List tool allows users to upload identifiers to create
custom lists, perform set operations such as unions and intersections, and execute template queries with lists.
When used with gene identifiers, the List tool automatically provides gene set enrichment for GO and pathways,
with a choice of statistical parameters and background gene sets. M aizeM ine is particularly useful for tracking
gene identifiers across gene sets to facilitate meta-analysis. Query results can be downloaded in several formats
(tab delimited, GFF3, Fasta, BED, JSON, and XM L).
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
P19
Making YOUR data and databases FAIR; Functional gene annotation and more!
(submitted by Lisa Harper <lisaharper@me.com>)
Full Author List: Harper, Lisa 1; Dietze, Mandy 2 3; Gardiner, Jack 4; Schaeffer, Mary 4; Cannon, Ethalinda 2 3; Portwood,
John 2 3; Walsh, Jesse2 3; Woodhouse, Margaret 3; Andorf, Carson 2 3
1
USDA-ARS Albany, CA
2
USDA-ARS Ames, IA
3
Iowa State University, Ames IA
4
University of Columbia, Missouri
At M aizeGDB we value your input as we work towards making the best resource possible for you! Here we
report new strategies for functional gene annotation through literature curation, suggestions for standard
nomenclature, and new features on the gene model pages. We also have suggestions for you to make your data
comply with the FAIR principles (https://www.force11.org/group/fairgroup/fairprinciples,
https://www.ncbi.nlm.nih.gov/pmc/articles/PM C4792175/). We present the steps AgBioData member databases
are now taking to make all public agriculturally related databases more interoperable and easy to navigate. At
this poster, we are also soliciting your suggestion for improved content and organization. Please stop by!
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
66
P20
MaizeGDB: new resources for maize researchers
(submitted by John Portwood <john.portwood@ars.usda.gov>)
Full Author List: Portwood, John L. 1; Cannon, Ethalinda K.S. 1 2; Schott, David2; Cho, Kyoung T ak 2; Dietze, Miranda2;
Walsh, Jesse R. 1; Harper, Lisa C. 1; Woodhouse, Margaret 2; Gardiner, Jack M. 2; Schaeffer, Mary A. 3; Andorf, Carson
M.1
1
USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011
2
Iowa State University, Ames, IA 50011.
3
University of Missouri-Columbia, Columbia, MO 65203
M aizeGDB, the USDA-ARS maize genetics and genomics database, is a highly curated, community -oriented
informatics service to researchers focused on the crop plant and model organism Zea mays. M aizeGDB
facilitates maize research by curating and maintaining a database that serves as the central repository for the
maize community. With the availability of more reference quality genomes for maize, M aizeGDB has become
more sequence-centric, while still maintaining traditional maize genetics datasets. The research focus of the
maize community has continued to evolve, making it necessary to continually redefine data access and data
analysis tools. In this poster we present an overview of new services and data types provided by M aizeGDB.
New genome sequences are incorporated into M aizeGDB and made accessible through the annotation/assembly
pages, BLAST databases, and genome browsers. Recently added genomes include B73v4, W22v2, M o17, M o17Yan, PH207, CM L247, B104, EP1, F7, Ki11, and NC350. M aizeGDB is responsible for stewardship of the
maize representative genome assembly (B73), including the improvement of associations between the B73 gene
models and gene models for all other assemblies. New resources include CornCyc 8.0, a tool allowing users to
query metabolic pathways on the B73v4 assembly and SNPversity, a tool allowing users to compare SNPs across
a diverse set of inbred lines. New tools under development include M aizeM ine (an InterM ine instance),
M aizeDIG (a tool for tagging phenotypes in images and linking them to genes), and PedNet (a tool for
visualizing pedigree networks).
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
67
P21
Mining maize with Gramene
(submitted by Marcela Karey Tello-Ruiz <mmonaco@cshl.edu>)
Full Author List: T ello-Ruiz, Marcela K. 1; Wei, Sharon 1; Olson, Andrew1; Preece, Justin 2; Gupta, Parul2; Naithani,
Sushma2; Stein, Joshua1; Jiao, Yinping1; Wang, Bo 1; Kumari, Sunita1; Lee, Young K. 1 3; Kumar, Vivek 1; Muna,
Demitri1; Bolser, Dan 4; D'Eustachio, Peter 5; Papatheodorou, Irene 4; Kersey, Paul4; Jaiswal, Pankaj2; Ware, Doreen 1 6
1
Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA 11724
2
Dept Botany & Plant Pathology, Oregon State University; Corvallis, OR, USA 97331
3
Division of Biological Sciences and Institute for Basic Science, Wonkwang University; Iksan, Korea 54538
4
EMBL-European Bioinformatics Institute, Wellcome T rust Genome Campus; Hinxton, CB10 1SD, UK
5
Dept Biochemistry & Molecular Pharmacology, NYU School of Medicine; New York, NY, USA 10016
6
USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit; Ithaca, NY, USA 14853
Have you ever needed to know if the maize gene you work on has an ortholog in sorghum, or Arabidopsis? Has
the gene family that you are working on expanded or contracted relative to other crop or model grass species? Is
the biochemical pathway you work on conserved in sorghum and soybean? If so, you may want to explore these
questions in the Gramene database. Gramene (http://www.gramene.org) is an integrated resource for
comparative functional analysis in plants. Gramene provides researchers with access to 53 genomes, and
pathways for 75 plants species, including Zea mays B73 (maize). Gramene builds upon Ensembl and Reactome
software, and is committed to open accesses and reproducible science based on the FAIR principles, providing
both human and machine access to the data. Gramene provides integrated search capabilities and interactive
views to visualize gene features, gene neighborhoods, phylogenetic trees, gene expression profiles, pathways,
and cross-references. Powerful phylogenetic approaches, including protein-based gene trees with stable IDs and
whole-genome DNA alignments, enable traversing between maize and other plant species. Gramene hosts
curated rice pathways, and uses these curated pathways to generate orthology -based projections for other species.
M aize data includes the hosting of the maize RefGen_V4 assembly includes: i) functional descriptions for ~30K
genes, ii) sub-genome designation and ohnologs, iii) transposable elements, and iv) V3-V4 gene ID conversion
table and assembly converter to lift over genomic coordinates between V2, V3, and V4. Variation data includes
the Panzea’s 2.7 GBS (~720K SNPs in 16,718 lines) and maize HapM ap2 (~55 million SNPs in 104 lines) data
sets. Visualizations of EBI Expression Atlas data are integrated into the search results panel, and both genome
and pathway browsers. Other annotation tracks include methylome signatures, genome-wide long non-coding
RNAs, and nascent transcriptomes. Gramene is supported by an NSF grant IOS-1127112, and partially from
USDA-ARS (1907-21000-030-00D).
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
68
P22
MOA (MNase Open Access) mapping: A new and efficient method for genomewide open chromatin profiling in maize, demonstrated with developing earshoots
(submitted by Savannah Savadel <sds14d@my.fsu.edu>)
Full Author List: Savadel, Savannah D. 1; Vera, Daniel2; Lung, Pei-Yau3; Zhang, Jinfeng3; Bass, Hank W. 1
Department of Biological Science, Florida State University, T allahassee, FL, USA, 32306
2
T he Center for Genomics and Personalized Medicine; Florida State University; T allahassee, FL, 32306
3
Department of Statistics, Florida State University, T allahassee, FL, USA, 3 2306
1
Chromatin structure is dynamic and intimately linked to gene regulation and other genetic functions. Our lab has
developed a nuclease sensitivity profiling method (DNS-seq) that reveals sites of open chromatin linked to
biological traits such as growth and yield (Rodgers-M elnick et al,. PNAS, 2016). Here we set out to develop a
new M NAse-based open chromatin mapping technique (M OA) based on isolation and sequencing of small,
subnucleosomal-sized fragments from light nuclease digests of chromatin from formaldehyde-fixed nuclei. Size
selected libraries (~50-130 bp genomic fragments) sequenced at ~20 million reads per sample efficiently
highlight open chromatin regions. We have found that these “small, light -digest” fragments produce many of the
M Nase-Sensitive Footprint signals from differential nuclease sensitivity (DNS) mapping (requiring over 300
million reads/replicated sample). We carried out M OA mapping on field-grown earshoots staged by size as 0-1
cm, 1-2 cm, 2-3 cm, 3-5 cm. One of these, the 1-2 cm earshoots (FES on GenoM aize browser), is one of the core
reference tissues that has been fully profiled by DNS-seq (NSF PGRP project IOS 1444532). We will map the
reads to the B73 genome and segment the coverage peaks using iSeg. Comparative analysis of DNS vs. M OA
will improve our interpretation of each and allow us to test our prediction that M OA will uncover sub
nucleosomal regions with developmentally variable occupancy. Experimental advantages of M OA-seq include
the small amount of tissue required (< ~ 1g), the ability to use frozen tissues allowing for flexibility in harvest
scheduling, and the relatively small number of sequence reads required. As a result, this innovation adds to the
methods for identifying and monitoring activity of maize regulatory regions compared across multi-samples.
Epigenomic profiling data will further improve our understanding of plant genome structure and function.
Funding acknowledgement: National Science Foundation (NSF)
P23
New software to identify and explore the orphan genes of maize
(submitted by Eve Wurtele <mash@iastate.edu>)
Full Author List: Arendsee, Zebulun 1; Li, Jing1; Singh, Urminder 1; Seetharam, Arun 1
Iowa State University, Ames, IA, USA 50011
1
The premise that new genes can arise from non-genic DNA sequences, borne out from massive sequencing data,
sharply contrasts with the long- accepted view that novel gene functions primarily arise from a slow process of
accumulated mutations and rearrangements of already -established genes. We hypothesize that a major role of
orphan genes is to enable evolutionary adaptation to new environments. Because orphan genes have no homologs
in other species, many current tools do not identify them efficiently. We describe new softwares designed to
identify and delineate the genomic context of orphan genes, and to develop hypotheses as to the possible function
of each gene. As maize genomes are sequenced, the orphan genes of these genomes can be categorized in the
context of the adaptation and selection as the result of evolution and of human intervention for improved
agronomic traits. We apply the tools to a systematic analysis of orphan genes across maize races and lines, and
describe the insights and challenges from this comparative genomic analysis.
Funding acknowledgement: National Science Foundation (NSF)
69
P24
Organ-specific maize metabolic models from ensemble modelling
(submitted by Georg Basler <basler@mpimp-golm.mpg.de>)
Full Author List: Basler, Georg1; Nikoloski, Zoran 1 2
1
Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
2
University of Potsdam, 14476 Potsdam, Germany
Different plant organs show markedly different transcriptomics, proteomics, and metabolomics profiles largely
due to differences in the underlying cellular networks. Here, we focus on reconstruction of organ-specific
metabolic models for maize (i.e., root, shoot, and leaf) by integrating various omics-data with stoichiometric
genome-scale metabolic models. Several computational strategies for extraction of tissue- and organ-specific
models have already been proposed [1], and their performance in plants tested in our group for the case of A.
thaliana [2]. Our main result consists of designing a combined modeling approach which uses the different
computational methods for model extraction, aimed at leveraging the advantages of the existing solutions to
generate an ensemble of consensus models. We validate the generated models against pathway -based evidence
from various sources to select models with high predictive accuracy. We demonstrate that the ensemble
modeling approach results in more specific and more predictive functional models than those obtained by the
individual approaches. The models provide the prerequisite for combining the organ- and tissue-specific models
into a functional multi-organ model.
[1] S. Robaina-Estévez, Z. Nikoloski (2017) On the effects of alternative optima in context-specific metabolic
model predictions. PLoS Comput Biol 13(5): e1005568. doi:10.1371/journal.pcbi.1005568
[2] S. Robaina-Estévez, D. M . Daloso, Y. Zhang, A. R. Fernie, Z. Nikoloski (2017) Resolving the central
metabolism of Arabidopsis guard cells. Scientific Reports 7 (8307) doi:10.1038/s41598-017-07132-9
Funding acknowledgement: M ax Planck Society
P25
Parallel transposase tagging (PTT-seq) technology is a cost-effective alternative
for traditional Sanger sequencing
(submitted by Xiang Gao <caugxiang@163.com>)
Full Author List: Gao, Xiang1; Ma, Xuxu1; Li, Xinchen 1; Mo, Weipeng1; Liu, Han 1; Song, Weibin 1; Zhao, Haiming1;
Lai, Jinsheng1
1
State Key Lab of Agrobiotechnology and National Maize Improvement Center ，Department of plant genetics and
breeding, China Agricultural Universit y, Beijing, 100193,P.R.China
DNA sequencing is fundamentally important for the genetics of all species. The traditional sequencing
technology called Sanger sequencing was developed 40 years ago. Over the last decade, tremendous advances
have been made by introducing the second or third generation sequencing technologies like the Illumina, Pacbio
or Nanopore sequencing, with the cost of sequencing per base pair rapidly decreased. However, all the next
generation sequencing technologies have a common feature -- sequencing millions of DNA fragments all
together, and being not able to track the identity of individual fragment. Therefore, the traditional Sanger
sequencing is still broadly used around the world by being able to obtain the sequencing information of any
given individual fragments. Here we present our newly developed parallel transposase tagging (PTT -seq)
technology. The PTT-seq is based on our novel strategies of barcoding the hyperactive Tn5 transposons so that
the subclone libraries of each individual plasmids to be sequenced can be generated parallelly in high-throughput
format. The subclone libraries of individual plasmids can be pooled together and then be sequenced using any of
the next generation sequencing platform. Implementation of our PTT -seq technology can result in dramatic cost
reduction as comparing to traditional Sanger sequencing. As an example, over 10,000 maize seed cDNA clones
were sequenced rapidly with minimum cost while the identities of each individual clones correctly tracked,
demonstrating that the PTT-seq can be a cost-effective alternative for traditional Sanger sequencing in many
sequencing/genotyping applications.
Funding acknowledgement: National Natural Science Foundation of China (91435206; 31421005), 948 project
(2016-X33)
70
P26
Predicting crop leaf parameter from leaf reflectance spectra
(submitted by Urte Schlüter <u.schlueter@hhu.de>)
Full Author List: Schlüter, Urte 1; Heckmann, David2; Denton, Alisandra K1; Weber, Andreas PM 1
1
Plant Biochemitry, Heinrich Heine University, Düsseldorf, Germany, 40227
2
Computer Science, Heinrich Heine University, Düsseldorf, Germany, 40227
Harnessing natural variation in photosynthetic capacity is a promising route towards yield increases, but
physiological phenotyping is still too laborious for large-scale genetic screens. Here, we evaluate the potential of
leaf reflectance spectroscopy to predict parameters like specific leaf area, chlorophyll content, C/N ratio and
photosynthetic capacity in Zea mays leaves. The method is fast and non-destructive so that high numbers of
plants can be evaluated. Suitable models for prediction of leaf parameters from the leaf reflectance spectra were
obtained using partial least square regression with recursive feature elimination. A minimum of about 50 samples
from each species was required for reliable model development. In greenhouse material, the C/N ratio was the
parameter resulting in the highest correlation between predictions and observations, but the final intra-species
models could also predict photosynthetic parameters such as initial slope of the A-Ci curve and the maximal
assimilation capacity with high accuracy. The obtained models will now be tested in leaf material from the field.
Our results indicate that leaf reflectance phenotyping is an efficient method for improving crop photosynthetic
capacity.
Funding acknowledgement: BM BF
P27
Regulatory networks and kernel length related genes identified by eQTL
analysis in 5 DAP maize kernels
(submitted by Jun Zhao <zhaojun01@caas.cn>)
Full Author List: Pang, Junling1; Zong, Na1; Fu, Junjie2; Song, Dandan 1; Wang, Jing1; Wang, Guoying2; Zhao, Jun 1
Biotechnology Research Institute, Chinese academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing
100081, China
2
Intitute of Crop Sciences, Chinese academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081,
China
1
Early maize kernel development produces most cells comprising the mature kernel and is thus closely related to
final grain yield. However, the regulatory networks controlling gene expression during the early phases of maize
kernel development remain unclear. In this study, by analyzing RNA sequencing data derived from 318 inbred
lines, we identified 22,966 eQTLs regulating 18,377 expressed genes in 5 DAP maize kernels. Based on this, the
regulator-target relationships between 4,408 trans-eQTLs and 4,980 genes were established by setting further
criteria, in which putative molecular links of auxin, brassinosteriod, and/or cytokinin signaling pathways with
cellular processes including cell cycle and division, cell differentiation and cell wall organization/ biogenesis
were predicted. Furthermore, 137 genes that are expressed and regulated by eQTL at 5 DAP were revealed
significantly associated with kernel length by an approach integrating eQTL with QTT analyses. These data lay
the groundwork for fully understanding the molecular mechanisms underlying maize kernel development and
provide candidate genes for molecular breeding.
Funding acknowledgement: National Key Basic Research Program of China (grant no. 2014CB138205)
71
P28
Regulatory Networks Governing Nitrogen Use Efficiencyt in Maize
(submitted by Lifang Zhang <zhangl@cshl.edu>)
Full Author List: Zhang, Lifang1; Olson, Andrew1; Bagman, Anne-Maarit 2; Gaudinier, Allison 2; Frank, Mary 3; liseronMonfils, Christophe 1; Kumar, Vivek 1; Abbitt, Shane3; Shen, Bo 3; Bradat, Siobhan 2; Ware, Doreen 1 4
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA, 11724
2
Dept. of Plant Biology and Genome Center, UC Davis, Davis, CA, USA, 95616
3
DuPont-Pioneer, Johnston, IA, USA, 50131-1004
4
USDA-ARS-NAA, Ithaca, NY, USA, 14853
Nitrogen (N) is an essential micronutrient for plants. M aximizing Nitrogen Use Efficiency (NUE) in plants is a
critical way to increase crop production and reduce negative impacts on environment. In order to explore the
gene regulatory network (GRN) that controls these processes, we have profiled the transcriptome of maize in
response to N limitation. Based on this profile, we have used yeast one-hybrid (Y1H) technology to
systematically map the gene regulatory network that governs the genes that are known to be involved in the
process of nitrogen uptake, assimilation, utilization, remobilization and transcriptional regulation in maize. We
have compared this regulatory network with an NUE network in Arabidopsis, conducted correlation analysis
using expression data and identified key transcription factors that regulate maize genes involved in NUE.
Funding acknowledgement: United States Department of Agriculture (USDA), Pioneer
P29
Sequence analysis of european maize inbred line F2 provides new insights into
molecular and chromosomal characteristics of presence/absence variants.
(submitted by Johann Joets <johann.joets@inra.fr>)
Full Author List: Darracq, Aude 1; Vitte, Clémentine 1; Nicolas, Stéphane1; Duarte, Jorge2; Pichon, Jean-Philippe2;
Mary-Huard, T ristan 1 3; Chevalier, Céline1; Bérard, Aurélie4; Le Paslier, Marie-Christine4; Rogowsky, Peter 5;
Charcosset, Alain 1; Joets, Johann 1
1
GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisT ech, Univ. Paris-Saclay, Gif-sur-Yvette, France.
2
BIOGEMMA, Chappes, France.
3
MIA, INRA, AgroParisT ech, Université Paris-Saclay, Paris, France.
4
EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, Evry, France.
5
Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA,
Lyon, France.
M aize is well known for its exceptional structural diversity, including copy number variants (CNVs) and
presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize
adaptation. While PAVs have been described in this important crop species, they have been only scarcely
characterized at the sequence level and the extent of presence/absence variation and relative chromosomal
landscape of inbred-specific regions remain to be elucidated.
De novo genome sequencing of the French F2 maize inbred line revealed 10,044 novel genomic regions larger
than 1 kb, making up 88M b of DNA, that are present in F2 but not in B73 (PAV). This set of maize PAV
sequences allowed us to annotate PAV content and to analyze sequence breakpoints. Using PAV genotyping on a
collection of 25 temperate lines, we also analyzed Linkage Disequilibrium in PAVs and flanking regions, and
PAV frequencies within maize genetic groups.
We highlight the possible role of M M EJ-type double strand break repair in maize PAV formation and discover
395 new genes with transcriptional support. Pattern of linkage disequilibrium within PAVs strikingly differs
from this of flanking regions and is in accordance with the intuition that PAVs may recombine less than other
genomic regions. We show that most PAVs are ancient, while some are found only in European Flint material,
thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this
material. Characterization of such PAVs will provide useful material for further association genetic studies in
European and temperate maize.
Funding acknowledgement: Agence Nationale de la Recherche ANR-10-GENM -0003 ANR-10-BTBR-01-01,
France Agrimer
72
P30
Sequence shattering and chromothripsis-like genome rearrangements following
biolistic transformation in rice and maize
(submitted by Jianing Liu <jl03308@uga.edu>)
Full Author List: Liu, Jianing1; Nannas, Natalie 2; Shi, Jinghua3; Fu, Fangfang4; Aspinwall, Brooke1; Dawe, R. Kelly 1 4
1
Department of Genetics, University of Georgia, Athens, GA 30602
2
Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323
3
Bionano Genomics, San Diego, CA 92121
4
Department of Plant Biology, University of Georgia, Athens, GA 30602
We biolistically transformed linear 48 kb phage lambda molecules into rice and maize and analyzed the results
by sequencing and optical mapping. Among a total of 8.2 M b of inserted lambda analyzed, the average fragment
size was ~200-500 bp. Fragments were joined by microhomology -mediated and non-homologous end joining,
and organized in random arrangements. Optical mapping confirmed that one event contained a ~2.4 M b insertion
with a collage of thousands of small lambda fragments. Further analysis revealed similar rearrangements of the
chromosomes in the transformed plants. There was clear evidence of large scale deletions, as well as degradation
and reassembly of large chromosome fragments, including one entire rice chromosome. The structure of the
inserts strongly resembles the outcome of chromothripsis, a chromosome fragmenting process frequently
observed in late stage cancers. We suggest that particles frequently enter and exit nuclei to settle in the
cytoplasm, where they form micronuclei that undergo degradation that occasionally rejoin with the nucleus.
Funding acknowledgement: National Science Foundation (NSF)
P31
Soil-based machine vision seedling emergence assay for studying cold tolerance
in maize
(submitted by A. Mark Settles
<settles@ufl.edu>)
1
2
2
1
2
Full Author List: Miller, Nathan D. ; Settles, A. Mark ; Baier, John W. ; Spalding, Edgar P. ; Gustin, Jeffery L.
Department of Botany, University of Wisconsin, Madison, WI
2
Horticultural Sciences Department, University of Florida, Gainesville, FL
1
Seedling emergence is a critical stage in the establishment of a successful crop. Germination and robust seedling
establishment are selected traits during the development of new varieties but with inefficient, largely manual
methods. We developed an in-lab, soil-based machine vision platform to automatically measure emergence
parameters, including rate, median time, duration, and percent. The assay is scalable, accommodates chemical or
environmental treatments, and can be used with different soil types. A single camera monitors 168 kernels by
time-lapse imaging. One current platform uses twelve cameras to monitor 2,016 kernels in parallel. A custom
software tool employing machine learning processes the time-lapse images to determine the point of emergence.
A public version of application runs on the CyVerse cyberinfrastructure. M aize seedling percent emergence is
measured with a 2% False Negative Rate and median time to emergence is measured with a 30 minute temporal
resolution. Cold tolerance of 40 diverse inbred lines was assayed by sowing and imbibing kernels in 5℃ soil for
5 days. Flats were transferred to 24℃ for the emergence assay. The treatment protocol gave a broad distribution
of cold sensitivity. Total emergence after cold conditions ranged from 20% to over 100% of control conditions.
M ean emergence time after cold treatment varied from 4 to 7 days after the shift to 24℃ and mean emergence
time did not correlate with percent emergence relative to control conditions. Several tropical lines were the most
cold tolerant while some European and M idwestern dents were consistently cold sensitive suggesting that cold
tolerance is not naturally selected by latitude and that tropical lines can be a source of cold hardy alleles. We are
in the process of screening QTL mapping populations with parental inbred lines that have contrasting cold
sensitivities.
Funding acknowledgement: National Science Foundation (NSF)
73
P32
Structural variation analysis in the Wisconsin Diversity Panel using multiple de
novo genome assemblies
(submitted by Patrick Monnahan <pmonnaha@umn.edu>)
Full Author List: Monnahan, Patrick J1 2; Brohammer, Alex B1; McGaugh, Suzanne E 2; Hirsch, Candice N1
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
2
Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108
1
Analysis of structural variation in maize has previously been limited by access to only a single reference genome
assembly. With multiple de novo assemblies available within the species, we are able to expand our
understanding of the extent of structural variation that exists within maize. To this end, we have sequenced the
inbred lines in the Wisconsin Diversity (WiDiv) Panel to 10-40x sequence depth. Using a number of recently
developed algorithms including LUM PY, M etaSV, and Genome STRiP, we have genotyped inbred lines from
the WiDiv panel for structural variants relative to the B73, PH207, and W22 reference genome assemblies. Loci
across the assemblies have been linked using a series of colinear chains. We are working towards using a
machine learning approach to provide confidence to structural variation genotype scores across algorit hms and
assemblies. This information will ultimately be used to link genotypes and phenotypes in an association mapping
framework to determine if structural variants preferentially affect certain traits and if the distribution of effect
sizes differs between structural variants and more traditional, SNP-based effects.
Funding acknowledgement: National Science Foundation (NSF)
P33
The NUPRIME project: nuclease profiling of four reference tissues as a resource
for maize epigenomics.
(submitted by Hank Bass <bass@bio.fsu.edu>)
Full Author List: Bass, Hank W 1; Vera, Daniel L 2; Lung, Pei-yau3; Liu, Yuhang3; Girimurugan, S B3 4; T urpin, Zach
M1; Savadel, Savannah D1; Kyle, Kathleen E 1 2; Dennis, Jonathan H1; Onokpise, Kome U5; Zhang, Jinfeng3
1
Department of Biological Science, Florida State University, T allahassee, FL, USA
2
Center for Genomics and Personalized Medicine, Florida State University, T allahassee, FL, USA
3
Department of Statistics, Florida State University, T allahassee, FL, USA
4
Department of Mathematics, Florida Gulf Coast University, Fort Myers, FL, USA
5
College of Agriculture and Food Sciences, Florida A&M University, T allahassee, FL, USA
The goal of this project (referred to as NUPRIM E) is to develop micrococcal nuclease (M Nase) profiling as a
foundational resource for integration of maize epigenomic data. The web page at maizenucleosome.org describes
the project, supported by the Plant Genome Research Program (NSF IOS 1444532). We previously showed that
particular genomic regions are highly susceptible to variation introduced by differences in the extent to which
chromatin is digested with M Nase (Vera et al., 2014 Plant Cell). We exploited this digestion-linked variation to
simultaneously map nucleosome occupancy and open chromatin, defining the functional portion of the maize
genome (Rodgers-M elnick et al., 2016, PNAS). The open chromatin is nuclease hypersensitive and operationally
defined by differential nuclease sensitivity (DNS). Here we present DNS-seq chromatin profiles on four distinct
maize B73 tissues; root tip, coleoptilar nodes, earshoot, and mid-maturation endosperm. Two-week hands-on
workshops have been conducted to train other scientists to apply DNS-seq chromatin profiling to their own
samples, ranging from maize and sorghum to arabidopsis and pine. We also developed and applied a new peakcalling algorithm, iSeg (Girimurugan et al., BM C Bioinformatics, in revision, 2018), to identify discrete sites of
open chromatin and facilitate comparative genomics. These data will be made and released through our UCSC
maize genome browser, http://www.genomaize.org/.
Funding acknowledgement: National Science Foundation (NSF)
74
P34
The practical haplotype graph: using a simplified pan-genome to impute
genotypes from skim sequence
(submitted by Peter Bradbury <pjb39@cornell.edu>)
Full Author List: Bradbury, Peter J1; Casstevens, T erry 2; Ilut, Dan 3; Johnson, Lynn 2; Miller, Zachary 2; Punta, Ramu2;
Romay, Maria C2; Buckler, Edward S1 2
1
USDA-ARS; Ithaca, NY 14853
2
Institute for Genomic Diversity; Cornell University; Ithaca, NY 14853
3
School of Integrative Plant Science; Cornell University; Ithaca, NY 14853
The Practical Haplotype Graph provides a general, graph-based, computational framework that can be used with
a variety of sequencing methods to infer high-density genotypes directly from low-coverage sequence. The
framework combines existing software with custom code implemented in a series of Docker modules that allows
users to build custom analysis pipelines that can run on a variety of system architectures. The method first loads
haplotypes from a population to a relational database. To genotype an individual, a graph is constructed from the
haplotypes stored in the database. Sequence from the individual is then used with an HM M (hidden M arkov
model) to identify the most likely path through the graph. The resulting path is translated to variant calls and
output in VCF format. By integrating an entire species worth of prior informat ion, the PHG pipeline can produce
an accurate whole genome sequence from any sequencing approach. Potential applications range from basic
genomic research into chromatin structure to applied plant breeding.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA), Bill and M elinda Gates Foundation
P35
Tracing the heritability of agronomic traits in maize
(submitted by Junpeng Shi <shijunpeng_cau@163.com>)
Full Author List: Shi, Junpeng1; Wang, Baobao 1; Liu, Zhipeng1; Ma, Xuxu1; Wang, Xin 1; Xie, Shaojun 1; Zhao,
Hainan 1; Sun, Silong1; Zhou, Yingsi1; Zhao, Haiming1; Song, Weibin 1; Lai, Jinsheng1
1
State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics
and Breeding, China Agricultural University, Beijing, 100193, P. R. China
Remarkable morphological changes were accumulated along the modern breeding process of maize (Zea mays
ssp. mays). While, a comprehensive dissection of the underlying genetic architecture is challenging. To this end,
we resequenced 775 temperate maize breeding accessions and constructed a high-density map of ~63.60 million
SNPs. Purifying selection was detected to keep the deleterious mutations towards low frequency during modern
breeding. Despite the fact that only 9 of 20 agronomic traits have significantly associated loci (P < 6.3 × 10-8),
genome-wide SNP based heritability (h2 SNP) was estimated to be as high as ~0.77 (an average of ~0.37),
indicating that SNPs with small effects may jointly contribute to the “heritability”. By partitioning the h2 SNP
into SNPs with different allele frequency spectrums, we found the low frequency (M AF < 0.01) alleles, which
were rarely analyzed in traditional association studies due to limited sample size and genotyping efforts, could
contribute as much as ~17.1% of phenotypic variance. Our findings provide novel insights into the genetic
architecture of complex agronomic traits and will benefit the design of molecular breeding and genome selection
(GS) in maize.
Funding acknowledgement: National Key Research and Development Program of China (2016YFD0100802;
2016YFD0101803; 2017YFD0101100) and the National Natural Science Foundation of China
(9143520013;31421005)
75
P36
Tripsacum de novo transcriptome assemblies reveal parallel gene evolution in
maize and Tripsacum after ancient polyploidy
(submitted by Christine Gault <cg449@cornell.edu>)
Full Author List: Gault, Christine M 1; Kremling, Karl A2; Buckler, Edward S3
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
2
Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
3
USDA-ARS, Ithaca, NY 14853
1
Following a whole genome duplication event, plant genomes reduce in size. When there isn’t selective pressure
to maintain duplicate gene copies, one copy is lost. M aize and its sister genus, Tripsacum, share a genome
duplication event that occured 5-26 million years ago. It is unknown whether Tripsacum grasses and maize have
maintained a similar set of genes under purifying selection because few genomic resources for Tripsacum exist.
Here we present high quality de novo transcriptome assemblies for two species: Tripsacum dactyloides and
Tripsacum floridanum. The transcriptome assemblies have L50 lengths of 1,442 bp and 1,452 bp in Tripsacum
dactyloides and Tripsacum floridanum, respectively. Core plant eukaryotic genes are well represented because
84% and 86% of BUSCO genes are completely assembled in Tripsacum dactyloides and Tripsacum floridanum,
respectively. A previous proteomics study by Walley et al. (2016) identified p rotein-encoding maize genes by
analyzing 33 tissues. We hypothesized that these protein-encoding genes are resisting fractionation in both maize
and Tripsacum, and that the remaining genes in the genome are more likely to decay into pseudogenes. Proteinencoding maize transcripts and their Tripsacum homologs have higher GC content, higher gene expression
levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum
homologs. These results indicate that genome fractionation is occuring in a similar fashion in two genera after a
shared ancient polyploidy event. The Tripsacum transcriptome assemblies provide a high-quality genetic
resource that can frame the maize genome in a larger evolutionary context.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
76
P37
Using two parent genome mapping to identify expression level quantitative loci
in maize roots
(submitted by Alexandra Asaro <aasaro@wustl.edu>)
Full Author List: Asaro, Alexandra 1; Dilkes, Brian 2; Baxter, Ivan 3
Washington University in St. Louis, Donald Danforth Plant Science Center; St. Louis, Missouri, USA 63132
2
Purdue University; West Lafayette, Indiana, USA 47907
3
USDA-ARS, Donald Danforth Plant Science Center; St. Louis, Missouri, USA 63132
1
Roots of young plants undergo highly regulated cell differentiation that patterns root architecture and physiology
and has lifelong effects on the structural integrity, water-use efficiency, and nutrient flow of the plant. To
understand how gene expression in maize roots impacts different aspects of plant structure and function, we
measured transcript levels in two-week-old roots of 218 greenhouse-grown plants belonging to the maize
Intermated B73 x M o17 (IBM ) recombinant inbred population. After performing quality control steps, we
retained an average of 19.6 million reads per sample. The high levels of sequence diversity in maize can cause
artifacts in alignment-based methods of expression quantification, especially if one of the parents is the reference
sequence. If RILs that contain the B73 allele at a particular locus have an inflated expression level of that
transcript due to alignment differences, expression QTL (eQTL) mapping may detect a false positive association
between the B73 allele and expression of a transcript. To date, there has been no well-tested and standardized
method for dealing with mapping bias in a bi-parental RIL population. We have devised an approach utilizing the
reference genomes of each parent to account for mapping bias. By using reference genomes from both B73 and
M o17 for eQTL mapping, as well as the difference in expression values between references, we can detect
instances of false positive eQTL that arise from reference genome discrepancies including variation in paralogs
between references. The results of parent-sample alignments to the congenic and dysgenic references can identify
loci likely to encode cis-eQTL arising from alignment bias and help to validate cis-eQTL driven by true
expression differences. After using both references to confirm a high-confidence set of eQTL, we intend to
perform network analyses and gene ontology enrichment tests to identify functional gene regulatory modules in
the developing maize root.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
P38
A system biology approach to identify biochemical markers representative of
high yielding maize lines
(submitted by Bertrand Hirel <bertrand.hirel@inra.fr>)
Full Author List: Hirel, Bertrand1
Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité
Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisT ech, Equipe de Recherce
Labellisée, Centre National de la Recherche Scientifique 3559, F– 78026 Versailles
1
We have developed a systems biology approach in order to identify metabolic pathways that could play a major
role in the control of grain production in maize. Using nineteen genetically distant maize (Zea mays L.) lines
from Europe and America, metabolomic, biochemical, fluxomic, and metabolic modelling approaches were
combined in order to identify key metabolic and enzymatic markers representative of high yielding lines. Both
correlation studies and metabolic network analyses allowed the description of a maize ideotype with a high grain
yield potential. Such an ideotype is characterized by low accumulation of soluble amino acids and carbohydrates
in the leaves and high activity of enzymes involved in the C4 photosynthet ic pathway and in the biosynthesis of
amino acids derived from glutamate. Chlorogenates appear to be important markers that can be used to select for
maize lines that produce larger kernels. We will discuss how these markers could be further used for breeding
and agronomic purposes under high and low fertilization input, using genetic engineering, mutagenesis and
association genetics.
Funding acknowledgement: INRA
77
P39
An opaque phenotype and altered mitochondrial respiratory chain are caused by
a maize rug3 mutation
(submitted by Peng Liu <mcliup@ufl.edu>)
Full Author List: Liu, Peng1; Lundgren, Jennifer M. 1; Li, Chengcheng2; Wu, Shan 1; Wohlgemuth, Stephanie E. 2;
McCarty, Donald R1; Koch, Karen E. 1
1
Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida,
Gainesville, FL 32611
2
Animal Sciences Department, and Animal Molecular and Cellular Biology Program, University of Florida,
Gainesville, FL 32611
The importance of C partitioning and C/N balance in kernels led to a focus on genes that could affect these
features. An “opaque” phenotype, for example, is indicative of defects in the protein-rich vitreous layer. Here, a
new opaque mutant was identified from the UniformM u maize population and confirmed by transgenic
complementation to arise from disruption of RUG3 (RCC1/UVR8/GEF-like3). The rug3 mutant kernel had a
normal starchy endosperm, but a defective vitreous layer. Protein profiles showed that the proportion of zeins
was significantly decreased. The visible kernel phenotype was severe when grown in spring, but less altered
during the autumn planting season in Florida. Analysis of transcripts showed deficient splicing of mitochondrial
(mt) mRNAs, including those for complex I of the respiratory chain. RUG3, which belongs to the RCC1
superfamily, promotes folding and subsequent splicing of group II introns from mt genes. The RUG3 splicing
factor functions with other diverse, nuclear-encoded splicing factors that are targeted to mitochondria. These
other factors include PPR proteins (Pentatricopeptide Repeat), and maturases. Although RCC1 proteins have
similar structures to one another, their functions are quite diverse, ranging from guanine nucleotide exchange for
Ran GTPase, to UV-B light signaling, and mt mRNA splicing. M aize RUG3 mediates splicing of the mt gene,
nad2, which encodes a subunit of complex I. Although plants have evolved alternative pathways for electron
transfer, ATP production relies heavily on complex I. Disruption of complex I and its specific effect on
respiration and other mitochondrial functions thus affects the development of kernels. Transcriptomic profiles
suggested that mutants had lower levels of mRNAs for biosynthesis of both starch and storage proteins, but also
increased abundance of transcripts for constituents of the entire respiratory chain. The latter might possibly result
from a compensation effect mediated by ROS or an energy -sensing system.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
78
P40
Apoplasmic phloem loading in Zea mays L. requires three SWEET sucrose
transporters
(submitted by Margaret Bezrutczyk <Margaret.Bezrutczyk@hhu.de>)
Full Author List: Bezrutczyk, Margaret 1 2; Hartwig, T homas1 2; Horschmann, Marc 2; Char, Si Nian 3; Yang, Jinliang4;
Yang, Bing3; Frommer, Wolf B. 1 2; Sosso, Davide2 5
1
Institute for Molecular Physiology, Heinrich Heine University, Düsseldorf, Germany 40225
2
Department of Plant Biology, Carnegie Science, 260 Panama Street, Stanford, CA, USA 94305
3
Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA 50011
4
Department of Agronomy and Horticulture, Universit y of Nebraska-Lincoln, Lincoln, NE, USA 68588
5
Inari Agriculture Inc., Cambridge, MA, USA 02139
Crop yield depends on efficient allocation of sucrose from leaves to seeds. Sugar is transported from the leaves
where it is synthesized, to phloem for long distance transport, to sink tissue such as seeds and roots. In
Arabidopsis, phloem loading is mediated by a combination of SWEET sucrose effluxers and subsequent uptake
by SUT1/SUC2 sucrose/H+ symporters. However, it is not clear that this is true for monocots: rice does not
appear to require SUT-medated apoplasmic transport for phloem loading, whereas maize does require SUT1. We
analysed the contribution of SWEETs to phloem loading in maize. Three leaf-expressed SWEET sucrose
transporters, ZmSWEET13 paralogues a, b, and c, are among the most highly expressed genes in the leaf
vasculature. Genome-edited triple knock-out mutants were severely stunted. Photosynthesis in mutant plants was
impaired and leaves accumulated high levels of soluble sugars and starch. RNA-seq revealed profound
transcriptional deregulation of genes associated with photosynthesis and carbohydrate metabolism. GWAS
analyses may indicate that variability in ZmSWEET13s correlates with agronomical traits, specifically flowering
time and leaf angle. This work provides support for cooperation of three ZmSWEET13s with ZmSUT1 in
phloem loading in Zea mays L., and suggests a potential target for improving photosynthesis and sugar
partitioning efficiency.
Funding acknowledgement: Syngenta, Carnegie Institution for Science
P41
barren stalk3 is required for axillary branch development and maps to the same
location as barren stalk2.
(submitted by Norman Best <bestn@missouri.edu>)
Full Author List: Best, Norman B1; Skirpan, Andrea1; Yao, Hong1; McSteen, Paula1
1
University of Missouri, Columbia, MO, 65211
Zea mays (maize) bears female reproductive inflorescences, ears, on axillary branches. Both initiation and
maintenance of the female axillary meristems are necessary for their proper development. Previously
characterized barren stalk (ba) mutants have determined that auxin is required for initiation of these axillary
branches. The ba mutants, ba1 and ba2, encode a transcription factor and interacting protein, respectively, that
function downstream of auxin to control development of axillary meristems. A new mutant, barren stalk3 (ba3),
was identified in 1990 in an Ubiquitous transposon active population by Pan and Peterson as a novel locus
controlling this process. The ba3 mutant failed to initiate an axillary ear branch and the grooves on the stem that
normally bear ears do not develop. In the B73 genetic background, ba3 mutants have shorter tassel branches and
fewer secondary branches but there was no effect on plant height or tassel length. An enhancer of the ba3 mutant
phenotype was discovered when introgressed into the M o17 background. The ba3 mutants were significantly
shorter for plant height and tassel length and there were fewer primary and secondary tassel branches on ba3
mutants as compared to normal siblings. Therefore, the ba3 locus was necessary for ear initiation without
affecting plant height and the mutant phenotype was enhanced by maize standing variation and we infer that the
ba3 gene is necessary for axillary meristem initiation or maintenance. We used a next generation sequencing and
bulk-segregant analysis approach to map the ba3 locus to the short arm of chromosome 2, indicating that it
could, in fact, be a new allele of ba2. Current endeavors are underway to identify the causative mutation of the
ba3 phenotype and confirm if it is an allele of ba2. These results indicate that there may only be two identified
barren stalk loci in maize.
Funding acknowledgement: National Science Foundation (NSF)
79
P42
Biochemical and structural characterization of a new maize receptor-like kinase
likely involved in drought stress.
(submitted by Viviane Cristina Heinzen da Silva <vchsilva@gmail.com>)
Full Author List: da Silva, Viviane Cristina Heinzen 1 2; Aquino, Bruno2 ; Biazotti, Bárbara Bort1 2; Pauwels, Laurens3 4; Arruda,
Paulo 1 2
1
University of Campinas (UNICAMP), Center for Molecular Biology and Genetic Engineering (CBMEG), Campinas, Sao
Paulo, Brazil.
2
Structural Genomic Consorcium (SGC-UNICAMP), Campinas, Sao Paulo, Brazil.
3
Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Gh ent, Belgium
4
VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
Protein kinases and receptor-like kinases (RLKs) are key regulators of virtually every physiological process. However,
despite their importance, most plant kinases are “under-explored”. By analyzing the gene expression profile of maize
plants subjected to drought stress we have selected some promising targets including a gene that encodes a leucine -rich
repeat receptor-like kinase (LRR-RLK). Here we describe the cloning, expression, purification and crystallographic
structure of the kinase domain of Zm00001d028770. Small molecules inhibitors were identified to be used chemical
biology studies towards the understanding of the mechanism of action of this LRR-RLK protein in plant response to
drought stress. IT C analysis confirmed the kinase inhibitor ENMD-2076 as a ligand to kinase domain with high
affinity. T his maize LRR-RLK seems not have kinase activity as neither AT P nor GT P binds its kinase domain. We are
using CRISPR/Cas9 genome editing to produce loss of function mutants to understand the function of this LRR-RLK
kinase better. A CRISPR/Cas9 construct was generated expressing Cas9 under control of the ZmUBI promoter and two
sgRNAs targeting Zm00001d028770 expressed by OsU6 -2 pol III promoters. T he primary focus of this work is to
develop tools to establish a chemical biology platform to study the maize kinase set potentially involved in drought
stress response.
Gene / Gene Models described: Zm00001d028770
Funding acknowledgement: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Fundação de
Amparo à Pesquisa do Estado de São Paulo (FAPESP)
P43
Characterization and functional analysis of maize Terpene synthetase6 (TPS6) Gene
(submitted by Zhihong Lang <langzhihong@caas.cn>)
Full Author List: Li, Shengyan1 ; Wang, Hai1 ; Li, Mengtao1 2 ; Wang, Guiping1 ; Cang, Jing2 ; Lang, Zhihong1
1
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China 100081
2
College of Life Science, Northeast Agricultural University, Harbin, China 150030
Maize plants emit a complex blend of secondary metabolites to defend the biotic stress and abiotic stress. T erpene
synthetases were key enzymes catalyzing secondary metabolite terpenes biosynthesis. T PS6 gene encoded a
sesquiterpene synthetase, which catalyzed β-macrocarpene and β-bisabolene. In prior studies, T PS6 expression was
induced by bacteria and pest damage, indicating that T PS6 gene may be involved in the process of disease and insect
defense. In our studies, no T PS6 gene expression was detected in B73 maize leaf and root with JA or SA induction and
T PS6 gene mainly expressed in maize root not leaf induced by ABA hormone. T o further elucidate the T PS6 gene’s
transcriptional regulation, the different truncated T PS6 promoter’s activity were analyzed in transgenic Arabidopsis
thaliana and the result showed -400 bp (AT G as +1) promoter included the sufficient cis-elements and had the same
activity as the full length promoter (1500 bp). A high-throughput screening of an Arabidopsis transcription factor
library using 400 bp promoter region as the bait identified a DREB transcription factor as candidate regulator. Within
the 400 bp promoter region, we found an 8 nt cis-element was necessary to gene expression. Ninety-six maize inbred
lines were re-sequencing and 44 inbred lines missed the 8 nt sequence which resulted in no T PS6 gene expression in
maize root induced by ABA. T he other 52 inbred lines including 8 nt sequences in their promoters could induce T PS6
gene expression in root. T he role of 8 nt cis-element to T PS6 expression was ongoing study. T he transgenic maize
plants with T PS6 gene overexpression and CRISPR-Cas9 knock-out were obtained. GC-MS showed the release of βmacrocarpene and β-bisabolene in OX-transgenic maize root and leaf. T he further works focus on the T PS6
transcriptional regulation mechanism and functions in disease, pest, and drought defense.
Gene / Gene Models described: TPS6; GRMZM2G127087
Funding acknowledgement: National Natural Science Foundation of China (Grant No. 31601702 t o Shengyan Li and
31570272 to Zhihong Lang)
80
P44
Cloning and characterization of a gene which disrupts carbohydrate partitioning
in maize
(submitted by David Braun <braundm@missouri.edu>)
Full Author List: Leach, Kristen A. 1 4; Liu, Peng4; Baker, R. Frank 1; McCubbin, T yler J. 1; Julius, Ben T . 1; Brush,
Parker L. 1; Barron, Brady 1; Wagner, Ruth 2; Grote, Karen 2; Peevers, Jeanette2; Jackson, Dave3; Chomet, Paul2; Koch,
Karen E. 4; Braun, David M. 1
1
Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri,
Columbia, MO 65211
2
Monsanto, Chesterfield, MO 63017
3
Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724
4
Horticultural Sciences Department, University of Florida, Gainesville, FL 32611
Carbohydrate partitioning is the process through which plants distribute photoassimilated carbon to distal
growing and storage tissues. The physiological aspects governing this process are well characterized; however,
the underlying genetic mechanisms are poorly understood. To gain better insight into the genes controlling
carbohydrate partitioning, we screened an EM S-mutagenized population for plants that displayed phenotypes
characteristic of the inability to effectively transport carbon, such as reduced plant height, leaf chlorosis, and the
hyperaccumulation of starch in the leaf. Through this screen we identified many mutant plants displaying these
phenotypes, including a mutant identified as carbohydrate partitioning defective6 (cpd6). An additional mutant,
cpd84, displayed strikingly similar phenotypes to cpd6, and, through complementation testing, was identified as
being allelic. In addition to the above phenotypes, cpd6 mutant leaves display a reduction in photosynthesis and
have increased levels of sugars and starch. The mutation responsible for the cpd6/84 phenotype was identified
through genetic fine mapping. Sequencing of the candidate gene revealed that each mutant allele was caused by a
premature stop codon, with the position of the cpd84 mutation being downstream of the cpd6 mutation. We are
currently conducting experiments to identify the cell-type specific expression, subcellular localization of the
encoded CPD6 protein, and determine its activity. Through identifying Cpd6 and similarly functioning genes we
are increasing our knowledge of the regulation of carbohydrate partitioning, which will contribute to the
development of crops with improved yields and stress tolerance.
Funding acknowledgement: National Science Foundation (NSF)
P45
Development of an amenable system for site-specific addition to a maize BChromosome
(submitted by Nathan Swyers <ncs89f@mail.missouri.edu>)
Full Author List: Swyers, Nathan C1; Cody, Jon P 1; Graham, Nathaniel D 1; McCaw, Morgan E 1; Zhao, Changzheng1;
Albert, Patrice1; Birchler, James A1
1
University of Missouri; 310 T ucker Hall; Columbia, MO, 65211
Currently, transgenic crops are created by random integration of a gene into the crop plant. This works for single
gene traits, such as herbicide resistance, but not as well for complex traits, which require multiple genes to be
expressed. For multiple transgenes to be expressed in a crop plant, several genes are randomly integrated into the
plant. Identifying plants that have all the separate transgenes integrated becomes a very difficult task. Gene
stacking at a single location in the genome would make combining multiple transgenes into plants a simpler
process. M y presentation focuses on the development of a system that allows for transgenes to be sequentially
added to a specific site in the maize genome. The system would work by utilizing two recombinases, Cre
recombinase and ɸC31 Integrase, to remove a selectable marker and to integrate transgenes. An initial construct
containing a selectable marker, flanked by loxP sites, which are acted upon by Cre recombinase, and an attP site,
is transformed into a maize plant. The selectable marker is then removed from the integrated transgene by
exposure to Cre recombinase. Two amendment constructs would enable modification of the integrated construct
by utilizing complementary attP and attB sites, which are acted upon by ɸC31 Integrase. The amendment
constructs contain cargo and a promoterless selectable marker which, upon successful recombination with the
initial site, would restore expression of the selectable marker. Successful demonstration of this system would
simplify inclusion of multiple transgenes, and the synthesis of multi-gene pathways in plants.
Funding acknowledgement: National Science Foundation (NSF)
81
P46
Effect of sugar levels on the low oxygen response of maize roots
(submitted by Maria-Angelica Sanclemente <sanangelma@gmail.com>)
Full Author List: Sanclemente, Maria-Angelica1; Della Porta, Adriana 1; Singh, Jugpreet 2; Ma, Fangfang3; Koch, Karen 1
2
1
Plant Molecular and Cellular Biology, University of Florida, USA, Gainesville, FL 32611
Horticultural Sciences, University of Florida, USA, Gainesv ille, FL 32611
3
Horticultural Sciences, Shandong Agricultural University, China, T aian, Shandong
2
Hypoxia (limited oxygen availability) typically leads to energy imbalances with deleterious effects at cellular-to
whole-plant levels. Sugar availability is central to hypoxia tolerance because fermentable substrates are essential
for recycling ATP. In maize, early work indicated sugar and oxygen modulate accumulation of mRNAs encoding
a small group of anaerobic proteins (ANPs). The objective of work presented here was to identify genome-wide
effects of sugar levels on the hypoxic response of maize. Toward this end, root tips were cultured under aerobic
(20% O2) or hypoxic (0.2% O 2) conditions with either physiologically abundant glucose (2%) or limited glucose
(0.2%). Transcriptome responses were quantified throughout treatments by RNA-seq. The combination of sugar
and oxygen levels tested here led to major transcriptome restructuring within 3h. The response was consistent
with altered metabolic profiles observed within the same time-frame. Sugar- and oxygen-responsive mRNAs
were examined separately. The number of sugar-responsive genes was constricted by hypoxia while low glucose
shifted the profile of low-oxygen responsive genes, possibly due to starvation. Over-represented transcripts were
mostly associated with stress tolerance and survival including those for carbohydrate metabolism and glycolysis.
Regardless of oxygen levels, physiologically abundant glucose had a significant effect on transcripts associated
with RNA processing and protein synthesis. Co-expression network analysis identified genes with similar
expression patterns across different sugar levels. Low glucose limited the number of co-expression relationships
of ANP transcripts indicating that the negative effects of hypoxia on root transcriptome are exacerbated by
starvation. Changes in transcriptional relationships throughout the treatments were consistent with coordination
of transcriptome restructuring and changes in sugar status. Results presented here show novel contributions of
sugars to co-expression relationships among transcripts under low oxygen conditions and the potential
contributions to their modulation.
Funding acknowledgement: National Science Foundation (NSF)
P47
Effect of water-deficit on phenotypes and transcriptomes of developing tassel in
maize
(submitted by Lei Wang <wanglei01@caas.cn>)
Full Author List: Zhang, Min 1; Xu, miaoyun 1; Wang, Lei1
Biotechnology Research Institute, Chinese Academy of Agricultral Science
1
M aize often exhibits asynchronous pollination under abiotic and biotic stress conditions, but the molecular basis
of asynchronous pollination has not been elucidated. Tassel development is a key process which affects the
anthesis-silking interval(ASI). In this study, we observed significantly increased ASI in the inbred lines of B73
and Chang7-2 under water deficit, and both inbreds displayed delaying pollen shedding and longer barren tip
length with decreased yields. Our transcriptome analysis identified 1931and 1713 differentially expressed genes
(DEGs) in immature tassels of B73 and Chang7-2 between well-watered and water deficit. We also identified 28
transcription factors from co-DEGs of two inbreds, some of which were known to regulate development,
flowering and stress processes. Collectively, we demonstrate a molecular association of the regulations of tassel
development with water deficit stress at the early vegetative stage. This finding extends our understanding to t he
molecular basis of maize tassel development under drought stress.
82
P48
Elucidating the transcriptional regulatory network controlling SUT and SWEET
genes in maize
(submitted by Nick Ferrigno <nferrigno@mail.smcvt.edu>)
Full Author List: Ferrigno, Nick K1 ; Eldridge, Brian Z 1 ; Tidd, Jess F1 ; Braun, David M 2 ; Lubkowitz, Mark A1
1
Saint Michael's College; Colchester, VT USA 05439
2
Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia,
MO USA 65203
Carbohydrate partitioning describes the process of how sugars (typically sucrose) produced during photosynthesis are
distributed from source organs (primarily leaves) to sink organs (e.g., roots, stem s, flowers, and fruits) where these
sugars are catabolized, anabolized, or stored. In maize, phloem loading in source organs requires sucrose crossing the
apoplasm (cell wall space) between the mesophyll and companion cells in leaves. In many sink tissues, such as kernels,
phloem unloading likewise requires sucrose to transit the apoplasm between companion cells and parenchyma cells.
T he coupled activities of two families of transporters—one that imports sucrose and one that exports—underlie sucrose
movement across membranes. T he Sucrose T ransporter (SUT ) gene family encodes sugar -proton symporters, most of
which import carbohydrates from the apoplasm. SUT s work in conjunction with the SWEET transporters (Sucrose Will
Eventually be Exported T ransporters), which function as passive efflux proteins. T o elucidate the regulatory network
that governs SUT and SWEET genes expression, we are using a yeast one hybrid screen to identify transcription factors
that control their expression. To this end we have cloned SUT and clade III SWEET promoters into yeast expression
vectors and begun screening a library consisting of 2200 maize transcription factors (Burdo et al., 2014, Plant J
80:356). Here we present the results of our initial screening efforts and current underst anding of SWEET and SUT gene
regulation.
Funding acknowledgement: National Science Foundation (NSF)
P49
Enhancement of maize disease resistance by CRISPR/Cas9 editing of LOX and
WRKY genes
(submitted by Borrelli Marocco <virginiamaria.borrelli@unicatt.it>)
Full Author List: Borrelli, Virginia 1 ; Lanubile, Alessandra1; Rogowsky, Peter2 ; Brambilla, Vittoria3 ; Fornara, Fabio 3;
Marocco, Adriano1
1
Dipartimento di Scienze delle Produzioni Vegetali Sostenibili, Università Cattolica del S. Cuore, Via Emilia Parmense 84,
29122 Piacenza (Italy)
2
Laboratoire Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon (ENSL), Alle d’Italie 46,
69364 Lyon Cedex 07 (France)
3
Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano (Italy)
Fusarium verticillioides (Fv) causes ear rot in maize and contaminates the kernels with fumonisins, a family of
mycotoxins that affects feed and food and considered carcinogenic for humans and animals. Several studies were
conducted to identify maize genes associated with host plant resistance to Fv infection and fumonisin accumulation. It
is known that plant lipoxygenase (LOX)-derived oxylipins regulate defense against pathogens and that the host pathogen lipid cross-talk influences the pathogenesis.
T he genome editing technology of Clustered Regularly Interspaced Short Palindromic Repeat/associated Cas9
(CRISPR/Cas9) was applied in order to investigate the possible implication
of the lipoxygenase gene ZmLOX6 and the transcription factor ZmWRKY125 in the resistance mechanisms against Fv.
T he enhanced expression of these genes was previously observed by RNA-seq experiments in maize resistant
genotypes and GWAS resulted in a SNP significantly associated with ZmWRKY125.
T he CRISPR cloning was based on a double cloning using two different guides (sgRNA) for one gene target. T he
constructs under the maize promoter ZmpUBI in the binary vector p1609 were transformed into the maize A188 line
using Agrobacterium tumefaciens mediated transformation. Edited ZmLOX6 and ZmWRKY125-expressing maize plants
will be characterized for Fv resistance using in vivo assays.
In parallel, maize mutants carrying Mu insertions in the ZmLOX4 gene were screened for Fv resistance and the
expression profiles of 15 genes of the LOX pathway were studied. T he fumonisin content and the enzymatic
lipoxygenase activity will be also investigated in the lox4 mutant kernels.
Gene / Gene Models described: GRMZM2G109130;GRMZM2G109056;GRMZM2G102760;GRMZM2G040095;
GRMZM2G104843;GRMZM2G015419;GRMZM2G009479; ;
Zm00001d033623;Zm00001d033624;Zm00001d013493;Zm00001d002000;Zm00004b024196;Zm00001d015852;
83
P50
Exploration of the molecular mechanism of CMS-S
(submitted by Senlin Xiao <forestxiao@genetics.ac.cn>)
Full Author List: Senlin, Xiao 1; Youhui, T ian 1; Huabang, Chen 1
Institute of Genetics and Developmental Biology, Beijing, China
1
Two CM S-S specific chimeric open reading frames, orf355 and orf77, were considered as CM S candidate genes,
the amounts of its 1.6-kb transcripts were previously shown to be greatly reduced in fertility -restored
microspores relative to the amounts in sterile plants. However, little is known regarding its mechanism of action.
In this study, we found that transgenic plants(M aize and Arabidopsis) containing M TS-orf355-GFP construct
exhibiting typical gametophytic male sterility, which comfirmed that orf355 was the CM S gene. The
mitochondrial OXPHOS activity was obviously impaired at microspore stage in CM S-S tassel, from which the
CM S-S microspore start to collapse. Retrograde reponse was activated in CM S-S tassel compared with fertile
ones. We found that the NAD/NADH redox state ratio reduced in both tassel and ear mitochondrial at
microspore stage,while further reduced in tassel but keep constant in ear. This indicate exsiting of a tassel
specific regulator mediate the collapsion of mircrospore. By yeast-one-hybrid screening, we identified an tassel
specific transcription factor named DBP4, which may participate in this process. DBP4 binding to orf355
promotor with the DRE/CRT element. The expression level of DBP4 increase dramaticaly at microspore stage in
CM S-S tassel, but not change in control fertile tassel. DBP4 was an stress responsive transcription factor,
analysis its promotor identified several typical cis UPR(unfolded protein response) element. Overexpression of
DBP4 in Arabidopsis resulting in gametophatic male sterility.
Funding acknowledgement: National Natural Science Foundation of China
P51
Functional characterization of maize auxin signaling modules in yeast
(submitted by Britney Moss <mossbl@whitman.edu>)
Full Author List: Moss, Britney L 1; Cates, Robert 1; Daly-Jensen, Kathleen 1; Klaeser, Hannah 1; Jackson, Kristina1;
Chen, Zongliang2; Gallavotti, Andrea 2
1
Department of Biology; Whitman College; Walla Walla, WA, USA 99362
2
Waksman Institute; Rutgers University; Piscataway, NJ, USA 08854
The hormone auxin regulates myriad processes during the life of a plant - from root and shoot development to
environmental responses. Understanding how auxin regulates such diverse processes necessitates
characterization of the specific signaling modules (receptors, repressors, transcription factors) that enable plant
cells to detect and respond to auxin. Recapitulation of the Arabidopsis nuclear auxin signaling system in yeast
has shown that auxin repressors (Aux/IAAs) exhibit a range of auxin-induced degradation rates which can be
tuned depending on identity of the co-expressed auxin receptor and of specific amino acid sequences within the
repressors. Subsequent studies confirmed that Aux/IAAs show similar degradation differences in planta and that
Aux/IAA degradation dy namics are highly correlated with the rate of developmental events. We are now using
this yeast system to functionally annotate auxin signaling modules crucial during maize reproductive
organogenesis. We have identified the subset of maize Aux/IAAs expressed in developing inflorescences and
have utilized the yeast system to confirm that these repressors degrade in response to auxin and exhibit different
degrees of hormone sensitivity. Efforts are now centered on characterizing transcriptional repression across this
subset of maize Aux/IAAs. This work is providing new insights to inform our understanding of how auxin action
is specified by context-specific deployment of auxin signaling components during plant development.
Gene / Gene M odels described: ZmIAA1, ZmIAA2, ZmIAA4, ZmIAA5, ZmIAA8, ZmIAA9, ZmIAA10, ZmIAA12,
ZmIAA14, ZmIAA16, ZmIAA20, ZmIAA21, ZmIAA25, ZmIAA27, ZmIAA28, ZmIAA29; GRM ZM2G079957,
GRM ZM2G159285, GRMZM2G104176, GRMZM2G004696, GRMZM2G167794, GRMZM2G057067,
GRM ZM2G037368, GRMZM2G142768, GRMZM2G077356, GRMZM2G121309, GRMZM5G864847,
GRM ZM2G147243, GRMZM2G115357, GRMZM2G130953, GRMZM2G035465, GRMZM2G163848
Funding acknowledgement: National Science Foundation (NSF), M J M urdock Charitable Trust, Whitman
College
84
P52
GBS identification of genomic loci associated with embryo twins in ig1 mutants
(submitted by Samuel Hokin <shokin@carnegiescience.edu>)
Full Author List: Hokin, Samuel1; Evans, Matthew MS1; Chettoor, Antony 1; Tang, Vicki1
1
Carnegie Institution for Science Department of Plant Biology, Stanford, CA USA 94305
M aize embryo twins occur rarely, in fewer than 0.1% of ovules in most maize lines. The INDETERM INATE
GAM ETOPHYTE1 (IG1) gene encodes a protein required for regulation of embryo sac development; when this
gene is mutated, the occurrence of embryo twins increases dramatically, depending on the genotype, reaching as
high as 11% of M o17 ovules.
B73 ig1 plants have a low embryo twin rate, and hybrid B73/M o17 ig1 plants display an intermediate rate,
suggesting a single genetic modifier present in M o17. We employed a transgenic M o17 line carrying an ig1-O
W23 segment on chromosome 3 to produce a mapping population in which one chromosome is pure M o17 and
the other carries the ig1 locus on a 50% B73, 49% M o17+1% other background. Seeds from this population were
sorted into groups containing twin and non-twin embryos, and checked via PCR for the presence of the ig1 locus.
Embryo tissue was then sequenced and mapped to the B73v4 genome using a GBS protocol. The resulting maps,
from 48 twin and 45 non-twin samples, reveal two strongly segregated loci, on chromosomes 8 and 9. Several
SSR markers display significant segregation in nearby regions. The B73 Chr8 locus maps to Chr8 on M o17 (v1)
while the B73 Chr9 locus maps to Chr5 on M o17. We therefore posit that M o17 contains a genetic modifier
which promotes embryo twin production in ig1 mutants on its chromosomes 5 and 8.
Funding acknowledgement: National Science Foundation (NSF)
P53
Genetic variability for nitrate uptake in a core collection of European and
American maize (Zea mays L.) lines.
(submitted by Isabelle Quilleré <isabelle.quillere@inra.fr>)
Full Author List: Quilleré, Isabelle 1; Brulé, Lenaïg1; Hirel, Bertrand1
Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon,
Unité Mixte de Recherche 1318, INRA Agro-ParisT ech, Equipe de Recherche Labellisée, Centre National de la
Recherche Scientifique (CNRS) 3559, F-78026 Versailles cedex, France.
1
Nitrogen use efficiency (NUE) in crops can be defined as the grain yield per unit of available nitrogen (N)
already present in the soil and added as N fertilizer. Thus, improving NUE in crops is a way of reducing both the
cost and the detrimental environmental effects associated with N fertilization. NUE is the product of N uptake
efficiency and N utilization efficiency. At high N input, variation in NUE was explained by variation in N uptake
capabilities. Generally, cereals such as maize are inefficient at acquiring N from the soil. Thus, identifying
genotypes that are more efficient in capturing mineral N resources and identifying both the phenotypic traits and
the biological mechanisms controlling the ability of maize to take up N is of major importance. To explore N
uptake efficiency, a core collection of nineteen maize inbred lines originating from different countries of Europe
and America, was grown in hydroponics under non-limiting N supply. When the plants had 4 visible leaves,
(nitrate) NO3- uptake was measured using 15N labeled NO3-. In parallel, the architecture of the root system
including seminal and nodal roots was analyzed using the WinRhizo software and the accumulation of mRNAs
encoding NO3- transporters was measured using Quantitative Real-Time (Q-RT)-PCR. We found that within this
natural population of maize lines, there is a very large variability for NO3- uptake efficiency, which is not
necessarily correlated with the architecture of the roots and the accumulation of mRNAs encoding high and low
affinity NO3- transporters.
Funding acknowledgement: Institut National de la Recherche Agronomique (INRA)
85
P54
Genome imbalance impacts global gene expression and small RNA expression in
maize
(submitted by Xiaowen Shi <shix@missouri.edu>)
Full Author List: Shi, Xiaowen 1; Hou, Jie2; Yang, Hua1; Chen, Chen2 ; Cheng, Jianlin 2; Birchler, James A1
Division of Biological Sciences, University of Missouri, Columbia, MO 65211
2
Computer Science Department, University of Missouri. Columbia, MO 65211
1
It has been long known that genome imbalance caused by changing the dosage of individual chromosomes
(aneuploidy) has a more detrimental effect phenotypically than by varying the dosage of complete sets of
chromosomes (polyploidy). An explanation of this phenomenon could be that genes with varied copy number
exhibited a dosage effect. Later on, several studies illustrated that those dosage-sensitive modifiers are likely to
be transcription factors and signaling components, which usually compose protein complexes. A gene balance
hypothesis attempting to address the molecular basis for genome imbalance demonstrates that altering the
stoichiometry of members of oligomeric complex will affect the function of the complex as a whole. If the
complex affected plays a critical regulatory role in gene expression, it would consequently alter global gene
expression. Despite all these findings, the mechanism of genome imbalance is still unclear. In order to investigate
how genome imbalance affects gene expression, we performed an RNA-seq study of maize leaf tissue from
aneuploidy and polyploidy series. Ratio distributions of experimental and control reads were generated to
examine the trend of gene expression in aneuploidy or polyploidy in comparison to the diploid control. The result
indicates genes both on the varied chromosome and the remainder of the genome show significant change of
expression. In general, we observed a greater spread of modulation in aneuploids than polyploids. Recently, noncoding RNAs are discovered to play a key role in the regulation of gene expression. To understand whether noncoding RNAs are involved in genome imbalance, we analyzed the expression of small RNAs (20-24nt) in
aneuploids and polyploids. This study will gain insight into the mechanism of genome balance and guide us to
understand gene regulatory networks and genome function in maize.
Funding acknowledgement: National Science Foundation (NSF)
P55
Genomic analyses of the genetic basis for shaping maize plant architecture for
adapting to increased planting density
(submitted by haiyang wang <wanghaiyang@caas.cn>)
Full Author List: Wang, Haiyang1
1
State Key Laboratory for Conservation and Utilization of Subtropical Agro -Bioresources, South China Agricultural
University, Guangzhou 510642, China
Increasing planting density has been a primary factor for the increased maize grain yield in the past few decades.
High-density tolerant ideal plant architecture can optimize canopy architecture, improve photosynthetic
efficiency, and prevent lodging, thus resulting in overall high grain yield. The complexity of maize genome has
impeded the identification and functional studies of key genes controlling plant architecture in maize. Recently,
we showed that in Arabidopsis, phytochorme B (phyB) and PIFs-mediated light signaling pathway interacts the
miR156/SPL pathway to regulate different aspects of plant architecture (including leaf production, stem
elongation, branching and flowering) in response to shade or high density planting. To investigate whether this
genetic pathway also operates in maize, we conducted a systematic study of the maize PIFs and SPL gene family
using the CRISPR-cas9 knockout and overexpression strategies. Progress on functional characterization of maize
PIFs and SPLs in regulating various aspects of plant architecture will be presented.
In a further effort to identify the key regulatory genes and genetic pathways regulating plant architecture in
maize, we collected 350 maize inbred lines (US-public and EX-PVP lines, as well as breeding lines used in
China from 1960s to 2010s) and conducted multi-year and multi-location field experiments. Remarkable
morphological changes were detected in plant architecture associated with high density planting during maize
breeding, including early flowering, reduced ear height, more upright leaf angle, reduced tassel branches number,
and shortened anthesis-silking interval. We also resequenced these 350 lines (more than 10X depth for each line)
and obtained ~25 millions high quality SNPs. GWAS analysis allowed us to confirm several known genes and
dozens of novel candidate genes that may have played pivotal roles in shaping maize architecture for adapting to
high density planting.
Funding acknowledgement: National Science Foundation of China (NSFC)
86
P56
Heritable differences in C4 photosynthetic sub-type across diverse maize germplasm
indicate utility in discover and breeding
(submitted by Jacob Washburn <jdw297@cornell.edu>)
Full Author List: Washburn, Jacob D1 ; Strable, Joshua1; Buckler, Edward S. 2
1
Cornell University; Ithaca, NY, USA 14853
2
USDA-ARS; Ithaca, NY, USA 14853
Maize, Sorghum, Sugarcane, and other important crop species rely on C4 photosynthesis for carbon fixation and
growth. T he current dogma is that C4 photosynthesis in maize is done primarily through the efficient NADP -ME C4
sub-type pathway. However, work stretching back over a decade indicates that in conjunction with NADP -ME, maize
also utilizes the PCK sub-type of C4 photosynthesis, which is estimated to contribute up to 25% of overall
photosynthetic product. T his mixture of sub-types is hypothesized to enhance maize productivity an d/or enable greater
environmental flexibility. Still, the outstanding question remains: How much, if any, of the ratio between NADP -ME
and PCK in maize is determined by genotype, and how much is determined by environment? In other words, is the C4
sub-type ratio in maize heritable, variable, and potentially useful in breeding?
RNAseq data from across the Maize 282 association panel and NAM founder lines was used to demonstrate that
NADP-ME:PCK ratios in diverse inbred lines of maize vary considerably. T hese expression data were validated
through in situ hybridization on mature maize leaves from representative inbred lines, as well as a replicated growth
chamber experiment in controlled high- and low-light intensities. Quantitative genetic modeling of the NADP-ME:PCK
ratio reveals a heritability of 0.54, indicating the potential utility of this trait in variant discovery, genomic selection,
and maize breeding.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture (USDA)
P57
High resolution interactomics in the maize leaf growth zone, using AN3 as a case study
(submitted by Michiel Bontinck <mibon@psb.ugent.be>)
Full Author List: Bontinck, Michiel1 2 ; Besbrugge, Nienke1 2; Nelissen, Hilde1 2 ; Van Leene, Jelle1 2; Eeckhout, Dominique1 2 ;
Persiau, Geert 1 2 ; Demuynck, Kirin 1 2; De Jaeger, Geert1 2 ; Inzé, Dirk1 2
1
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
2
VIB Center for Plant Systems Biology, Ghent, Belgium
Plant organ growth is driven by coordinated cell proliferation and expansion. T he maize leaf is an excellent model
system to study the complex regulation between these two developmental processes because it has a large growth zone
in which dividing and expanding cells are organized in a linear fashion. T his allows for high resolution sampling of
dividing and expanding cells while still maintaining sufficient input for genome-wide molecular techniques. Combining
such a sampling strategy with affinity purification techniques such as AP -MS and ChIP-seq allows the construction of
dynamic interaction networks surrounding known growth regulators.
Such a dynamic network was generated in our lab surrounding ANGUST IFOLIA3 (AN3), also called GRF-interacting
Factor1 (GIF1), a transcriptional coactivator involved in leaf development. T andem Affinity Purification (T AP -MS)
showed that AN3 stably interacts with a SWI/SNF chromatin remodeling complex throughout the growth zone but
interacts differentially with multiple GRF (Growth Regulating Factor) transcription factors depending on the
developmental context. Quantification of these differential interactions shows enrichment of several GRFs in the
division zone, GRF1 being the most prominent, while GRF4 and GRF10 interact stably throughout the growth zone.
By performing the reverse T AP -MS using GRF1 and GRF10 as bait proteins, we show th at GRF1 binds specifically to
AN3/GIF1, while GRF10 binds specifically to the other two members of the GIF family, GIF2 and GIF3. Strikingly,
T AP-MS using the GRF proteins as bait failed to identify any SWI/SNF complex components, hinting that AN3 might
bind to the SWI/SNF complex and the GRF proteins independently, comprising two discrete types of proteins
complexes.
Our current research focusses on extending this growth network to include the target genes of AN3, GRF1 and GRF10
by using ChIP-seq and to overlay the different types of interactomics data to understand how the network around AN3
and GRFs changes throughout the maize leaf growth zone.
Funding acknowledgement: ERC
87
P58
INDETERMINATE1 direct targets and regulatory mechanisms
(submitted by Vincenzo Rossi <Vincenzo.Rossi@crea.gov.it>)
Full Author List: Monticolo, Francesco 1; Zambelli, Federico 2; Galli, Mary 3; Minow, Mark 4; Gallavotti, Andrea 3;
Colasanti, Joseph 4; Pavesi, Giulio 2; Rossi, Vincenzo 1
1
Research Centre for Cereal and Industrial Crops, Council for Agricultural Research and Economics, Bergamo, I 24126, Italy
2
Department of BioSciences, University of Milan, Milan, I-20133, Italy
3
Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
4
Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
INDETERM INATE1 (ID1) protein is a zinc-finger transcription factor that acts as a key regulator of the
autonomous flowering p athway in maize. ID1 regulates the expression of florigenic genes, such as Zea mays
CENTRORADIALIS8 (ZCN8) in mature leaf. ID1 also controls different aspects of carbohydrate metabolism,
establishing a physiological energy state in the plant that promotes the transition to flowering. Previously, RNA
sequencing transcriptome analysis of wild-type and null id1 mutant plants was conducted to find ID1 targets in
immature and mature leaf. Since ID1 is expressed exclusively in immature leaf, ID1 must act indirect ly to
regulate expression of its mature leaf targets. For example, evidence suggests that ID1 is required to establish a
specific histone modification pattern in ZCN8 chromatin, which is maintained throughout leaf development and
facilitates florigen expression in mature leaf.
The goal of the present study is to identify ID1 direct targets (i.e. sequences directly bound by ID1) at a genomewide level. To this end, we employed ChIP-seq and DAP-seq approaches in combination with previous RNA-seq
data. This was followed by ChIP-seq to analyze alterations in histone modifications at loci bound by ID1, to
assess whether the establishment of specific histone modification patterns is a common feature of ID1 regulatory
mechanisms.
Our work has produced a list of putative ID1 direct targets, containing different transcription factors, which
provide information to analyze mechanisms within the intricate regulatory network, involving ID1 control of
flowering. These findings will be illustrated in the present poster, along with data describing the connection of
ID1 with histone modifications of its targets.
Funding acknowledgement: EPIGEN - The Epigenomics Flagshop Project (CNR/M IUR) - Italy, National
Science Foundation (NSF - USA), Natural Sciences and Engineering Research Council (NSERC) of Canada
P59
Investigating seed mineral composition of Korean landrace corns (Zea Mays L.)
(submitted by Gibum Yi <gibumyi@gmail.com>)
Full Author List: Yi, Gibum 1; Lim, Sooyeon 1
1
Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826,
Korea
M aize kernel is one of the greatest agricultural products in the world and used for various purposes as food, feed,
and industrial materials. M anipulating the chemical composition of maize seeds has great impacts on its
nutritional and industrial value. M aize is also a good target for mineral biofortification to solve the mineral
malnutrition problems from which over 2 billion people are suffered. In this study, we collected maize
germplasms including Korean landraces and quantified the amount of minerals in whole kernels and detected
relationships among amount of minerals and seed phenotypes including texture and color. Twelve minerals were
quantified by ICP-AES from 47 maize germplasms including 25 Korean landraces, 7 Korean cultivars or inbred
lines, 4 inbred lines of USA, and 11 landraces from other countries. The amounts of Fe and S are significantly
different among the groups with different seed colors. And the amounts of K, P, and S showed possible
relationships to seed texture phenotype. Strong positive relationships were detected between the amount of P and
those of K, M g, and M n, respectively. Between the amounts of M n and M g, a strong positive relationship was
also detected. These results provide information about Korean corn landraces which was not intensively studied
so far. Furthermore, the landraces which showed high mineral contents could be used as materials for a
biofortification breeding program.
Funding acknowledgement: Rural Development Administration of Korea
88
P60
Maize genomics, genetic engineering and gene editing research and services at
the Wisconsin Crop Innovation Center
(submitted by Heidi Kaeppler <hfkaeppl@wisc.edu>)
Full Author List: Kaeppler, Heidi F. 1 2; Petersen, Michael W. 2; Collier, Ray 2; Miyamoto, Amy J. 2; Martinell, Brian 2;
Williams, Edward J. 2; Lor, Vai S.N. 1 2; McFarland, Frank 1 2; Mahoy, Jill A. 2; Spalding, Edgar 2 3; Kaeppler, Shawn M. 1 2
1
Department of Agronomy, University of Wisconsin, Madison, WI 53706
2
Wiscsonsin Crop Innovation Center, University of Wisconsin, Middleton, WI 53562
3
Department of Botany, University of Wisconsin, Madison,, WI 53706
Genetic engineering and gene editing systems are critical components in the advancement of maize functional
genomics and epigenomics research, and genetic crop improvement efforts. Limitations in current public maize
bioengineering systems, including genotype dependency, low efficiency, intellectual property restrictions, and
lack of automation and capacity have created a significant bottleneck in the advancement of maize translational
genomics investigations. The Wisconsin Crop Innovation Center (WCIC) was established in January , 2017, at
the University of Wisconsin to advance basic and applied translational and functional genomic research in crop
plants, including maize, through technology development, collaboration, and fee-for-service transformation,
gene-editing, and phenotyping activities. Current maize-related research and service activities underway at
WCIC include genetic investigation of genotype-dependent tissue culture response, development of novel,
transformable maize germplasm, investigation and implementation of high efficiency, genotype-independent
transformation and gene editing protocols including meristem and nanoparticle-based systems, and automation of
protocols for high throughput production. B73-derived near isogenic lines containing a small genomic segment
from A188 imparting embryogenic, regenerable culture response have been developed and recently transformed
via Agrobacterium-mediated DNA delivery. Transformation/editing protocols are also being developed for B73
and sequenced maize ex-PVP lines including PH207, PHJ89, PHJ40, PHB47, and LH145. Successful delivery of
transgene DNA to specific target cells in maize meristem explants was documented and optimization of the
meristem-based selection protocol is underway. WCIC seeks collaborations with partners that have need for
large-scale projects. Initial fee-for-service rates for specific services and genotypes are available on the WCIC
website with additional services added over time. WCIC is open to discussion of start -up collaboration rates for
significant projects with partners that can provide constructs and manage products in the short -term, and have the
potential to utilize the capacity of WCIC in the future.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA), Department of Energy (DOE)
89
P61
Maize RNA Binding Motif Protein48 (RBM48) is required for minor intron
splicing and promotes endosperm cell differentiation
(submitted by Jacob Corll <jbcorll123@gmail.com>)
Full Author List: Corll, Jacob1; Bai, Fang2; Shodja, Donya1; Brigolin, Christian J. 1; Davenport, Ruth 3; Feng,
Guanqiao 2; Martin, Federico 2; Spielbauer, Gertraud2; Steinhauer, T yler 1; T seung, Chi-Wah 2; Barbazuk, W. Brad3; Lal,
Shailesh K. 1; Settles, A. Mark 2
1
Department of Biological Sciences, Oakland University, Rochester, MI 48309
2
Horticural Sciences Department, University of Florida, Gainesville, FL 32611
3
Department of Biology, University of Florida, Gainesville, FL 32611
The last eukaryotic common ancestor had two classes of introns that were spliced by different spliceosome
complexes. The vast majority of introns, termed U2-type introns, are spliced by the major spliceosome. There are
also rare U12-type introns, which are spliced by the minor spliceosome. The biological significance of these rare
minor intron genes (M IGs) are not well understood. M utations in minor spliceosome genes disrupt normal
growth and development in both plants and animals. There are relatively few splicing factors that have been
shown to be specific to the minor spliceosome. We found that the maize RNA Binding M otif Protein48
(RBM 48) is a minor spliceosome factor that functions to promote cell differentiation and repress cell
proliferation. Transposon-induced mutations in rbm48 cause a rough endosperm (rgh) defective kernel
phenotype that alters endosperm cell differentiation to promote aleurone differentiat ion over basal endosperm
transfer cells and embryo surrounding region. M oreover, rbm48 endosperm is more proliferative in a callus
culture system than normal sibling endosperm tissues. RNA-seq and RT-PCR data show that rbm48 mutants
have splicing defects in approximately 60% of M IGs, while U2-type introns are largely unaffected. These
developmental and molecular phenotypes are similar to the maize rgh3 mutant, which also encodes a U12
splicing factor. RBM 48 is highly conserved among organisms that retain the minor spliceosome. Protein-protein
interactions and co-localization between RBM 48, RGH3, and U2 Auxiliary Factor (U2AF) subunits suggests
major and minor spliceosome factors may form complexes as part of recognizing introns. M aize RBM 48 also
shows a conserved interaction with the maize homolog of human Armadillo Repeat Containing Protein7
(ARM C7). Our data predict that RBM 48 will have a conserved function in U12 splicing throughout eukaryotes
and that a major function of U12 splicing in maize is to promote endosperm cell differentiation.
Funding acknowledgement: National Science Foundation (NSF), Research Excellence Fund (REF)
P62
Maximizing photosynthesis efficiency in maize
(submitted by Claudiu Niculaes <claudiu.niculaes@tum.de>)
Full Author List: Niculaes, Claudiu1; Eggels, Stella1; Avramova, Viktoriya 1; Bauer, Eva1; Schön, Chris-Carolin 1
1
Plant Breeding, T UM School of Life Sciences Weihenstephan, T echnical University of Munich; Freising; Germany;
D-85354
The theoretical solar use efficiency of photosynthesis is far from being achieved in intensively managed maize
cultures, indicating that a large and currently untapped potential for yield increase exists. We aim to improve the
efficiency of C4 photosynthesis by making use of natural variation to elucidate the factors contributing to carbon
13
13
isotope discrimination (Δ C) in maize. In C3 plants, Δ C is used as a desirable physiological trait in breeding
due to the fact that it is influenced mainly by stomatal conductance, and therefore is an accurate predictor of
13
yield under drought. In C4 plants, carbon fixation is more complex and the factors contributing to Δ C are not
well characterized.
A maize introgression library was used to identify genomic regions which influence Δ 13C. From this library, near
isogenic lines carrying defined segments of the donor parent inserted into the genetic background of the recurrent
parent were developed and were analyzed in controlled growing conditions as well as in field trials. The
existence of a link between Δ 13C, stomatal conductance, assimilation and yield parameters is investigated.
In parallel, a fine-mapping approach is being implemented to narrow down the genomic region responsible for
one Δ13C QTL and allow for selection and characterization of candidate genes.
Funding acknowledgement: Deutsche Forschungsgemeinschaft (DFG), Bundesministerium für Bildung und
Forschung (BM BF)
90
P63
Meiotic recombination landscape in maize: impact of chromosome axis and heat
stress
(submitted by Bing Liu <bl472@cornell.edu>)
Full Author List: Liu, Bing1; Pawlowski, Wojtek P. 1
School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United State
1
M eiotic recombination plays a prominent role in creating genomic diversity by driving exchanges of genetic
information between chromosomes. Studies in maize have revealed that several factors including genomic and
epigenomic features shape the landscape of meiotic recombination. However, less is known about how
chromosome structure; e.g. the chromosome axis and the synaptonemal complex (SC) regulate the progression
and outcomes of meiotic recombination. It has been shown that high-temperature stress affects meiotic
recombination patterns and we hypothesize that this interaction is mediated by dynamic changes in chromosome
axis. M odulation of temperature may serve as a strategy to manipulate the recombination landscape to allow
crossover formation in chromosome regions that exhibit recombination suppression in normal temperature
conditions. We are conducting experiments to examine the meiotic recombination landscape and dynamics of
recombination events in heat-stressed maize plants, and especially focus on the examination of axis behavior in
response to temperature increase. We expect to observe an alteration of meiotic recombination frequency and
shift of crossover distribution on the chromosomes, which might be induced by altered axis activity. Our study
should contribute to elucidating the role of chromosome axis in meiosis and explaining how environmental
factors affect plant genomic diversity by influencing meiotic recombination.
Funding acknowledgement: National Science Foundation (NSF)
P64
Miniature seed 2109 encodes a nitrate transporter protein required for maize
seed development.
(submitted by Jing Wang <1964263754@qq.com>)
Full Author List: Yang, Bo 1; Wang, Jing1; Zhang, Xiangbo 1; Zhao, Haiming1; Song, Weibin 1; Li, Xuexian 2; Lai,
Jinsheng1
1
State Key Lab of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and
Breeding, China Agricultural University Beijing 100193, P.R.China
2
Department of Plant Nutrition, College of resources and environmental sciences, China Agricultural University
Beijing 100193, P.R.China
The plant nitrate transporter 1/peptide transporter (NRT1/PTR) family comprises low-affinity nitrate transporters
and di/tripeptide. Some members also recognize other substrates such as carboxylates, phytohormones (auxin and
abscisic acid), or defence compounds (glucosinolates). Little is known about members of this gene family in
maize (Zea mays). In this study, we isolated a mutant with reduced seed size from an EM S-mutagenized
mutation pool of B73. Gene cloning and characterization indicated that M N2109 encoded a putative transporter
that belong to the NRT1/PTR family. This conclusion was based on findings that M N2109 contained a conserved
PTR2 region and 12 transmembrane domains, and that the M N2109-GFP fusion protein was localized in the
plasma membrane. A detailed function analysis of M N2109 showed that M N2109 was a pH dependent lowaffinity nitrate transport protein, M N2109 also acted as a K + efflux transporter. The M N2109 gene was
specifically expressed in the BETL cell type of maize endosperm. The BETL in mn2109 was impaired compared
with its wild type, consistented with this seed phenotype. We found that ZmM RP1 regulated the expression of
M N2109 gene. The results of RNA-seq indicated that the metabolic pathway of amino acid
biosynthesis、hormone biosynthesis and starch biosynthesis impaired strongly in mn2109 seeds. Our study
+
indicated that M N2109 acted as a nitrate transporter、K efflux transporter, was thus critical for normal BETL
cell type and endosperm development in maize.
Funding acknowledgement: Natural Science Foundation of China
91
P65
Modulation of cold sensitivity and early seedling performance by priming in 27
maize NAM parental inbred lines
(submitted by Gokhan Hacisalihoglu <gokhan.h@famu.edu>)
Full Author List: Hacisalihoglu, Gokhan 1; Gustin, Jeff 2; Miller, Nathan 3; Kantanka, Sarfo 1; Settles, Mark 2
1
Florida Agricultural and Mechanical University, Biological Sciences Department, T allahassee, FL 32307
2
Horticultural Science Department, University of Florida, Gainesville, FL 32611
3
Department of Botany, University of Wisconsin, Madison, WI 53706
Seedling emergence is an important factor for yield, particularly under challenging planting conditions. In the US
corn belt, maize is planted in early spring, as soon as soil temperatures are permissive to germination. At that
time, temperatures often drop below normal, which can delay or even kill the seedling. Seed pre-treatments have
been shown to improve germination in cold conditions in crops such as rice and cabbage, but are largely
unpublished in maize. To assess the effects of pre-treatments on early maize cold tolerance, twenty-seven inbred
parents of maize Nested Association M apping (NAM ) population were primed using a synthetic solid matrix and
then tested for cold tolerance using a soil-based emergence assay. Primed kernels were incubated at 10C for 5
days, and then transferred to 24C for emergence. DSLR cameras were used to capture images every 30 min to
obtain emergence profiles of each seedling. Emergence time was determined from the time-lapsed images and
multiple measures including final emergence percentage, time to 50% emergence, and emergence rate were
extracted for each genotype. The cold treatment reduced total emergence of several genotypes. However, priming
pre-treatment protected the sensitive genotypes allowing nearly full emergence. We also used single-kernel near
infrared reflectance spectroscopy to determine seed density, weight, oil, protein, and starch for the kernels prior
to planting. By combining kernel characteristics and emergence time, we found small, but highly significant
correlations between the kernel and early seedling performance. The current status of this project will be
presented including the further research results and analysis.
Funding acknowledgement: National Science Foundation (NSF)
P66
Opaque11 is a central hub of the regulatory network for maize endosperm
development and nutrient metabolism
(submitted by Rentao Song <rentaosong@cau.edu.cn>)
Full Author List: Feng, Fan 1; Qi, Weiwei1; Lv, Yuanda3; Yan, Shumei1; Xu, Liming1; Yang, Wenyao 1; Yuan, Yue2;
Chen, Yihan 1; Zhao, Han 3; Song, Rentao 1 2
1
Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University,
Shanghai 200444, China
2
National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
3
Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences,
Nanjing 210014, China
M aize (Zea mays) endosperm is a primary tissue for nutrient storage and is highly differentiated during
development. However, the regulatory networks of endosperm development and nutrient metabolism in maize
remain largely unknown. M aize opaque11 (o11) is a classic seed mutant with a small and opaque endosperm
showing decreased starch and protein accumulation. We cloned O11 and found that it encodes an endospermspecific bHLH transcription factor (TF). Loss-of-function of O11 significantly affected the transcription of
carbohydrate/amino acid metabolism and stress-response genes. Genome-wide binding site analysis revealed
9,885 O11-binding sites distributed over 6,033 genes. Using chromatin immunoprecipitation sequencing (ChIPseq) coupled with RNA sequencing (RNA-seq) assays, we identified 259 O11-modulated target genes. O11 was
found to directly regulate key TFs in endosperm development (NKD2 and ZmDof3) and nutrient metabolism (O2
and PBF). M oreover, O11 directly regulates cyPPDKs and multiple carbohydrate metabolic enzymes. O11 is an
activator of ZmYODA, suggesting its regulatory function through the M APK pathway in endosperm
development. M any stress-response genes are also direct targets of O11. M oreover, eleven O11-interacting
proteins were identified, including ZmICE1, which co-regulates stress-response targets and ZmYODA with O11.
Therefore, this study reveals an endosperm regulatory network centered around O11, which coordinates
endosperm development, metabolism and stress responses.
Funding acknowledgement: National Natural Science Foundation of China (NSFC)
92
P67
Phosphoenolpyruvate carboxykinase mutants reveal interaction of C 4
photosynthesis and nitrogen utilization in maize
(submitted by Jennifer Arp <jarp@danforthcenter.org>)
Full Author List: Arp, Jennifer J1 ; Rhodes, Brian H2 ; Moose, Stephen P 2; Allen, Douglas K1 3; Brutnell, Thomas P 1 4
1
Donald Danforth Plant Science Center, St. Louis, MO 63132
2
Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801
3
United States Department of Agriculture, Agricultural Research Service, St. Louis, MO 63132
4
Enterprise Institute for Renewable Fuels Donald Danforth Plant Science Center, St. Louis, MO 63132
Crop breeding efforts will need to increase yields while decreasing the use of non -renewable resources and minimizing
detrimental impacts on the soil, water, and air in order to continue to provide food for an increasing world population.
Modifications to photosynthesis present an opportunity to increase crop yields. Maize and other C 4 plants evolved a
more efficient type of photosynthesis where initial carbon fixation and Calvin cycle activity are spatially separated into
the mesophyll and bundle sheath, in order to reduce losses associated with photorespiration. Three subtypes of C 4
photosynthesis exist, and maize utilizes the NADP -malic enzyme (NADP -ME) pathway in combination with the
phosophoenolpyruvate carboxykinase (PEPCK) pathway. In the PEPCK pat hway, aspartate is used as a transfer
molecule between mesophyll and bundle sheath cells, and also acts in nitrogen metabolism, linking the two pathways.
Perturbation of the PEPCK pathway is a potential route to increase photosynthetic output and metabolic flexibility for
the plant under stress. T his project uses a mutant approach to characterize the effect of the pathway at the
physiological, biochemical, and transcriptomic levels. Ds insertion mutations were identified in the maize PEPCK1
gene, and the pepck1-Ds plants were grown under low and high nitrogen in a nitrogen responsive field site during the
summers of 2016 and 2017 to determine the effect of the PEPCK pathway under nitrogen stress. At the V8 growth
stage, tissue was sampled along the developmental gradient of the leaf, and RNAseq was performed to determine the
extent of compensation from the NADP -ME pathway in the mutant. Among agronomic traits, pepck1 -Ds mutants
flowered later, were taller, and had smaller kernels and heavier cobs than controls. T he vegetative tissues contained
more nitrogen and retained more biomass, indicating that pepck1 -Ds plants were deficient in nitrogen and sugar
remobilization.
Funding acknowledgement: United States Department of Agriculture (USDA)
P68
Regulation of cuticle deposition during juvenile vegetative phase in maize
(submitted by Giulia Castorina <giulia.castorina@unimi.it>)
Full Author List: Castorina, Giulia 1 ; Chiara, Matteo2; Domergue, Frédéric3; Horner, David2; Consonni, Gabriella1
University of Milan, Department of Agricultural and Environmental Sciences; Via Celoria 2; Milan, Italy; 20133
2
University of Milan, Bioscience Department; Via Celoria 26; Milan, Italy; 20133
3
UMR 5200 CNRS - Université de Bordeaux Bâtiment A3 - INRA Bordeaux Aquitaine; 71 Avenue Edouard Bourlaux - CS
20032; Villenave d'Ornon, France; 33140
1
T he cuticle, a hydrophobic film covering the aerial organs of plants, constitutes the first barrier against biotic and
abiotic stresses, especially water loss. In addition to its roles in plant protection, cuticle has been shown to have
important functions in plant and floral development. T he MYB transcription factor ZmMYB94/fused leaves1 (fdl1) is a
key regulator of cuticle deposition in maize embryo and seedling. Its action is required to establish a precise boundary
between seedling organs, thus preventing fusion between coleoptile, first and second leaf.
T o gain insight into the role of FDL1 in seedling development and to obtain information on FDL1-dependent genetic
regulation of cuticle biosynthesis, we analysed the biochemical profile of fdl1-1 mutant and wild type plants at different
stages of seedling development. We also performed an Illumina based RNA-sequencing experiment in which
transcriptomes from the fdl1-1 mutant and wild type plants were compared.
Biochemical analysis showed that wax and cutin components were significantly affected in the fdl1-1 mutant compared
to wild type. Moreover, a gene ontology and pathway analysis of the about 1600 differentially expressed genes led to
the identification of novel gene candidates implicated in lipid metabolism in maize. Variation in their expression nicely
correlated with cuticular differences observed at the biochemical level. Among them, we detected genes involved in
fatty acid elongation pathway as well as in wax and cutin biosynthesis and transport. Their expression may be directly
or indirectly affected by ZmMYB94. T hese results along with the analysis of the expression of these genes in response
to drought stress conditions will be presented.
Gene / Gene Models described: fused leaves1 (fdl1); GRMZM2G056407
93
P69
Rhizosphere signaling in arbuscular mycorrhizal symbiosis of maize.
(submitted by Uta Paszkowski <up220@cam.ac.uk>)
Full Author List: Albinsky, Doris1; Manley, Bethan 1; Nadal, Marina1; Oldroyd, Giles2; Sawers, Ruairidh 3; Brutnell,
T homas4; Paszkowski, Uta 1
1
University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge CB2 3EA, UK
2
Sainsbury Laboratory University Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
3
Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y
de Estudios Avanzados, Instituto Politécnico Nacional (CINVEST AV-IPN), Irapuato, México
4
Danforth Center 975 N. Warson Rd. St. Louis, MO 63132, USA
The arbuscular mycorrhizal (AM ) symbiosis is a fascinating mutualistic interaction between roots of most land
plants and fungi of the Glomeromycotina. The development of this life-long association starts with reciprocal
recognition in the rhizosphere. The interaction proceeds towards extensive root colonization which culminates in
the formation of highly branched hyphal structures, the arbuscules, within root cortex cells. It is here where bidirectional nutrient exchange occurs, the basis for mutualism in AM symbioses.
Pre-symbiotic plant-fungal recognition is manifested in a well-orchestrated exchange of signals that leads to
reprogramming of both symbionts for the anticipated association. The nature of some of the signals has been
discovered in recent years, providing a first insight into the typ e of chemical language spoken between the two
symbiotic partners. Importantly, these discoveries suggest that the dialogue is complex and that additional factors
remain to be unveiled. I will introduce some of our recent observations which have led us to p ropose
fundamentally new signaling mechanisms operating during pre-symbiotic communication of this intimate plantfungal partnership.
Funding acknowledgement: BBSRC, Bill & M elinda Gates Foundation, Gatsby
P70
Site specific recombinases: Tools for genetic engineering in maize
(submitted by Jon Cody <joncody@mail.missouri.edu>)
Full Author List: Cody, Jon P 1; Graham, Nathaniel D1; Zhao, Changzeng1; Swyers, Nathan C1; James, Birchler A1
Division of Biological Sciences, University of Missouri, Columbia, MO 65211
1
Site-specific recombinases activate strand-switching reactions between two DNA recognition sites in a targeted
and precise manner. Depending on recombinase site positioning and orientation, reactions result in the
integration, excision, or inversion of specific sequences. If recombinase technology is coupled with conventional
genetic engineering methods in plants, it could possibly increase the efficiency of the transformation process by
eliminating random transgene incorporation, targeting genes of interest to specific locations in the maize
genome, including engineered minichromosomes. Additionally, recombinases could give researchers more
control over established transgenic lines by enabling the removal of selectable markers through breeding
strategies, a process that would subsequently allow gene stacking with a single selectable marker. This project
demonstrated functionality of a collection of different recombinases (Cre, Flip, R, PhiC31 Integrase, and PhiC31
Excisionase) in maize. Recombinase technology will serve as the framework for future genome engineering
projects, including targeted transgene integrations and engineered minichromosomes.
Funding acknowledgement: National Science Foundation (NSF)
94
P71
Strigolactone biosynthesis in Zea mays (maize)
(submitted by Changsheng Li <c.li3@uva.nl>)
Full Author List: Li, Changsheng1; Dong, Lemeng1 ; Bouwmeester, Harro J. 1
1
Plant Hormone Biology group, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park
904, 1098 XH Amsterdam, T he Netherlands
Strigolactones are plant hormones regulating a.o. shoot branching, root architecture and secondary stem growth, which
are also exuded from the roots into the rhizosphere where they serve as host detection signals for beneficial arbuscular
mycorrhizal (AM) fungi. Parasitic plants of the Orobanchaceae family that infect the roots of their host plants have
evolved a mechanism to detect strigolactones, and use them as germination stimulants, ensuring that after germination a
host is nearby. Parasitic plants are a major threat to agricultural crops and are difficult to control. Multiple structural
strigolactone variants have been identified and interest ing differences in biological activity such as in mycorrhizal
branching and parasitic plant germination stimulatory activities have been observed. In maize root exudate, two
canonical strigolactones - 5-deoxystrigol and sorgomol - have been reported. Recently, we demonstrated the occurrence
of seven new strigolactones in maize root exudate, of which two were identified as zealactone and zeapyranolactone.
T he core pathway of strigolactone biosynthesis, up to carlactone, has been identified. However, the enzy mes
responsible for the formation of specific strigolactones after carlactone, as it now seems three different pathway branches, are largely unknown.
In this project, candidate genes involved in the strigolactone biosynthetic pathway were identified using co-expression
analysis using the known core strigolactone biosynthetic pathway genes ( D27, CCD7 and CCD8) as bait. In our further
analysis, a combination of heterologous expression (transiently in Nicotiana benthamiana and other systems), advanced
analytical chemistry and transformation will be utilized to elucidate the downstream biosynthetic pathways of
strigolactones in maize. T his will enable us to create maize lines with altered strigolactone profiles, allowing us to
study the biological relevance of t he structural diversity in these (rhizosphere) signaling molecules.
Funding acknowledgement: China Scholarship Council (CSC) for funding Li, Changsheng
P72
The maize Oxalyl-CoA Decarboxylase1 acting downstream of Opaque7 is required
for oxalate degradation and central metabolism and affects seed nutritional quality
(submitted by Jun Yang <yangjun@sibs.ac.cn>)
Full Author List: Yang, Jun 1 ; Fu, Miaomiao1 2 ; Ji, Chen1 2 ; Huang, Yongcai1 2; Wu, Yongrui1
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai
Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
2
University of the Chinese Academy of Sciences, Beijing 100049, China
1
Oxalate is a widely synthesized organic acid in animals, plants and other organisms. Excessive accumulation of this
acid is toxic to cell growth and organ development. Degradation pathways for oxalate in Oxalobacter formigenes have
been well understood; however, the genes and biochemical reactions for oxalate metabolism in plants have not been
fully characterized. Here, we reported the characterization of a new maize opaque endosperm mutant, which exhibits a
smaller seed size and shorter plant height compared with the wild type (WT ). We cloned this mutant gene and
determined that it encodes an oxalyl-CoA decarboxylase1 ( OCD1; EC4.1.1.8). Ocd1 is generally expressed in all
detected tissues and was specifically induced by oxalate treatment. T h e accumulation of oxalate in the ocd1 seed and
seedling is significantly higher compared with WT , indicating that the oxalate breakdown is blocked in ocd1. T he
permeability of the seed coat in ocd1 is also apparently affected. T he ocd1 phenotype is similar to that of opaque7 (o7),
a classic maize high-lysine mutant. T he O7 homologue in Arabidopsis encodes oxalyl-CoA synthetase (EC 6.2.1.8) and
is able to catalyze oxalate into oxalyl-CoA and CO2. We purified the recombinant OCD1 protein and determined that it
could further degrade oxalyl-CoA, the product of O7, into formal-CoA and CO2. Mutations in ocd1 caused dramatic
metabolic alterations in endosperm. T he synthesis of the major storage-protein zeins is significantly reduced and that of
non-zeins is compensatorily elevated, leading to a higher lysine level in ocd1 compared with WT . T argeted
metabolomics analyses showed that oxaloacetate, a precursor of oxalate was increased, while NADH (NAD+) which is
produced during citric acid cycle was reduced in the ocd1 endosperm. Our findings demonstrate that OCD1 acts
downstream of O7 in oxalate degradation and affects endosperm development, central metabolism and nutritional
quality in maize seed.
Gene / Gene Models described: Oxalyl-CoA decarboxylase; GRMZM2G175171
Funding acknowledgement: Natural Sciences Foundation of China
95
P73
The maize TFome and the GRASSIUS database: Resources for regulomics in the
grasses
(submitted by John Gray <john.gray5@utoledo.edu>)
Full Author List: Gray, John 1; Fabio, Gomez Cano 3; Ouma, Wilberforce2; Wasikowski, Rachael1; Maina, Eric3; Doseff,
Andrea4; Grotewold, Erich 3
1
Department of Biological Sciences, University of T oledo, T oledo, Ohio, USA 43606
2
Molecular and Cellular Imaging Center, Ohio Agricultural Research and Development Center/The Ohio State
University, Wooster, Ohio, USA, 44691
3
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA 48824
4
Departments of Physiology, and Pharmacology & T oxicology, Michigan State University, East Lansing, Michigan,
USA 48824
Gene regulatory networks are central to all cellular processes. In plants, they help link molecular targets with
agronomic traits of functional value including biofuel/biomass production, biomaterials, nutritional health, and
stress tolerance. M aize provides an attractive system for investigating the architecture of gene regulatory
networks (GRNs) and the underlying gene regulatory grids (GRGs) in cereal crops. To advance the study of
regulomics in cereals we developed several years ago the M aize Transcription Factor ORFeome (TFome). The
first public release of the maize TFome contained 2,034 clones corresponding to 2,017 unique Transcription
factor (TF) and CoRegulator (CR) gene models in recombination-ready vectors (Burdo et al., The Plant Journal.
2014 80:356-66). The entire collection is available through the Arabidopsis Biological Resource Center (ABRC),
and has been requested multiple times with a total of over 15,000 clones so far distributed. The potential for this
resource to greatly accelerate the discovery of GRNs in plants is demonstrated by its employment to build a
protein-DNA-interaction (PDI) network for the phenylpropanoid pathway (Yang et al., 2017. M ol Plant, 10:498–
515). As a parallel resource, we developed GRASSIUS (grassius.org) as a gene regulatory information
knowledgebase for the grasses. GRASSIUS consists of three interlinked databases that contains a collection of
TFs classified into different families (GrassTFDB); transcriptional co-regulators (GrassCoRegDB); and promoter
sequences (GrassPROM DB) for maize and other grasses including rice, sorghum, sugarcane, and Brachypodium.
GRASSIUS is home to the maize TFome and is being updated to host experimentally determined TF/coregulator
protein-DNA interactions (PDIs) and newly annotated maize transcription start sites (TSSs) derived from Cap
Analysis of Gene Expression (CAGE) experiments. The utility of GRASSIUS combined with the maize TFome
to the scientific community is to accelerate elucidation of regulatory mechanisms that are vital for engineering
cereal crops with improved agronomic traits. This project was funded by NSF grant IOS-1125620.
Funding acknowledgement: National Science Foundation (NSF)
96
P74
Tissues lignification, cell wall p-coumaroylation and degradability of maize stems
depend on water status
(submitted by Fadi El Hage <fadi.el-hage@inra.fr>)
Full Author List: El Hage, Fadi1 2; Legland, David3 ; Borrega, Nero 1; Jacquemot, Marie-Pierre1; Griveau, Yves1; Coursol,
Sylvie1 ; Méchin, Valérie1 ; Reymond, Matthieu1
1
UMR 1318, Institut Jean-Pierre Bourgin, INRA-AgroParisTech, CNRS, Universite Paris-Saclay, Versailles, France
2
Ecole Doctorale 567 Sciences du Vegetal, University Paris-Sud, University of Paris-Saclay, bat 360, Orsay Cedex 91405,
France
3
UR1268 Biopolymères, Interactions et Assemblages, INRA, Nantes, France.
In the context of both climate change and replacement of fossil resources, water supply and biomass valorization
are two urgent issues for providing sustainable systems of production. M aximizing maize biomass valorization is
of interest to make biofuel conversion competitive and to increase forage energetic value for animal fodder. One
way to estimate these valorizations is to quantify the cell wall degradability. Degradability is influenced by the
biochemical composition and structure of the cell wall and also by the lignin distribution in different plant
tissues. Recently, few evidences underline that cell wall components and their distribution is also influenced by
environmental factors. The aim of this study is to evaluate the impact of water supply on cell wall degradability
and composition, and on distribution of lignin in cell type in maize internodes. Dedicated high throughput tools
for the quantification of cell wall composition (NIRS predictive equations) and for the distribution of lignin in
the different tissues (plugins for image analysis) have been developed. This allowed us to efficiently and
accurately phenotype over 528 maize internodes from 11 inbred lines cultivated during 3 years under two
contrasted irrigation scenarios in South of France. Overall, our results clearly demonstrate that water deficit
induces an upheaval of lignin content and distribution along with a reduced lignin p -coumaroylation which
impacts cell wall degradability. M oreover, responses to water supply varied between lines, underscoring
biochemical and histological targets for plant breeding.
Funding acknowledgement: Biomass For the Future (ANR-11-BTBR-0006-BFF) funded by the French National
Research Agency under an Investment for the Future program (ANR-11-IDEX-0003-02); the LabEx Saclay Plant
Sciences-SPS (ANR-10-LABX-0040-SPS).
P75
Validation and functional characterization of the maize lateralrootless 1 (lrt1) gene
(submitted by Marcel Baer <Marcel.Baer@uni-bonn.de>)
Full Author List: Baer, Marcel1 ; Müller, Verena1 ; T aramino, Graziana2 ; Multani, Dilbag2 ; Hochholdinger, Frank1
1
INRES, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
2
Pioneer Hi-Bred International Inc., Johnston, IA 50131, USA
The monogenic recessive mutant lrt1 was identified in a segregating F2-generation of an EM S mutagenized B73
population (Hochholdinger and Feix, 1998). The lrt1 mutant is deficient in lateral root formation in the
embryonic primary and seminal roots during early postembryonic development (Husakova et al., 2013).
The lrt1 gene was fine mapped by a combination of molecular markers and bulk segregant analysis-sequencing.
Co-segregation analyses of homozygous wild type and mutant seedlings showed that a candidate gene cosegregated with the mutant phenotype. Confirmation of the candidate gene by independent mutant alleles and
CRISPR/Cas9 knock out of the gene is under way.
qRT-PCR experiments of the candidate gene demonstrated that the putative lrt1 mutation leads to down
regulation of lrt1 expression in primary roots to less than 20% compared to the expression level in wild type
primary roots. Furthermore, lrt1 showed the highest transcript level in the meristematic zone of the primary root,
whereas no significant differences in lrt1 expression were observed between the different root types at different
developmental stages.
After confirmation of the candidate gene a more detailed expression analysis by in situ hybridization experiments
will be performed. To determine the subcellular localization of LRT1, C- and N-terminal GFP-fusions will be
generated.
References:
Hochholdinger F., Feix G. (1998a): Early post-embryonic root formation is specifically affected in the maize mutant lrt1. Plant J. 16:
247-255.
Husakova E., Hochholdinger F., Soukup A. (2013): Lateral root development in the maize (Zea mays) lateralrootless 1 mutant. Ann.
Bot., 112:417-428.
97
P76
Why does maize produce benzoxazinoids and transgenic Arabidopsis not?
(submitted by Aleksej Abramov <aleksej.abramov@tum.de>)
Full Author List: Abramov, Aleksej1; Hoffmann, Thomas2; Stark, Timo 3; Schwab, Wilfried2 ; Frey, Monika1
Chair of Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technical University of Munich, Freising
Germany
2
Biotechnology of Natural Products, Center of Life and Food Sciences Weihenstephan, Technical University of Munich,
Freising Germany
3
Chair of Food Chemistry and Molecular Sensory Science, Center of Life and Food Sciences Weihenstephan, Technical
University of Munich, Freising Germany
1
Secondary metabolites constitute the chemical defense arsenal of plants. Specific active compounds out of a reservoir
of hundreds of thousands are characteristically found in specific plant families. Benzoxazinoids are plant defense
compounds mainly produced by grasses. T he main benzoxazinoids (BXs) DIBOA and DIMBOA, are synthetized in the
seedling and confer resistance against pathogens and herbivores. BX biosynthesis is connected to the tryptophan
pathway, all required genes are known from maize and hence theoretically BX biosynthesis ca n be expressed
transgenically in every plant. T o assess the effects of BXs on plant physiology, development and defense we are
working on a transgenic expression of the whole biosynthesis pathway in Arabidopsis thaliana, a dicot with no
endogenic BX production.
All maize enzymes of DIBOA biosynthesis, the indole synthase BX1, four cytochromes P450s (BX2 to BX5) and a
cytosolic UGT (BX8), could be functionally expressed in S. cerevisiae and A. thaliana. T he expression of the whole
pathway chain however so far could not produce the final biosynthesis product DIBOA. In HPLC and LC-MS analyses
intermediates of the BX pathway have shown to be readily modified, e.g. by glycosylation in A. thaliana and N.
benthamiana. Modification is by oxygenases and gycosyltransferases. T o avoid such modifications of xenobiotics in
planta, intermediates have to be captured. T his might take place in a protein complex called metabolon. Such a
metabolon hypothetically exists in maize. T he P450-oxidoreductase is a known nucleation sit e and the soluble UGT
BX8 could also contribute to the complex formation. T he impact of these proteins for BX biosynthesis is currently
investigated in A. thaliana and S. cerevisiae. For the evolution of secondary metabolic pathways (ER-)membrane
domains that recruit enzyme complexes might be essential: the diffusion of toxic intermediates will be reduced and at
the same time the efficiency of the catalysis will be increased.
Gene / Gene Models described: Bx1, Bx2, Bx3, Bx4, Bx5, Bx8; GRMZM2G086489
Funding acknowledgement: SFB924, DFG (Deutsche Forschungsgemeinschaft)
P77
Zma-miR169q/NF-YA14 module is involved in salt stress tolerance in maize
(submitted by Miaoyun Xu <xumiaoyun@caas.cn>)
Full Author List: Zhu, Ming1 2 ; Xing, Lijuan 1; Zhang, Min 1; Wang, Lei1; Xu, Miaoyun1
1
Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese
Academy of Agricultural Sciences, Beijing 100081, China
2
School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
Soil salinity is a major threat to maize productivity worldwide. Plants must adjust their developmental and
physiological processes to cope with salt stress. Gene regulation involved by miRNA is essent ial in these adaptive
processes. However, the functions of the miRNA in plant saline stress responses are poorly understood. Here, we
identified and functionally characterized a maize salt -tolerance miRNA, miR169q, which targets a nuclear factor Y,
subunit A (designated as ZmNF-YA14). T he zma-miR169q overexpression line was hypersensitive to salt stress and
accumulated more reactive oxygen species (ROS) than the wild-type (WT ) under salt stress. Conversely, T he zmNFYA14 overexpression line was resistant to salt stress and accumulated less reactive oxygen species (ROS) than WT .
We showed that miR169q was preferentially expressed in root and reduced under salt stress, meanwhile expression of
ZmNF-YA14 was increased responding to salt stress. We also showed Superoxide Dismutase (SOD) activity was
enhanced in zmNF-YA14 overexpression line compared to WT . RNA-seq analysis revealed that miR169q/NF-YA14
module regulated expression of antioxidant system related genes, which potentially scavenge ROS. Chromatin
immunoprecipitation assays revealed that zmNF-YA14 bound directly to the cis-element CCAAT in the promoter of
the maize peroxidase 1 (PER1). Our findings highlight the critical role of miR169q/NF-YA14 module as a regulator of
salt tolerance in maize.
Gene / Gene Models described: ZmNF-YA14; GRMZM2G038303
Funding acknowledgement: the National Key Research Program of China (grant No. 2016YFD0101002), T he National
Key Basic Research Program (grant No. 2014CB138205)
98
P78
ZmbZIP22 is a new transcription factor for 27-kD γ-zein gene
(submitted by Chaobin Li <chaobinli@cau.edu.cn>)
Full Author List: Li, Chaobin 1; Yue, Yihong2; Ling, Huiling2; Xing, Yingying2; Zhu, T ongdan 2; Song, Rentao 1 2
National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
2
Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University,
Shanghai 200444, China
1
Zeins are the most abundant storage proteins in maize kernel, affecting maize nutrient quality and kernel
hardness. The 27-kD γ-zein is a highly expressed zein that plays crucial role for zein protein body formation. So
far, several transcription factors (TFs) (O2, PBF1 and OHPs) have been identified for the 27-kD γ-zein gene
transcription. However the complexity of 27-kD γ-zein transcription regulation is not fully revealed. In this
study, a new factor binds to the 27-kD γ-zein gene promoter was identified through probe affinity purification
and mass spectrometry analysis. This new factor belongs to bZIP type TF (hence named as ZmbZIP22) and is
endosperm specifically expressed. ZmbZIP22 can directly bind the ACAGCTCA box in 27-kD γ-zein promoter,
and trans-activates the promoter in tobacco cells. The bZIP22 mutants were generated by CRISPR/Cas9, and the
27-kD γ-zein gene expression was significantly decreased in mutant kernels. ChIP-seq analysis confirmed that
ZmbZIP22 binds the 27-kD γ-zein gene promoter in vivo, and also identified additional direct targets of
ZmbZIP22. M oreover, ZmbZIP22 can interact with other TFs of 27-kD γ-zein gene, such as PBF1, OHP1 and
OHP2, but not with O2. Transactivation assay with combinations of these TFs revealed different interaction
mode to the transcription activity of 27-kD γ-zein promoter. These results suggested that ZmbZIP22 is a
functional TF for 27-kD γ-zein gene, and it coordinates the regulation of 27-kD γ-zein promoter with other
known TFs.
Funding acknowledgement: National Natural Science Foundation of China (NSFC)
P79
A phenomics-based dynamic model of growth and yield to simulate hundreds of
maize hybrids in the diversity of European environments
(submitted by Francois Tardieu <francois.tardieu@inra.fr>)
Full Author List: Lacube, Sebastien 1; Parent, Boris1; T ardieu, Francois1
INRA LEPSE Montpellier France F34000
1
Under soil water deficit, plants limit transpiration by decreasing leaf area to save water for the end of the crop
cycle. A large genetic diversity is observed in maize for the processes involved in this response. We aimed to
predict which combination of trait values related to leaf growth would be beneficial in the diversity of European
environments. For this purpose, we have first analysed the genetic and environmental controls of leaf elongation
and widening. A series of experiments revealed that leaf elongation is related to plant water status whereas leaf
widening is related to the carbon available to plant. A GWAS analysis also revealed that elongation and
widening depend on different alleles. This analysis resulted in a model that allows simulating leaf area in a large
variety of environmental scenarios. This model resulted in estimated leaf area and yield that were close to those
observed in 15 fields over Europe. The model was then used to determine ideotyp es of leaf growth adapted to the
different environmental scenarios. Results indicate that sensitive hybrids perform better in southern Europe under
rainfed conditions while less-sensitive genotypes perform better in northern Europe or in irrigated fields.
However, the best combinations of parameters determined in an unconstrained phenotypic space were not
available in the observed genetic diversity. Overall, this study provides elements on where and when a
combination of trait values can give a comparative advantage on yield, together with the boundary of possibilities
within the current genetic diversity.
Funding acknowledgement: INRA, ANR
99
P80
A point mutation in maize hzMS1 gene causes the meiosis defects in heterozygous
mutants
(submitted by Wei Huang <wilsonhuang23@cau.edu.cn>)
Full Author List: Huang, Wei1; Shen, Yi2; Li, Yunfei1; Du, Yan 1; Cheng, Zhukuan 2; Jin, Weiwei1
1
National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improveme nt, China Agricultural
University, Beijing 100193, China
2
State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and
Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
M eiosis is a key process during plant gametes development, and is precisely regulated by a series genes. And
carbohydrate metabolism plays a vital role in the plant growth and development process. Whereas, how the
carbohydrate metabolism gene participates the meiotic process is limited known. Here, we studied a new type of
maize male sterile mutant hzms1, which showed heterozygous male sterile, causing by the chromosome arrested
at pachytene stage, while the homozygous mutants had no obvious defects. We mapped hzms1 positionally and
found that hzms1 possesses a point mutation in an invertase coding gene which hydrolyzes sucrose into glucose
hzms1
and fructose. To confirm the cloning result, we constructed transgenic vector pCambia3300-phzMS1:CDS
to
express the mutated copy in wildtype background, two independent transgenic lines showed the exactly same
phenotype to the heterozygous mutant; we also knockout hzMS1 using CRISPR-Cas9 assay, unexpectedly, the
fertility and meiosis process of hzMS1KO plants had no obvious difference to wildtype. Collectively, the SNP was
the cause of sterility of +/hzms1 plants. The hzMS1 was mainly expressed in meiotic anthers, with highest
abundance in early prophase microsporocytes. Enzyme activity analysis indicated that the wildtype protein had
stringent substrate towards sucrose, while the mutant exhibited no detectable activity. Further experimentations
are undertaking to reveal the molecular function of hzMS1 and its role in maize meiosis regulation.
Funding acknowledgement: National Science Foundation of China (NSFC)
P81
Analysis of leaf growth under mild drought in maize recombinant inbred lines.
(submitted by Tom Van Hautegem <tohau@psb.vib-ugent.be>)
Full Author List: Van Hautegem, T om 1 2; T akasaki, Hironori3; Demuynck, Kirin 1 2; Storme, Veronique1 2; Inze, Dirk 1 2;
Nelissen, Hilde1 2
1
Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.
2
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
3
Institute of Environmental Research and T echnology, Graduate School of Science and Engineering, Saitama
University, Saitama City, Japan.
Plants absorb light energy with their leaves, and convert the energy to carbohydrates, making leaf growth an
important yield component. Two main determinants for leaf size are the maximal growth rate (leaf elongation
rate; LER) and the duration of the growth period (leaf elongation duration; LED). Here, we studied how changes
in environmental conditions affect LER and LED by applying a mild drought stress to a selected panel of a
B73xH99 recombinant inbred line (RIL) population. The mild drought stress negatively affects the maximal
growth rate, but remarkably prolongs the duration of growth, suggesting that the prolonged growth duration
compensates, at least partly, for the reduction in growth rate. To test the hypothesis that the prolonged duration of
the reduced growth rate in mild drought treated maize plants represents a pausing that can be restored to ‘normal’
growth rates when water becomes available, we re-watered drought treated plants at different time points during
their growth. Depending on the growth phase of the leaf upon re-watering, growth could be either fully restored
by increasing the maximal growth rate or partially restored by prolonging the duration of growth. These
phenotypic analyses were complemented with RNAseq transcriptome data to have a molecular view on the
recovery of LER and/or prolongation of LED after re-watering. The observed differences in the recovery
potential of plants is a useful trait for breeding towards drought tolerance.
Funding acknowledgement: European Research Council (ERC)
100
P82
Bioremediation analysis of water pollutants and pathogens within household
water in rural south India
(submitted by David Perez <Dp15g@my.fsu.edu>)
Full Author List: Perez, David1; Clark, Clayton J. 1
Florida State University; FAMU-FSU College of Engineering; T allahassee, Florida, USA 32310
1
Unsafe drinking water is recognized as a leading factor in diarrheal diseases, responsible for about 5 million
annual deaths globally, six hundred thousand deaths alone coming from India. An international field study was
fashioned to document the techniques used by an the Indian Social Service Institute in Southern India to
construct, develop, assemble and distribute bio-sand filters (BSFs), a cost-effective water filtration system, for at
home use. The field study used BSFs to combat microbiological contaminants in household water by using a
mass of organic and inorganic charged compounds that create an environment used to remediate contaminated
water. M ore importantly, this study assessed the logistics and efficiency of BSFs in Pudukkotai, Tamil Nadu.
The three month study created concrete BSFs and filled them with sand and gravel from the surrounding
environment to create a naturally occurring biological filtration system. Laboratory analyses were performed in
five day increments on water samples using indicator strips that tested for pH, NO3-, NO2-, PO4-3, alkalinity
and water hardness. An increase or decrease in nutrient levels over time from this analysis would indicate the
growth or decay of a microbiological community within the BSF. Water analysis did not indicate a growth of a
biological layer, called Shmutzdecke, which indicates the method used for assembly of a BSF must be
configured for greater efficacy. The study is on-going and once an effective system of configuration is produced
this BSF project is expected to construct and distribute 50 filters within the year for the villages located within
Pudukkottai.
P83
Characterization and cloning of needle1 (ndl1), a temperature sensitive mutant
affecting reproductive organogenesis
(submitted by Qiujie Liu <qiujieliu@waksman.rutgers.edu>)
Full Author List: Liu, Qiujie 1 2; Galli, Mary 1; Gallavotti, Andrea 1 2
1
Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854 -8020
2
Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901
ndl1 is a temperature sensitive mutant that develops tassels with fewer branches and spikelets, and ears with
unorganized kernels and partially barren tips. When grown at higher temperature, ndl1 affects root development
as well. Scanning Electron M icroscopy and in situ hybridizations with early markers for organogenesis suggest
that suppressed bract and axillary meristem initiation are defective in ndl1 inflorescences.
By a combination of map-based cloning and BSA RNA-seq approaches, we identified a candidate gene encoding
a mitochondria-localized protein with a missense mutation in a highly conserved amino acid. The homologous
genes in Arabidopsis have been reported to affect the function of the electron transport chain. In ndl1
inflorescences we observed high expression of the ALTERNATIVE OXIDASE-2 (AOX2) gene, a marker for
defects in the electron transport chain, whose expression is not affected in other mutants similar to ndl1.
We are currently following several complementary approaches to confirm the candidate gene. We developed
maize transgenic lines expressing the candidate gene from its native promoter and complemented the ndl1
phenotype. At the same time, we are employing CRISPR/Cas9 based approaches to generate new lesions in the
candidate gene, and to investigate the phenotype of loss of function mutants in both maize and Arabidopsis.
Funding acknowledgement: National Science Foundation (NSF)
101
P84
Characterization of a novel Kinesin protein required for Ab10 meiotic drive
(submitted by Kyle Swentowsky <kws67291@uga.edu>)
Full Author List: Swentowsky, Kyle W 1; Qiu, Weihong2; T seng, Kuo-Fu2; Dawe, R Kelly 1 3
Department of Plant Biology; University of Georgia; Athens, GA, USA 30 602
2
Department of Physics; Oregon State University; Corvallis, OR, USA 97331
3
Department of Genetics; University of Georgia; Athens, GA, USA 30602
1
Originally discovered 75 years ago, maize Abnormal Chromosome 10 (Ab10) lines display meiotic drive where
the segregation ratios of alleles linked to chromosome knobs are significantly altered from the expected 50:50. It
is estimated that meiotic drive in maize has had evolutionary consequences on a genome-wide level by affecting
segregation of alleles near knobs. The cytological cause of meiotic drive is neocentromere activity during female
meiosis where knobs are directed towards the poles and arrive before centromeres. During female meiosis in
plants, only the single lowest of the four cells survives and neocentromere activity favors the knob-containing
chromosome to migrate into what will become the functional megaspore. Knobs are composed of two distinct
tandem repeat arrays termed knob180 and TR1. Ab10 itself contains genes required for meiotic drive and
neocentromere activity, but prior to this work none of these genes had been described. We show that the distal tip
of Ab10 contains the eight-member Kindr (Kinesin driver) gene family and that Kindr is necessary for meiotic
drive and knob180 neocentromeres to occur. Kindr encodes a functional minus end-directed Kinesin-14A
homolog protein that is present in meiotic anthers and ears of Ab10 but not N10 plants. Furthermore,
immunolocalization studies show that KINDR colocalizes specifically with knob180 knobs during male meiosis.
Despite colocalization, KINDR does not undergo a direct protein-DNA interaction with knob180 DNA
sequences. In summary, our work has identified a novel Ab10 kinesin that contributes to meiotic drive by
facilitating meiotic neocentromere activity of the knob180 knobs.
Funding acknowledgement: National Science Foundation (NSF)
P85
Characterization of meiotic defects in the maize nrf4 mutant
(submitted by Wenjing She <wenjing.she@uzh.ch>)
Full Author List: She, Wenjing1; Chumak, Nina1; Bernardes de Assis, Joana 1; Pasquer, Frédérique1; Grossniklaus, Ueli1
1
Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
Apomixis is a form of asexual reproduction through seeds that leads to formation of offspring that is genetically
identical to the mother plant. Introduction of apomixis into the crop plants has the potential to revolutionize
agriculture by providing an ideal tool to fix complex genoty pes. If applied to including F1 hybrids, the heterosis
effect could be stably propagated over many generations.
Through a genetic screen in maize, we identified a recessive mutation - non-reduction in female 4 (nrf4) – that
mimics aspects of apomixis. Homozygous mutants produce up to 95% of unreduced embryo sacs and in a
fraction of those also no recombination occurred, mimicking apomeiosis, the first step of apomixis. To identify
the exact meiotic defects in the apomeiotic nrf4 mutant, we quantitatively analyzed the localization of meiotic
markers in nrf4 female meiocytes in comparison to wild-type meiocytes by whole-mount immunostaining [She et
al. (2018) M ethods M ol Biol 1675:443-454]. To shorten the generation time to facilitate this study, we
introgressed the nrf4 allele into the fast-flowering mini-maize background [M cGaw et al. (2016) Genetics
204:35-42]. Cytological analyses of female meiosis in the nrf4 mini-maize mutant by immunostaining revealed
multiple defects, for instance in the installation of key elements of the synaptonemal complex, the expression of a
meiosis-specific gene controlling the cell cycle, misalignment and decondensation of chromosomes on the
metaphase plate, as well as the distribution of H3Ser10p during metaphase I. Our findings suggest that
chromosome pairing, synapsis, and segregation during meiosis I are affected in the nrf4 mutant.
102
P86
Characterization of RAMOSA3 putative nuclear interactors and their role in
inflorescence development in maize
(submitted by Edgar Demesa-Arevalo <edemesaa@cshl.edu>)
Full Author List: Demesa-Arevalo, Edgar 1 ; DeBlasio, Stacy2; Claeys, Hannes1; Xu, Xiaosa1; Skopelitis, Tara1 ; SatohNagasawa, Namiko 3 ; Si Nian, Char4 ; Yang, Bing4 ; Jackson, David1
1
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY USA 11724
2
Boyce T hompson Institute for Plant Research, Ithaca NY USA 14853
3
Laboratory of Plant Genetics and Breeding, Akita Prefectural University, Akita Japan 010 -0195
4
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA USA 50011
T he classical maize mutant ramosa3 (ra3) shows branches in female inflorescences and increased branching in male
inflorescences; RA3 encodes a trehalose phosphate phosphatase enzyme, specifically expressed at the base of
inflorescence axillary meristems. RA3 is localized in nuclear and cytoplasmic speckles, and a RA3 catalytic-dead
transgene can partially complement ra3, suggesting additional roles other than catalysis of trehalose synthesis. Here we
ask if specific interactors can explain mechanistically how RA3 inhibits inflorescence branching and if RA3 functions
in gene expression regulation.
T o explore these hypotheses, we screened for RA3 physical interactors using yeast -two-hybrid screening and identified
some nuclear localized proteins. We focused on two candidates involved in gene regulation: Zea mays SCAFFOLD
AT T ACHMENT FACT OR B (ZmSAFB) and Zea mays VASCULAR PLANT ONE–ZINC FINGER (ZmVOZ). SAFB
has been described in animal systems as an RNA Recognition motif (RRM) protein involved in transcriptional co repression and splicing, but its functions in plants are not defined yet. In Arabidopsis, VOZ1 and VOZ2 redundantly
link flowering time with light sensing, with no obvious role in meristem branching or determinacy.
T o characterize their role in the RA3 pathway, we first identified homologs for ZmSAFB and ZmVOZ in the maize
genome, and CRISPR mutant alleles were generated. Genetic interactions with RA3 and our CRISPR alleles showed
Zmsafb enhances the ra3 phenotype. Additionally, ZmSAFB-mRFP1 transgenic lines showed constitutive expression in
a punctate pattern in nuclear compartments, and partial co-localization with RA3 and the active form of RNA POLII,
suggesting a role of ZmSAFB in transcriptional regulation. ZmVOZ1-RFP and YFP-ZmVOZ5 lines have also been
generated, and their localization patterns are under analysis. T hese tools will allow us to confirm physical interactions
with RA3 in planta, and by using cell biology, biochemical, genetic and genomic approaches we will determine how
ZmSAFB and ZmVOZ function in the RA3 pathway.
Funding acknowledgement: National Science Foundation (NSF), CONACYT -Mexico
P87
Characterization of the maize lil1-1 mutant defective in the Brassinosteroid C-6
oxidase
(submitted by Gabriella Consonni <gabriella.consonni@unimi.it>)
Full Author List: Castorina, Giulia 1 ; Zilio, Massimo1 ; Sangiorgio, Stefano 1; Gavazzi, Giuseppe1; Consonni, Gabriella1
Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy 20133
1
T he Brassinosteroids (BRs) hormones play an essential role in plant growth and development and mediate the plant
response to different environmental stimuli. BR biologically active molecules castasterone (CS) and brassinolide (BL)
are synthetized from sterols through a complex pathway, whose charact erization has been achieved with biochemical
analysis as well as with the isolation and subsequent characterization of mutants impaired in specific steps. T he main
feature of BR deficient mutant plants is their dwarf growth stature, due to reduced internode elongation. Here we
present the characterization of a mutant allele of the brassinosteroid-deficient dwarf1 (brd1, GRMZM2G103773) gene,
referred to as lilliputian1-1 (lil1-1), which was isolated through transpositional mutagenesis.
T he brd1 gene, encoding a brassinosteroid C-6 oxidase, controls the final steps of the BR pathway, while the nana
plant1-1 (na1) gene, encoding a 5α-reductase enzyme, is involved in earlier steps. Detailed phenotypic analysis of F2
progenies segregating for both na1-1 and lil1-1 mutants showed that the lil1-1 mutation causes a more severe reduction
in plant elongation and is epistatic to na1-1. T his observation suggests that an additional na1-independent branch,
leading to the production of CS precursors, might be present in the maize BR pathway.
T he lil1 mutant phenotype includes several characteristics, such as reduction in plant height, dark green leaves and
feminized male flowers, which are common to all BR related mutants. Our study highlights the presence of additional
traits not previously reported, including altered root gravitropic response and epicuticular wax deposition, which are
caused by BR deficiency in this mutant. In addition, by comparing lil1-1 mutant and wild type individuals grown in
well-watered and in drought stress condition, we assayed the effect of BR deficiency on the response to drought stress.
103
P88
Characterizing the function of kinectin in plants via Zea mays and Arabidopsis
thaliana
(submitted by Marschal Bellinger <mbell008@ucr.edu>)
Full Author List: Bellinger, Marschal Allen 1; Sidhu, Sukhmani1; Leon, Sareen 1; Aranda, Jocelyne 1; Allsman, Lindy 1;
Yang, Bing2; Rasmussen, Carolyn 1
1
Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, 92521, USA
2
Department of Plant Biology, Iowa State University, Ames, IA, 50011, USA
Establishment and maintenance of the division plane is essential for proper growth and development in
multicellular organisms. TANGLED1 (TAN1) promotes proper division plane orientation and localizes to the
future division site during mitosis. In Zea mays, tan1 mutants have disorganized cell architecture that leads to
rough leaf texture and short stature. A yeast-2 hybrid experiment identified KINECTIN1 (KNN1) as a candidate
TAN1-interacting-protein. Orthologs of this gene in animals encode integral endoplasmic reticulum (ER)
proteins that regulate the movement of motor proteins. We chose to investigate KNN1 for its potential role in the
division plane orientation and contributions to plant growth. Our hypothesis is that KNN1 is an ER localized
protein that contributes to proper growth and development through TAN1 interaction. M aize knn1 mutant alleles
were generated using CRISPR/Cas9. Homozygous loss-of-function knn1 single mutants have apparently normal
ER morphology with no obvious cell division plane orientation defects. KNN1-YFP colocalized with the
preprophase band, spindle and phragmoplast during mitosis and possibly co-localized with the ER, during
interphase in Arabidopsis thaliana. Our preliminary findings suggest that KNN1 may be required for growth in
maize.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
P89
CRISPR/Cas9 gene editing in the maize inbred line B104
(submitted by Laurens Pauwels <lapau@psb.vib-ugent.be>)
Full Author List: Vanderhaeghen, Rudy 1 2; Bossuyt, Shari1 2; Coussens, Griet 1 2; Aesaert, Stijn 1 2; karimi, Mansour 1 2;
Van Lijsebettens, Mieke 1 2; Inzé, Dirk 1 2; Pauwels, Laurens1 2
1
Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
2
VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
CRISPR/Cas9-mediated gene editing is revolutionizing plant breeding. Plant transformation and regeneration are
however new bottlenecks in efficient and genotype-independent application of gene editing. Here we report on
CRISPR/Cas9-mediated gene editing to create loss-of–function alleles in the maize inbred line B104. Recent
reports describe the use of the morphogenic regulators OVULE DEVELOPM ENT PROTEIN (ODP2) and
WUSCHEL (WUS2) to enhance maize transformation. We generated Golden Gateway -compatible building
blocks allowing combining these transcription factor modules easily with CRISPR/Cas9. First results with these
constructs in B104, PHP38 and PHN46 will be discussed. Use of these morphogenic regulators will allow shorter
procedures and higher throughput for generating loss-of–function alleles, supporting functional genomics in
maize.
Gene / Gene M odels described: ODP2, WUS2; GRM ZM2G14638, GRMZM2G028622
104
P90
Deposition of lipids in starch granules of maize endosperm is closely related to
zein synthesis and programmed cell death
(submitted by Bénédicte Bakan <benedicte.bakan@inra.fr>)
Full Author List: Gayral, Mathieu1; Fanuel, Mathieu1; Rogniaux, Hélène1; Dalgalarrondo, Michèle 1; Elmorjani, Khalil1;
Bakan, Bénédicte1; Marion, Didier 1
1
INRA, Biopolymers, Interactions, Assemblies, 44316 Nantes cedex 3, France
Presence of lipids within starch granules is a specificity of cereal endosperms. Although these lipids account for
only 0.7-1.5% of starch dry mass, they have strong impacts on assembly and properties of cereal starches.
Besides, cereal endosperms undergo a programmed cell death (PCD) during their development and its impacts on
the deposition of starch lipids is unknown. Furthermore, in contrast with chloroplasts, limited information is
available on amyloplast lipid homeostasis. Using Raman microspectrometry and M ALDI mass spectrometry
imaging, we established that the spatio-temporal deposition of storage proteins, i.e. zeins and the major starch
lipids, i.e. lysophosphatidylcholines (lysoPC), are closely related. Since zeins are synthesized in the endoplasmic
reticulum (ER), this suggests, in regard to what is known about chloroplast lipid homeostasis, that starch lysoPC
could derive from the ER. Transcriptomics strengthened this hypothesis since homologous genes of the
Arabidopsis ER-chloroplast lipid trafficking are also expressed in maize endosperm. However presence of
lysoPC within starch granules means that it is translocated through outer and inner amyloplast envelope
membranes in contrast to the mechanisms described in chloroplasts. In addition, during endosperm development,
palmitate content of amyloplast galactolipids decreased, in relation with a preferential trapping of palmitoyllysoPC by starch carbohydrates, suggesting a role of lysoPC in galactolipid synthesis. Finally, a gene encoding a
cytosolic patatin-like phospholipase A2 was overexpressed in the endosperm periphery. This gene, induced by
PCD in Arabidopsis, is a relevant candidate for the production of lysoPC from ER membranes. Altogether, our
results led us to propose a model where ER-amyloplast lipid trafficking directs the lysoPC in two routes, one
towards starch granules and the other towards galactolipid synthesis. Finally, lysoPC gradients fit well with those
of endosperm vitreousness and new gene candidates were identified that could be tested to improve this
important quality trait of maize crop.
Funding acknowledgement: Biogenouest, Fond unique interministériel
P91
DiSUMO-LIKE interacts with cell cycle and RNA pathways, and regulates early
embryo development in maize
(submitted by Kamila Kalinowska-Brandt <kamila.kalinowska@ur.de>)
Full Author List: Chen, Junyi1; Müller, Benedikt 1; Mergner, Julia2; Kalinowska, Kamila 1; Deutzmann, Rainer 3;
Schwechheimer, Claus2; Hammes, Ulrich Z. 1; Dresselhaus, T homas1
1
Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053
Regensburg, Germany
2
Plant Systems Biology, T echnical University of Munich, 85354 Freising, Germany
3
Laboratory for RNA Biology, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg,
Germany
Embryogenesis in maize and other flowering plants is initiated by an asymmetric zygote division, generating two
daughter cells that are the precursors of various cell lineages. Until now, little is known about the molecular
players regulating activation and progression of zygote development, establishment of asymmetry and the cell
plate formation. We have found that a cereal-specific ubiquitin-like modifier diSUM O-LIKE (DSUL) functions
in early embryo development in maize. Introduction of a DSUL-RNAi construct by sperm cells inhibits
completion of cytokinesis and generates non-separated zygotic daughter nuclei or multinucleate embryonic cells
lacking cell plates. DSUL localizes to the cytoplasm, nucleus and accumulates in the cell division zone.
Identification of DSUL targets suggests predominant roles of DSULylation in regulating the translation
machinery and in cell plate formation. A comparison of DSUL and SUM O1 localization patterns during the cell
cycle and of their target proteins reveals functional diversification between these two SUM O-family modifiers in
maize.
Gene / Gene M odels described: DiSUMO-LIKE (DSUL); GRM ZM2G073404
Funding acknowledgement: German Research Foundation (DFG)
105
P92
Diversity in the surface lipid composition of maize silks among Wisconsin Diversity
Panel inbreds in two environments
(submitted by Travis Hattery <thattery@iastate.edu>)
Full Author List: Hattery, Travis J1 ; Schroeder, Elly C2 ; Myers, Bryn M3 ; Moore, Riley D4 ; Lauter, Nick5 ; Hirsch, Candice
N.6 ; Yandeau-Nelson, Marna1
1
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011
2
Kinesiology Undergraduate Major, Iowa State University, Ames, IA 50011
3
Genetics Undergraduate Major, Iowa State University, Ames, IA, 50011
4
Biology Undergraduate Major, Iowa State University, Ames, IA, 50011
5
Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011
6
Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108
Extracellular surface lipids are specialized metabolites synthesized by epidermal cells that accumulate on aerial
portions of plants and provide a protective barrier against both biotic and abiotic stresses. Maize silks are rich in surface
lipids, accumulating predominantly hydrocarbons and minor amounts of fatty acids, which are the end-point and
precursor metabolites of the hydrocarbon biosynthetic pathway, respectively. T he underlying genetic networks that
organize the synthesis and localization of these surface lipids are not fully understood. T o dissect the genetic network,
we are profiling the surface lipids on silks from 500 genetically diverse inbred lines of maize that comprise the
Wisconsin Diversity (WiDiv) Panel. Silks that had emerged from encasing husk leaves were samp led in both
Minnesota and Iowa during Summer 2016 and extracted surface lipids were profiled via gas chromatography and flame
ionization detection. A high-throughput metabolomics analysis pipeline has revealed a set of approximately 50 unique
lipid metabolites. Across the 50% of the WiDiv panel profiled to date, a 14 -fold range in total metabolite accumulation
was observed. Herein, we will present a comparison of metabolome compositions from silks of inbreds profiled in
these two distinct environmental conditions. Potential diversity in the metabolic network will be probed by assessing
fatty acid precursor and hydrocarbon product relationships, providing insight into the mechanisms responsible for their
synthesis. Future work will include genome wide association studies to understand the underlying genetic networks
controlling these metabolites, and how this genetic network interacts with environmental perturbations.
Funding acknowledgement: National Science Foundation (NSF)
P93
early delayed kernel 1 (edk1) encodes a microtubule -located protein essential for
early endosperm development in maize
(submitted by Yongrui Wu <yrwu@sibs.ac.cn>)
Full Author List: Huang, Yongcai1 2 ; Wang, Haihai1; Huang, Xing1 2; Wu, Yongrui1
1
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai
Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
2
University of the Chinese Academy of Sciences
Maize (Zea mays) is a highly productive crop that is widely used as food and feed. T he seed size and plant height are
two critical agronomic traits related to the yield and are under control of multiple complex factors. In Arabidopsis and
rice, several signal pathways regulating the seed size have been extensively elucidated, while the related research in
maize still lacks, particularly at early seed development stage. Using EMS mutagenesis, we screened a small seed
mutant that is developmentally delayed at early stage (early delayed kernel 1, edk1). T he mutant plant is shorter
compared to the wild type (WT , A619). We cloned this gene and determined that the mutation in edk1 resulted in a
CGA → T GA transition, leading to a premature stop codon in the coding sequence. Cytohistological examination
revealed that the reduced seed size in edk1 was due to the decreased cell number rather than cell size in the endosperm.
Developmental defects in the cell wall ingrowth (CWI) at the basal endosperm transfer laye rs (BET L) were also
observed, which may partially contribute to its small seed size. edk1 was determined to be located on cortical
microtubules. Spatial and temporal expression analyses revealed that edk1 was most abundantly expressed between 2-3
DAP, preferentially enriched in the syncytium area during the endosperm development, indicating that EDK1 plays an
important role in nuclear divisions at syncytial stage. We propose that lack of EDK1 may affect the syncytial (and
cellularization) development, which in turn reduces the cell number and as a consequence the seed size in the later
endosperm development.
Funding acknowledgement: National Natural Science Foundation of China (91635303 to Y. W.), Chinese Academy of
Sciences (XDPB0401 and XDA08020107 to Y. W.)
106
P94
fun is: pleiotropy, unknown genes and double mutants
(submitted by Angus Vajk <vajking@berkeley.edu>)
Full Author List: Vajk, Angus1 ; Chuck, George1; Schulz, Burkhard2 ; Kim, Kitae1 ; Cheng, Miles1; Leiboff, Sam 1 ; Juarez,
Jazmin Abraham3 ; Hake, Sarah 1
1
UC Berkeley PGEC, Berkeley, CA, USA
2
UMass Amherst, Amherst, MA, USA
3
University of Maryland
Feminsed upright narrow (fun1) is a pleiotropic maize mutant that has a loss of auricle and thus a leaf angle defect, a
narrowing of leaves, and feminisation of tassel flowers and architecture. T he fun1-1 mutation contains a premature stop
codon in the last exon of a gene of unknown function that is conserved primarily as single copy across angiosperms
with high conservation in grasses. T he non-complementing fun1-2 allele also contains a premature stop codon in the
same gene. T hough neither functional nor predicted annotations of the gene or its homologues exist in the databases,
transient expression of YFP clones in Nicotiana benthamiana suggests protein localisation to the nucleus. Y2H and
RNAseq analysis have identified putative interactors of the protein and sketched the genetic landscape of the mutant.
An additive phenotype in the lg2;fun1 double mutant suggests that fun1 exists in a separate, later pathway than LG2.
T he extreme synergistic phenotype of the WAB;fun1 double and examination of the WAB;fun1;lg2 triple has allowed a
deeper interrogation of the lg2;fun1 interaction, showing that these genes operate in different areas of the ligular region.
On the other hand, the lg1;fun1 double loses the partial recovery of ligule seen in the lg1 single mutant, suggesting that
FUN1 also plays a role early in the ligule’s development, in the same ligular region as LG1. Feminisation in fun1 is a
result of a failure to abort the young silk, and, while the sk1;fun1 tassel loses silks, tassel architecture and florets
continue to show secondary feminine traits implying that feminisation of fun1 is not related to jasmonic acid
deficiencies. fun1 is epistatic to Bin1-RNAi transgenic mutants, implying that the fun1 mutation may block the
brassinosteroid response pathway, while a synergistic phenotype in the dwarf1;fun1 double mutant suggests that FUN1
doesn’t interact with the gibberellic acid pathway.
Gene / Gene Models described: GRMZM2G323353, GRMZM2G110242, GRMZM2G036297, GRMZM2G060216,
GRMZM2G021786; Zm00001d039435
Funding acknowledgement: National Science Foundation (NSF)
P95
Functional analysis of pollen-specific RALFs during reproduction in maize
(submitted by Lele Wang <lele.wang@ur.de>)
Full Author List: Wang, Lele1 ; Zhou, Liangzi1 ; Dresselhaus, T homas1
1
University of Regensburg; Universitätsstrasse 31; Regensburg; Bavaria; Germany; 93053
Small secreted peptides can be classified into two major groups, CRPs (cysteine-rich peptides) and non-CRPs. Previous
studies have shown that members of various CRP sub-classes are involved in different steps of the double fertilization
process of flowering plants. T o investigate the roles of CRPs during maize reproduction, we performed RNA -seq
analysis to identify CRPs with specific expression pattern during pollen tube growth and fertilization. We identified
three genes encoding rapid alkalinization factor (RALF) CRPs, which are highly and exclusively expressed in
germinated pollen tubes. T o understand the function of these pollen -specific RALFs during reproduction in maize,
RALF-RNAi lines were generated. During in vitro germination tests, pollen tubes from down-regulated lines were less
stable and burst much faster compared with wild type pollen tubes. T he effect of pollen cell wall instability and its
consequence is now investigated in vivo. Functional studies of RALFs in Arabidopsis thaliana revealed that peptides of
this gene family are involved in multiple aspects of plant growth and development. For example, it has been shown that
RALF1 interacts with the receptor-like kinase FERONIA in Arabidopsis root development and immune
signaling(Bergonci et al.,2014;Stegmann et al.,2017). Pollen expressed RALF4/19 can interact with FERONIA-like
receptor like kinases ANXUR1/2 and BUPs1/2. Int eraction of these receptors with ovule expressed RALF34 induces
burst of growing pollen tubes(Ge et al.,2017). Based on sequence alignment and expression pattern comparisons,
several putative FERONIA homologs were found in maize silks in a pollination -specific expression manner. Knockedout mutant lines with CRISPR-Cas9 of above mentioned pollen specific RALFs from maize and possible receptor-like
kinases have been generated and are currently being transformed. Moreover, we now study the specificity of
interactions between maize and Arabidopsis RALFs and their corresponding receptors.
Funding acknowledgement: Sonderforschungsbereiche924 (SFB924),Deytscge Forschungsgemeinschaft (DFG), China
Scholarship Council (CSC)
107
P96
Functional analysis of the heterotrimeric Gγ subunits in maize
(submitted by Jara Oppenheimer <jara.oppenheimer@uni-hamburg.de>)
Full Author List: Oppenheimer, Jara 1; Stateczny, Dave1; Maschmann, Sascha 1; Bommert, Peter 1
Universität Hamburg, Developmental Biology, 22609 Hamburg
1
Heterotrimeric G proteins are membrane-associated proteins involved in the transduction of extracellular
signaling by activating downstream effectors. However, it is a widely accepted fact that the mechanisms of G
protein activation and signaling in animals compared to plants are fundamentally different. G protein signaling in
plants affects a variety of physiological and developmental processes, which is also manifested in the pleiotropic
phenotype of heterotrimeric subunit mutants in various plant species, including Arabidopsis, rice and maize.
On average plants share one canonical Gα, one Gβ and multiple Gγ subunits. which can be classified into three
types: Type A Gγ subunits resemble the canonical type also present in animal systems, possessing a C-terminal
prenylation motif. Type B subunits are structurally similar to Type A, but lack the C-terminal prenylation motif.
Type C subunits are characterized through the presence of a long, cysteine rich C-terminal region.
The Gγ subunits have been shown to play important roles in development. Especially the Type C Gγ subunit,
DEP1, in rice has been shown to affect cell proliferation and inflorescence development.
As part of a functional genomics approach to elucidate the function of maize Type C Gγ subunits, we are
analyzing the tissue specific and subcellular expression pattern of the Type C maize Gγ subunits. We will present
in situ hybridization data in developing inflorescences. Initial data suggest an altered exp ression pattern in Gα
mutants compared to wild type. Furthermore initial subcellular localization data of YFP-tagged constructs
transiently expressed in tobacco leaves will be shown.
Additionally UniformM u insertion lines and M aize Targeted M utagenesis mutants for the DEP1-like Gγ subunits
were isolated to identify the role of the Gγ subunit in plant development.
Funding acknowledgement: German Research Foundation (Deutsche Forschungsgemeinschaft DFG)
P97
Functional characterization of male gametophyte genes under heat stress
(submitted by Xingli Li <xingli.li@ur.de>)
Full Author List: Li, Xingli1; Dresselhaus, T homas1; Begcy, Kevin 1
1
Cell Biology and Plant Biochemistry,University of Regensburg;Universitätsstraße 31; Regensburg, Germany,93053.
Genome-wide expression analysis is a powerful tool to identify genes affected by environmental stresses during
developmental programs. In maize, male gametogenesis is generally considered to be especially sensitive to
various stresses. Using the Leaf Collar M ethod (Begcy and Dresselhaus, 2017) we have dissected transcriptional
expression patterns from discrete pollen developmental stages. To understand mechanistically how heat stress
affects male gametophyte, we imposed a moderate (35°C) heat stress treatment on developing pollen at various
stages including the unicellular and bicellular stage. Heat stress resulted in shrunken pollen and reduced pollen
viability. We identified a set of genes including transcriptional regulators with a potential role to mitigate the
effect of heat stress during pollen development. To functionally characterize differentially expressed candidate
genes, we are currently generating maize CRISPR-Cas9 lines to study their function during male gametophyte
development under heat stress. Our findings suggest that several of these genes are preferred targets for heat
stress. Engineering such candidate genes could potentially help in the future to improve thermal resilience in
monocot plants.
References
Begcy K, Dresselhaus T (2017) Tracking maize pollen development by the Leaf Collar Method. Plant Reprod 30: 171-178
Funding acknowledgement: BayKlimaFit(BKF), China Scholarship Council(CSC)
108
P98
Functions of PP2A phosphatases in Arabidopsis stomatal development
(submitted by Chao Bian <chao.bian@rutgers.edu>)
Full Author List: Bian, Chao 1; Dong, Juan 1 2
1
Department of Plant Biology, Rutgers, the State University of New Jersey
2
T he Waksman Institute of Microbiology, Rutgers, the State University of New Jersey
Stomata guard cells control gas exchange between plants and the atmosphere. In Arabidopsis, stomatal
development is regulated by peptide ligands, membrane receptors, a mitogen-activated protein kinase (M APK)
cascade, and a set of transcriptional factors. The initiation of the stomatal lineage requires the activity of the
bHLH transcriptional factor SPEECHLESS (SPCH) and its partners. M ultiple kinases, including M APK3/6, the
GSK3-like kinase BIN2 and Cyclin-Dependent Kinase A;1, have been identified to regulate SPCH protein
stability through phosphorylation, yet no phosphatase has been characterized thus far.
In this work, we identified PP2A phosphatases as novel positive regulators in Arabidopsis stomatal develop ment.
PP2As form heterotrimeric complexes, each of which is composed of a scaffolding subunit (A), a regulatory
subunit (B), and a catalytic subunit (C). The single and double T-DNA insertional mutations in the three PP2A-A
genes exhibited decreased stomatal production, and both RNAi knocking down and CRISPR-Cas9 knocking out
all three PP2A-A subunits resulted in similar effects. Consistently, the PP2A-specific inhibitor Cantharidin (CT)
treatment of Arabidopsis seedlings suppressed stomatal formation. Furt hermore, we show that CT specifically
suppressed the SPCH protein abundance. Genetic analyses indicated that PP2As act downstream of the M APK
cascade, but upstream of SPCH. Considering PP2As were reported to participate in the brassinolide (BR)
hormone signaling, and BRs were found to regulate stomatal development through the BIN2 kinase, we are now
testing the potential connection between BR signaling and PP2A function. Our results suggest that PP2As
promote stomatal development through stabilizing the SPCH protein.
Funding acknowledgement: National Institutes of Health (NIH)
P99
Genetic control of maize floral development
(submitted by Beth Thompson <thompsonb@ecu.edu>)
Full Author List: Yang, Hailong1; Amoiroglou, Anastasia1; Nukunya, Kate1; Ding, Charlene1; De Luis Balaguer, Maria
Angels2; Sozzani, Rosangela 2; T hompson, Beth 1
1
East Carolina University; Greenville, NC 27858
2
North Carolina State University; Raleigh, NC, 27695
Flowers have an essential role in p lant reproduction and also produce fruits and seeds, which are a major food
source. Grass flowers (called florets) have a highly derived morphology and in addition to stamens and carpels
contain the grass-specific organs lodicules, palea and lemma. M aize spikelets contain two florets, which are the
product of the upper and lower floral meristems. In the tassel, both florets develop to produce two male florets
that are morphologically indistinguishable at maturity. In the ear, the lower floret aborts resulting in spikelets
with a single floret. To understand the gene regulatory networks that function in floral development, we used
lasercapture microdissection coupled with RNA-seq to identify genes specifically expressed in the upper and
lower floret. Approximately 600 genes are differentially expressed between the upper and lower floral meristems
in ears (FC>2; q<0.05) and are enriched for genes involved in transcriptional regulation, development and
hormone metabolism.
We have also begun analysis and positional cloning of the classical semi-dominant mutant, Polytypic1 (Pt1). The
Pt1 phenotype varies significantly depending on inbred background. In the A619 inbred background, Pt1
heterozygotes have a mild phenotype and are often male and female fertile, whereas in the B73 inbred
background, Pt1 heterozygotes are female sterile and tassels shed little pollen. Floral meristems in Pt1 mutant
ears are indeterminate and make abnormal floral organs. Interestingly, Pt1 homozygotes often have pin-like
inflorescences that produce few or no lateral primordia. Pt1 maps to bin 6.05 and we plan to identify candidate
genes using RNA-seq. Together, these approaches will uncover new genes and regulatory networks that function
in grass floral development.
Funding acknowledgement: National Science Foundation (NSF)
109
P100
Genetic control of stomatal conductance in maize and conditional effects to
water deficit and evaporative demand as revealed by phenomics
(submitted by Santiago Alvarez Prado <santiago.alvarez-prado@inra.fr>)
Full Author List: Alvarez Prado, Santiago 1; Cabrera-Bosquet, Llorenç1; Grau, Antonin 2; Coupel-Ledru, Aude3; Millet,
Emilie J4; Welcker, Claude1; T ardieu, François1
1
LEPSE, INRA, Univ. Montpellier, 34060 Montpellier, France
2
CNRS, Ecotron UPS-3248, 34980 Montferrier-sur-Lez, France
3
UMR AGAP, INRA Montpellier, 34398 Montpellier, France
4
Biometris, Wageningen University & Research, 6700 AA Wageningen, Netherlands
Plants tend to decrease transpiration under water deficit and/or high evaporative demand by closing stomata.
Stomatal conductance is central for the trades‐off between hydraulics and photosynthesis. We aimed at
deciphering its genetic control and that of its responses to evaporative demand and water deficit, a nearly
impossible task with gas exchanges measurements. Whole‐plant stomatal conductance was estimated via
inversion of the Penman–M onteith equation from data of transpiration and plant architecture collected in a
phenotyping platform. We have analyzed jointly 4 experiments with contrasting environmental conditions
imposed to a panel of 254 maize hybrids. Estimated whole‐plant stomatal conductance closely correlated with
gas‐exchange measurements and biomass accumulation rate. Sixteen robust quantitative trait loci (QTLs) were
identified by genome wide association studies and co‐located with QTLs of transpiration and biomass. They
accounted for 58% of the additive genetic variance and 40% of the genotype × environment interaction. Light,
vapour pressure deficit (VPD), or soil water potential largely accounted for the differences in allelic effects
between experiments, thereby providing strong hypotheses for mechanisms of stomatal control and explaining
part of the observed genotype × environment interaction. Light positively affected the allelic effects of three
QTLs (e.g. R2 = 0.74), whereas VPD and water deficit negatively affected the allelic effects of other four QTLs.
The combination of SNP effects, as affected by environmental conditions, accounted for the variability of
2
stomatal conductance across a range of hybrids and environmental conditions (R = 0.86). This approach may
therefore contribute prediction of stomatal control in diverse environments and to breeding for water efficient
maize.
Funding acknowledgement: INRA, ANR‐10‐ BTBR‐01 (Amaizing), FP7‐244374 (DROPS), FP7‐609398
(AgreenSkills+)
P101
Genetic mechanisms for bud suppression during maize domestication
(submitted by Dong Zhaobin <dongz@berkeley.edu>)
Full Author List: Dong, Zhaobin 1; Xiao, Yuguo 2; Whipple, Clint 2; Chuck, George1
U.C. Berkeley/PGEC, Albany, CA 94710
2
BYU, Provo, Ut, 84602
1
M any domesticated crop plants have been bred for reduced axillary branching compared to their wild ancestors.
In maize this has been achieved through selection for gain of function alleles of the TCP transcription factor
teosinte branched1 (tb1) nearly ten thousand years ago. Despite its importance, the precise genetic mechanism
for how tb1 was able to achieve bud suppression is unknown. By raising an antibody to TB1 and performing
chromatin immunoprecipitation and high through-put sequencing (CHiP seq) on very young axillary bud tissue,
we identified the genetic pathways necessary for TB1 function. For example, TB1 targets several hormone
pathways to effect axillary bud suppression, including auxins and gibberellins, but also targets genes controlling
sugar metabolism whose products are necessary to feed the growing bud. Interestingly, TB1 also targets several
previously described genes in the domestication pathway including teosinte glume archeticture1 (tga1) and
grassy tillers1 (gt1). This fact places tb1 near the top of the domestication hierarchy, demonstrating the critical
importance of this gene during the domestication of maize from teosinte.
Funding acknowledgement: National Science Foundation (NSF)
110
P102
Genome-wide analysis of small RNA-controlled gene networks in leaf
development
(submitted by Xiaoli Ma <xiaoli.ma@uni-tuebingen.de>)
Full Author List: Ma, Xiaoli1; Javelle, Marie2; Knauer, Steffen 1 2; Schnable, Patrick 3; Yu, Jianming3; Muehlbauer,
Gary 4; Scanlon, Mike5; T immermans, Marja C. P. 1 2
1
Center for Plant Molecular Biology Biology, University of T übingen, 72076 T übingen, Germany.
2
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
3
Department of Agronomy, Iowa State University, Ames, Iowa 50010, USA.
4
Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA.
5
Division of Plant Biology, Cornell University, Ithaca, New York 14850, USA.
In plants, stem cell niches serve as a stable source of cells for postembryonic growth and development. The shoot
apical meristem (SAM ) gives rise to all aerial organs of a plant, and its activity throughout the plant’s lifetime
therefore has to be tightly controlled in a spatiotemporal manner. To gain insight into gene regulatory networks
behind stem cell maintenance and organogenesis, we generated a high-resolution gene expression atlas of 12
distinct domains within the vegetative maize shoot apex using laser microdissection and RNA deep sequencing.
We also generated small RNA sequencing data that informs on the role of miRNAs in the maize shoot apex.
Together these data reveal a subfunctionalization of miRNA family members across the SAM subdomains, and
the regulation of miRNA accumulation in the stem cell containing SAM tip and vasculature. In addition, miRNA
degredome sequencing data, combined with information from the SAM atlas, predicts the presence of
mechanisms that further fine-tune the accumulation and activity of select small RNAs to regulate key meristem
genes.
Funding acknowledgement: National Science Foundation (NSF), Alexander von Humboldt Professorship.
P103
Grain abortion under drought in maize: expansive growth and hydraulics also
matter
(submitted by Claude Welcker <claude.welcker@inra.fr>)
Full Author List: T urc, Olivier 1; Oury, Vincent 1; Gibon, Yves2; Prodhomme, Duyen 2; T ardieu, François1; Welcker,
Claude1
1
LEPSE, INRA, Univ. Montpellier, Montpellier, France
2
BFP, INRA, Bordeaux, France
Yield maintenance under drought in maize (Zea mays) requires the rapid extension of styles and stigma (silks)
that collect pollen. We have shown that the control of grain set under moderate water deficits similar to those in
the field result from a developmental process linked to the timing of silk growth, in opposition to the common
view that abortion is linked to the sugar metabolism in ovaries. A switch to abortion occurs 2-3d after first silk
emergence in water-stressed plants, when silk growth stops simultaneously for all ovary cohorts, and explains
abortion rates in different treatments and positions on the ear. Analyses of transcripts and metabolites indicate
that the first molecular events occur in silks rather than in ovaries, and involve genes affecting expansive growth
rather than sugar metabolism. Sugar availability is preserved in ovaries until the switch to abortion, and the
disruption of carbon metabolism only occurs afterwards. Hence, changes in metabolite contents, transcript
amounts and enzyme activities involved in ovary sugar metabolism would be a consequence rather than a cause
of the beginning of ovary abortion. Patterns of silk growth responses to environment share common features with
those of leaf growth with both kinetic and genetic evidences. These findings have large consequences for
breeding drought tolerant maize and for modelling grain yields under drought.
Oury et al (2016) Plant Physiology 171: 986-996 and 171: 997-1008
Turc et al (2016) New Phytologist 212: 377–388
Dignat G et al (2013) Plant Cell and Environment 36: 1105-1119.
Funding acknowledgement: INRA, ANR‐10‐ BTBR‐01 (Amaizing), FP7‐244374 (DROPS)
111
P104
Heat stress induced male sterility during pollen development in maize
(submitted by Kevin Begcy <kevin.begcy@ur.de>)
Full Author List: Begcy, Kevin 1; Dresselhaus, T homas1
1
University of Regensburg, Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, Regensburg,
Germany.
Shifts in the duration and intensity of heat stress are expected to have a detrimental effect on plant development,
reproduction and yield. Increased male sterility has been reported and several factors associated to variations in
optimal temperatures have been shown to negatively affect male gametophyte (pollen) development. How the
specific stages of pollen developmental respond to increased temperatures is not understood. To elucidate the
mechanistic basis of heat stress sensitivity causing reduced male gametophyte viabilit y and partially arrested
development, we exposed maize plants to a moderate (35/30 °C day/night) heat stress for 48 hours at various
stages of pollen development. Physiological and biochemical analysis of maize plants heat stressed at the tetrad
stage of pollen development showed less pollen grains adhered to anthers, reduced pollen viability and
germination capability. Pollen grains also contained less starch. Next, we analyzed changes in gene expression
pattern. Approximately 300 genes were differentially expressed under heat stress condition at the tetrad stage.
Gene Ontology analysis of differentially expressed genes revealed that around 40 % of the genes found are
involved in metabolic processes. Detailed analysis showed that biosynthesis pathways used to generate energy
and lipids are especially affected by increased temperatures during the tetrad stage leading to male sterility and
thus affecting yield.
Funding acknowledgement: BayKlimaFit
P105
Hetero-fertilization along with failed egg-sperm cell fusion reveals single
fertilization involved in in vivo haploid induction in maize
(submitted by Xiaolong Tian <cautxl@163.com>)
Full Author List: T ian, Xiaolong1; Qin, Yuanxin 1; Chen, Baojian 1; Liu, Chenxu1; Wang, Lele1; Li, Xingli1; Dong, Xin 2;
Chen, Shaojiang1
1
National Maize Improvement Center of China, China Agricultural University, Yuanmingyuan West Road, Haidian
District, 100193 Beijing, China
2
Chongqing Academy of Agricultural Sciences, Jiulongpo District, Chongqing 401329, China
In vivo doubled-haploid technology is widely applied in commercial maize-breeding programs owing to its timesaving and cost-reducing features. The production of maize haploids during doubled-haploid breeding primarily
depends on the use of the Stock6-derived haploid inducer lines. Although the gene underlying haploid induction,
M TL/ZmPLA1/NLD, was cloned recently, how it functions is unknown. Hetero-fertilization can occur via a
single fertilization, which provides an indirect way to investigate single-fertilization events by studying the
hetero-fertilization phenomenon. We found that the hetero-fertilization rate increased significantly when female
maize lines were first individually crossed with pollen from the inducer CAU5 in dual-pollination experiments
for 4 h before the second pollination. We also examined ovule embryogenesis during haploid induction by
confocal laser-scanning microscopy and found that, sometimes, a sperm cell fused only with a central cell,
indicating that a single fertilization occurred during haploid induction. Consequently, we postulate that both
single fertilizations and chromosome eliminations contribute to haploid production in maize. We also discuss a
scheme for formation of hetero-fertilized and haploid kernels. Our results provide an efficient approach to
identify hetero-fertilized kernels for research on interactions between embryos and endosperm.
Funding acknowledgement: the National Key Research and Development Program of China
(2016YFD0101200), M odern M aize Industry Technology System (CARS-02-09)
112
P106
How to make maize seeds that look “not like dad”: insights in double
fertilization and prospects for novel breeding tools.
(submitted by Laurine Gilles <laurine.gilles@ens- lyon.fr>)
Full Author List: Gilles, Laurine M 1 2; Khaled, Abdelsabour 1 3; Laffaire, Jean-Baptiste2; Chaignon, Sandrine 1; Gendrot,
Ghislaine1; Laplaige, Jérôme1; Bergès, Hélène4; Beydon, Genséric4; Bayle, Vincent 1; Barret, Pierre5; Comadran, Jordi2;
Martinant, Jean-Pierre2; Rogowsky, Peter M 1; Widiez, T homas1
1
Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA,
Lyon, France
2
Limagrain Europe SAS, Research Centre, Chappes, France
3
Department of Genetics, Faculty of Agriculture, Sohag University, Sohag, Egypt
4
INRA, US1258 Centre National des Ressources Génomiques Végétales, Auzeville, France
5
INRA, UMR1095 Génétique, Diversité, Ecophysiologie des Céréales, Clermont -Ferrand, France
M ixing male and female genetic information during sexual reproduction is considered as key to the evolutionary
success of higher eukaryotes and is the basis of plant breeding. Sexual reproduction in flowering plants involves
double fertilization, characterized by two separate fusion events between the male and female gametes. A maize
line first reported in the 60s deviates from this classic pattern. Crosses using pollen from this so-called haploid
inducer line, trigger the development of the egg cell into a haploid embryo with only the maternal genome, a
process known as in vivo gynogenesis. Derivatives of this maize haploid inducer line have become the preferred
tool of numerous maize breeding companies, because it can produce perfectly homozygous plants in only 2
generations instead of 5 to 8 in classical breeding schemes.
Our recent results (Gilles et al., EM BO J), together with two other simultaneous independent studies (Kelliher et
al., Nature; and Liu et al., M olecular Plant), identified the major causal gene responsible for gynogenesis in
maize. Our map based cloning restricted the QTL to a zone containing a single gene coding for a patatin-like
phospholipase A, which was named Not like Dad (NLD) because haploid embryos do not have paternal
contribution. In all surveyed haploid inducer lines NLD carries a 4 pb insertion leading to a predicted truncated
protein. This frameshift mutation is responsible for haploid induction as complementation with wildtype NLD
abolishes the haploid induction capacity. Translational NLD::citrine fusion protein likely localizes to the sperm
cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma
membrane, contrary to the wildtype NLD protein. In conclusion, an intact sperm-specific phospholipase is
required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid
breeding tools in numerous crops.
Gene / Gene M odels described: Not Like Dad (NLD); Zm00001d029412
113
P107
Identification and characterization of LINC complex proteins in Zea mays L.
(submitted by Hardeep Gumber <hardeep@bio.fsu.edu>)
Full Author List: Gumber, Hardeep K 1; McKenna, Joseph 2; Estrada, Amado L 1; Jalovec, Alexis M 1; Graumann, Katja 2;
Bass, Hank W 1
1
Department of Biological Science, Florida State University, T allahassee, FL, USA 32306-4295
2
Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University,
Oxford,UK
The LINC (Linker of Nucleoskeleton to Cytoskeleton) complex serves as an essential multi-protein structure that
spans the nuclear envelope (NE). It connects the cytoplasm to the nucleoplasm and functions in both mechanical
and signal transduction across the NE. In eukaryotes, the multiple functions of the LINC complex include the
maintenance of nuclear shape, nuclear positioning within the cell, regulation of nuclear architecture, and
chromosome dynamics during mitosis and meiosis. We have previously characterized the LINC-resident SUN
domain proteins in meiotic prophase where they participate in tethering telomeres to the NE to ensure proper
chromosome interactions needed for segregation. Here, we have identified and classified a total of 21 genes
encoding candidate maize LINC complex proteins, grouped by their location in one of four cellular areas: the
nucleoplasm (lamin-like NM CP/CRWN, and CRWN-interacting proteins); the inner nuclear membrane (SUN
domain and NEAP proteins); the outer nuclear membrane (KASH and KASH-interacting proteins); and the
cytoplasm (cytoskeleton-binding proteins). These genes were identified through bioinformatic screens and
biochemical co-IP assays. Nuclear envelope localization of candidates was verified using heterologous fusion
protein expression assays. FRAP-based assays further revealed ZmSUN2-dependent reduction of mobility for
several of the KASH-FPs, indicative of KASH-SUN interactions. Transcriptome analysis revealed groups of
tissue-specific co-expressed LINC genes. Genetic analysis revealed two phenotypes of interest, nuclear shape in
root hair cells and stomatal complex development. Overall, we have identified genes encoding 9 KASH proteins
(M LKp1-MLKp7, M LKt1, MLKt2), 3 NEAP proteins (NEAP1A, NEAP1B, and NEAP2), 5 SUN proteins
(SUN1 - SUN5), and 4 CRWN or CRWN-binding proteins (NCH1, NCH2, KAKU4A and KAKU4B). These
findings were used to develop a summary working model of the entire maize LINC complex, providing a
framework for future studies of the plant nuclear envelope in a model crop species.
Funding acknowledgement: National Science Foundation (NSF)
P108
Identification of the translational landscape of Arabidopsis and Maize meiocytes
(submitted by Joke De Jaeger-Braet <joke.jaeger-braet@uni-hamburg.de>)
Full Author List: De Jaeger-Braet, Joke1; Brettschneider, Reinhold1; Schnittger, Arp 1
1
University of Hamburg; Biocenter Klein Flottbek; Hamburg, Germany, 22609
M eiosis is essential in sexually reproducing organisms to maintain genome size from one generation to another.
M oreover, meiosis is also the driving force for biodiversity, and hence, also the key for plant breeding. Recent
studies in yeast have revealed that translational regulation is important to control protein abundance during
meiosis. However in plants, as Arabidopsis and maize, meiotic gene regulation through translation is not known
yet, although there are strong indications for pervasive translational control. To gain insights into potential
translational regulation during meiosis in plants, we aim to identify the translatomes of dicoty ledonous and
monocotyledonous species, i.e. Arabidopsis and maize. To this end, we perform ribosome profiling experiments
of isolated reproductive organs. A comparison with what is known in yeast and animals will then address the
question whether the regulatory patterns and mechanisms are universally conserved and how translational
regulation might have evolved.
Next to insights into gene regulation, these approaches also promise to reveal unknown meiotic regulators.
114
P109
Integrated analysis of protein abundance, transcript level, and tissue diversity to
reveal developmental regulation of maize
(submitted by Yanfang Du <yanfangdu@webmail.hzau.edu.cn>)
Full Author List: Jia, Haitao1 ; Sun, Wei1; Li, Manfei1 ; Zhang, Zuxin1
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P.R. China
1
Integrated Analysis of Protein Abundance, T ranscript Level, and T issue Diversity to Reveal Developmental Regulation
of MaizeT he differentiation and subsequent development of plant tissues or organs are tightly regulated at multiple
levels, including the transcriptional, posttranscriptional, translational, and posttranslational levels. T ranscriptomes
define many of the tissue-specific gene expression patterns in maize, and some key genes and their regulatory networks
have been established at the transcriptional level. In this study, the sequential window acquisition of all theoretical
spectra-mass spectrometry technique was employed as a quantitative proteome assay of four representative maize
tissues, and a set of high confidence proteins were identified. Integrated analysis of the proteome and transcriptome
revealed that protein abundance was positively correlated with mRNA level with weak to moderate correlation
coefficients, but the abundance of key proteins for function or architecture in a given tissue was closely t empo-spatially
regulated at the transcription level. A subset of differentially expressed proteins, specifically tissue-specific proteins,
were identified, e.g., reproductive structure and flower development -related proteins in tassel and ear, lipid and fatty
acid biosynthetic process-related proteins in immature embryo, and inorganic substance and oxidation reduction
responsive proteins in root, potentially revealing the physiology, morphology and function of each tissue. Furthermore,
we found many new proteins in specific tissues that were highly correlated with their mRNA levels, in addition to
known key factors. T hese proteome data provide new perspective for understanding many aspects of maize
developmental biology.
Funding acknowledgement: National Science Foundation (NSF), Fundamental Research Funds for the Central
Universities
P110
Keeping Separate: mysterious boundaries and the grass leaf
(submitted by Annis Richardson <annisrichardson@berkeley.edu>)
Full Author List: Richardson, Annis E. 1; de Neve, Amber E.1 ; Johnston, Robyn2; Leiboff, Samuel1 ; Alexander, Martin A. 1 ;
Strable, Josh 2 ; Federici, Silvia2 ; Lewis, Michael W. 1; Sylvester, Anne W. 3; Scanlon, Michael2 ; Hake, Sarah1
1
UC Berkeley, Plant and Microbial Biology/ Plant Gene Expression Center, USDA-ARS, Albany, CA, USA 94710
2
School of Integrated Plant Science, Cornell University, Ithaca, NY, USA 14853
3
Department of Molecular Biology, University of Wyoming, Laramie, WY, USA 82071
Boundary formation is a fundamental step in organ development. Boundaries allow organ separation, influence growth,
polarity and shape, and act as the site of novel outgrowths (e.g grass ligules). Despite their importance, the gene
regulatory networks (GRNs) responsible for boundary formation in different species are not well understood. T his is
especially true of the grasses, which have a unique, modular leaf structure with a wrapped base (sheath), a middle hinge
region (ligule/auricle) and an upper flat region (blade). Grass leaf development requires the specification of three
distinct boundary types: within-organ (e.g. ligule), inter-whorl (i.e. between successive leaves) and intra-whorl (i.e.
between overlapping leaf margins). T o discover how these boundaries are defined we are using two groups of maize
mutants:
(1) Novel boundary mutants: fused-leaf1 (fsl1) and fused-leaf2 (fsl2) are intra- and inter-boundary mutants. We have
identified chromosome positions for fsl1 and fsl2 using bulk-segregant analysis and chromosome walking, and
surprisingly, neither mutation has implicated known boundary regulators. RNAseq of mature fsl1 embryos further
suggests that known organ boundary programs may not contribute to the fsl1 phenotype. (2) Ligule mutants: Mutations
in the grass specific transcription factors LIGULELESS1 (LG1) and LIGULELESS2 (LG2) cause ligule defects, but
how they define the within-organ boundary is unknown. We are using yeast -2hybrid, CoIP, ChiPseq and RNAseq, to
identify protein-protein interactions and directly regulated genes to elucidate the ligule GRN. T hrough this work we
will build GRNs for intra-, inter- and within-organ boundaries in the grass leaf. By contrasting monocot leaf boundary
programs with the dicot model Arabidopsis, we aim to determine how boundary specification is modulated in different
species, possibly explaining novel morphology changes like the grass ligule.
Gene / Gene Models described: LIGULELESS1, LIGULELESS2; GRMZM2G036297, GRMZM2G060216
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture (USDA)
115
P111
Kinetic and morphological tiller meristem development in domesticated and wild
Setaria
(submitted by Muriel Longstaff <mtlongstaff@gmail.com>)
Full Author List: Longstaff, Muriel T 1; Kelly, Jacob A1; Nielsen, T orrey 1; Brown, Brian 1; Xiao, Yuguo 1; Whipple,
Clinton J1
1
Department of Biology, Brigham Young University, Provo,UT USA 84602
Setaria is a panicoid grass related to maize and sorghum. Lateral branches called tillers grow in grasses and
commonly there are few to no tillers in domesticated grasses when compared to their wild ancestors. To explore
tiller growth in wild Setaria (S. viridis line A10) and domesticated Setaria (S. italica lines yugu1 and B100), we
measured axillary bud growth from 6 days after planting (DAP) up through 20DAP. We counted bud frequency
in all three lines of Setaria and performed a statistical analysis on several tiller growth-related features, such as
which leaves tillers originate from, the average number of tillers per inbred line, a comparison of primary versus
secondary tillers, and a comparison of axillary versus auxiliary tillers. Lastly, we checked the growth in S. viridis
and S. italica (B100 only) using scanning electron microscopy (SEM ). Within B100, SEM photos showed a
dynamic scale varying from fully mature axillary buds to no bud at all. We hope to further learn more about the
mechanisms contributed to the variation of tiller meristematic development in Setaria.
Funding acknowledgement: National Science Foundation (NSF)
P112
Leveraging next-generation sequencing technology for rapid gene cloning
(submitted by Madelaine Bartlett <mbartlett@bio.umass.edu>)
Full Author List: Klein, Harry 1; Xiao, Yuguo 2; Heeney, Michelle 1; Whipple, Clinton 2; Bartlett, Madelaine1
University of Massachusetts Amherst
2
Brigham Young University
1
Forward genetics remains a powerful mechanism for revealing the genes and gene networks that underpin
organismal form and function. Forward genetic screens have the capacity both to reveal unexpected roles for
known genes, and to reveal the functions of novel, uncharacterized genes. The size and complexity of the maize
genome has made the identification of the genes underlying mutant phenotypes time consuming and challenging.
However, the rise of next-generation sequencing (NGS) technology has allowed for the rapid identification of
mutant genes. We developed a user-friendly NGS-based bulked segregant analysis pipeline that can be used to
rapidly identify the lesions underlying mutant phenotypes in maize. We used this method to clone a number of
genes with roles in flower and inflorescence development. We focus here, in particular, on a novel role we have
uncovered for ramosa3 (ra3) in the development of unisexual flowers. Our method offers an unbiased, cost effective, simple strategy for rapid gene identification in maize.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
116
P113
MAC1 and AM1 play critical but independent roles to regulate the mitosis-tomeiosis transition of pollen mother cells in maize
(submitted by Ching-Chih Tseng <tsengyin@gate.sinica.edu.tw>)
Full Author List: T seng, Ching-Chih 1 2; Shi, Yun-Zhi1; Wang, Chi-T ing1; Kao, Yu-Hsin 1; Wang, Chung-Ju Rachel1
Institute of Plant and Microbial Biology, Academia Sinica, T aipei, 11529, T aiwan
2
Institute of Plant Biology, National T aiwan University, Taipei, 10617, Taiwan
1
In flowering plants, precursors of pollen mother cells (PM Cs) first proliferate by mitosis, and then enter meiosis
to produce haploid microspores. The mitosis-to-meiosis transition is a fundamental process for sexual
reproduction; however, it remains largely unknown. I monitored this transition by labeling DNA replication in
maize anthers and found that differentiated male germ cells first undergo asynchronous mitosis in an anther with
a gradually decreased mitotic rate until reaching cell cycle quiescence in all PM Cs. Next, the pre-meiotic S phase
is initiated synchronously, followed by meiotic prophase I. The multiple archesporial cells1 (mac1) mutant
showed that the mitotic quiescence is absent and successive mitotic cell divisions result in extra PM Cs.
Surprisingly, without the mitotic quiescence in an mac1 anther, the pre-meiotic S still occurs in some PM Cs,
whereas remaining PM Cs undergo mitosis or arrest at interphase. In contrast, the ameiotic1 (am1) mutant fails to
enter pre-meiotic S phase. After a prolonged quiescence in am1 PM Cs, asynchronous mitosis resumes. The
mac1;am1 double mutant exhibited an additive phenotype. Taken together, these results indicate that M AC1 and
AM 1 are required for the mitotic quiescence and pre-meiotic S phase, respectively, in an independent manner.
Gene / Gene M odels described: Ameiotic1; Multiple archesporial cells 1; Zm00001d013659; Zm00001d023681
P114
Maize genetics at the intersection of development and immunity
(submitted by Alyssa Anderson <alyssa.amy@berkeley.edu>)
Full Author List: Anderson, Alyssa A 1; Abraham Juarez, Maria J1; St. Aubin, Brian 2; Brunkard, Jacob1; Shen,
Zhouxin 3; Briggs, Steven P 3; Hake, Sarah C1
1
University of California, Berkeley, Ca, 94704
2
Michigan State University, East Lansing, Mi, 48824
3
University of California, San Diego, La Jolla, Ca, 92093
The intersection between plant immunity and development is apparent in the phenotypes of many auto-immune
mutants. However, the genetic mechanisms underlying this connection are not well established, especially in
maize. The maize mutant Liguleless narrow (Lgn-R) has a severe developmental phenotype that is background
dependent and temperature sensitive. In the B73 background, mutant plants are stunted with narrow leaves in
cooler climes and completely dead when grown in hot field locations. However, in the M o17 background the
Lgn-R mutants are difficult to distinguish from non-mutant siblings in our cool fields and only develop severe
mutant phenotypes in hot conditions. We have mapped the background dependent modifier of this mutant to
Sympathy for the ligule (Sol), a distant homolog of the Arabidopsis gene ENHANCED DISEASE RESISTANCE
4 (EDR4). The version of Sol found in M o17 is cap able of suppressing the mutant phenotype while the version
found in B73 is incapable of this function. Furthermore, Sol, which normally has low expression levels, seems to
be induced in the presence of certain PAM Ps under particular conditions. To further delve into this system we
generated large datasets, including an RNAseq and Phosphoproteome, for different combinations of the Lgn-R
mutation and the modifier, Sol. We also saw signs of an induced immune response within these datasets.
Therefore our data indicate that an immune response is potentially involved in the developmental defects found
in our mutant and that the modifier may interact with this response differently in the diverse maize inbred lines.
Further investigations into these genes should help to elucidate new aspects of both maize development and
immunity.
Gene / Gene M odels described: Liguleless narrow (Lgn); GRM ZM2G134382 (Lgn) ,GRM ZM2G075262
Funding acknowledgement: National Science Foundation (NSF)
117
P115
Maize leaf primordia microdomains show genetic signatures of proximal-distal
boundary patterning
(submitted by Josh Strable <jjs369@cornell.edu>)
Full Author List: Strable, Josh 1; Leiboff, Samuel2; Johnston, Robyn 1; Federici, Silvia1; Hake, Sarah 2; Sylvester, Anne 3;
Scanlon, Michael1
1
School of Integrated Plant Science, Cornell University, Ithaca, NY, USA 14853
2
Plant Gene Expression Center, USDA-ARS, Albany, CA, USA 94710
3
Department of Molecular Biology, University of Wyoming, Laramie, WY, USA 82071
Understanding the factors that pattern organ boundaries is a central topic in plant biology. The maize leaf is a
tractable developmental system as the ligule-auricle boundary between the distal blade and proximal sheath is
delineated early in young leaf primordia. However, precisely when during leaf ontogeny are proximal-distal
boundary (PDB) identities delimited remains an open question. We hypothesize that the competency to set up the
PDB is founded in cellular/tissue microdomains in early -staged primordia long before morphological evidence of
a PDB is observable in later-staged primordia. To identify genes that establish this "pre-PDB," we performed
laser microdissection RNAseq (LM -RNAseq) across four contiguous proximal-distal microdomains beginning at
the base of plastochron 4 (P4) leaf primordia, where the blade-sheath boundary is inconspicuous. Our analysis
identified 1,045 differentially expressed genes across microdomains that partition into 25 nodes by selforganizing map clustering. Within our clusters, we found significant enrichment for transcription factor activity
and hormone regulation gene ontologies. RNA in situ hybridization confirmed the spatiotemporal accumulation
of candidate genes in developing primordia. We expanded our P4 mircodomain analysis to examine the
expression pattern of genes in later-staged primordia, as well as and in liguleless (lg) mutants where the PDB is
disrupted. Additional LM -RNAseq datasets from B73 (P7), lg1 (P6) and lg2 (P4, P6, and P7) mutants were
combined to conduct a weighted gene co-expression network analysis (WGCNA) on a total of 61 LM -RNAseq
libraries, which grouped 23,912 similarly expressed genes into co-expression modules. Our leaf microdomainspecific co-expression modules showed significant enrichment for known biological processes and identified
leaf-specific expression modules. We found co-expression modules that contain LG1, LG2, and genes previously
unknown to participate in leaf development. Overall, our findings reveal genetic signatures of a PDB in
micordomains of early-staged primordia and highlight the power of analyzing multiple, high-resolution
expression datasets to study leaf patterning.
Funding acknowledgement: National Science Foundation (NSF)
P116
Male-specific argonaute (MAGO) proteins are necessary for meiosis in maize
(submitted by Robert Maple <R.Maple@warwick.ac.uk>)
Full Author List: Maple, Robert J. 1; Lee, Yang-Seok 1; T amim, Saleh 2; Rouster, Jacques3; Meyers, Blake4; GutierrezMarcos, Jose F. 1
1
School fo Life Sciences, University of Warwick, Coventry, West Midlands, United Kingdom, CV4 7AL
2
Plant and Soil Sciences, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711
3
Biogemma, Centre de Recherche de Chappes, Route d'Ennezat, 63720 Chappes, France
4
Donald Danforth Plant Science Center, 975 N. Warson RD., Room 384, St. Louis, MO 63132
Plants do not specify their germline until late in their life cycle. Hence, the plant germline is normally specified
from terminally differentiated somatic cells though the precise mechanism(s) are unknown. We have found that
male gametogenesis in maize is associated with the accumulation of distinct 21-nt phased small-interfering
RNAs (phasiRNAs) generated by male-specific argonaute (M AGO) proteins. M AGO1 accumulates in the
epidermis of pre-meiotic anthers while M AGO2 is found in developing meiocytes. We have found that M AGO
proteins are required for meiocyte development as mutants display chromosomal defects and male infertility. O ur
data suggest that M AGO proteins play an important role in maize male fertility.
Funding acknowledgement: BBSRC
118
P117
MicroRNAs targeting developmental transcription factors control maize leaf size by
switching cell proliferation to cell expansion
(submitted by Fatma Aydinoglu <faydinoglu@gtu.edu.tr>)
Full Author List: Aydinoglu, Fatma 1
1
Department of Molecular Biology and Genetics, Gebze T echnical University, Kocaeli, TURKEY
In maize, leaf size is determined both by cell division and cell expansion processes, which take place in three growth
zones: meristem, elongation and mature zones, located linearly from leaf base to tip. Elucidating the genes controlling
these processes is crucial for achieving increased leaf size. Recently microRNAs, endogenous non-coding small RNAs,
have attracted attention as tools for alteration of gene expression. In order to gain insight into the microRNA regulatory
networks behind the switching from cell proliferation to cell expansion in maize leaf, a miRNome analysis of 321
known maize microRNAs in the three distinct leaf growth zones was carried out. T o induce growth retardation,
ADA313 maize hybrid seedlings were subjected to low night temperatures, while a control group was gr own for
comperative studies. T he fourth leaf of each seedling was monitored and the growth zones sampled for molecular
analysis. T he cold treatment caused a 19% reduction in leaf elongation rate resulting in a 26% decrease in final leaf
size. T o understand differences in the cell dynamics along the growth zones, lengths of cells are located in the same cell
files were measured by DIC microscope and kinematic analysis of growth was performed. It was observed that the
length and number of dividing cells in the meristem remained unchanged during cold treatment, but cell production
declined by 30%. Genome wide analysis of microRNA displayed significantly differential expression along the growth
zones for 204 out of 321 miRNAs. Cluster analysis identified 23 miRNAs as meristem- spesific. In silico target
prediction suggested that these miRNAs target several transcription factors, and these interactions were validated by
qRT -PCR. T he findings clearly showed that many miRNAs play roles in controlling growth by switc hing between cell
proliferation and elongation through targeting of transcription factors, suggesting that these miRNAs could be
manipulated for crop improvement.
Funding acknowledgement: T he Scientific And T echnological Research Council Of T urkey (T UBIT A K) (115Z527)
P118
Modification of the expression of PIP2;5 plasma membrane aquaporin affects maize
water relations and growth
(submitted by Lei Ding <lei.ding@uclouvain.be>)
Full Author List: Ding, Lei1 ; Milhiet, T homas1 ; Van Lijsebettens, Mieke2 ; Inzé, Dirk 2; Nelissen, Hilde2 ; Chaumont, François1
Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
2
Department of Plant Systems Biology, VIB-Ghent University, Ghent, Belgium
1
Aquaporins are highly regulated water channels controlling the water flow across cell membranes. We previously
quantified the expression of plasma membrane intrinsic aquaporins (PIPs) in maize roots, leaves, stomatal complexes
and in reproductive organs at both RNA and protein levels and showed that the expression was dependent on the organ
developmental stage and environmental conditions.
In maize, PIP2;5 is the most highly expressed aquaporin in roots and its association with the presence of apoplast ic
barriers suggests a role in the regulation of radial water movement. Here, we investigated how deregulation of PIP2;5
expression affects water relations and plant growth using maize knockout (KO - W22 inbred) or overexpression (OE B104 inbred) lines.
When growing in hydroponic culture, the hydraulic conductivity of cortex cells (Lpc) and the whole roots (Lpr) was
lower in pip2;5 KO lines than in WT plants, as measured using a cell pressure probe or a hydraulic conductance flow
meter (HCFM), respectively. While the Lpc was higher in PIP2;5 OE plants compared with the WT plants, no
difference in the Lpr was recorded. In addition, the leaf hydraulic conductance (Kleaf) measured with the HCFM was
higher in the PIP2;5 OE than in WT plants.
When growing in soil in well-watered conditions, no difference in the photosynthetic rate, stomatal conductance, and
transpiration rate was observed between pip2;5 KO or PIP2;5 OE lines with their respective WT plants. On the other
hand, drought stress treatment (three days without watering) significantly decreased these parameters in pip2;5 KO
plants compared with the WT plants. We also found a less important decrease in the photosynthetic rate, stomatal
conductance and transpiration rate in the PIP2;5 OE plants compared with B104 WT plants under drought stress
condition. Altogether, these results indicate that PIP2;5 overexpression might be beneficial for plant growth under
drought stress.
Funding acknowledgement: T he Interuniversity Attraction Poles Programme-Belgian Science Policy (grant IAP7/29),
the “Communauté française de Belgique-Actions de Recherches Concertées” (grant ARC16/21 -075), MOVE-IN
Louvain fellowship, Fonds de la recherche scientifique (FRS-FNRS)
119
P119
MOP1 regulates germline specification and gamete development in maize
(submitted by Mario Arteaga-Vazquez <maarteaga@uv.mx>)
Full Author List: Oltehua-López, Omar 1; Michaud, Caroline2; Caballero-Pérez, Juan 3; Dorantes-Acosta, Ana1;
Grimanelli, Daniel2; Arteaga-Vázquez, Mario 1
1
Instituto de Biotecnología y Ecología Aplicada (INBIOT ECA), Universidad Veracruzana; Avenida de las Culturas
Veracruzanas 101; Xalapa, Veracruz, México 91090
2
Institut de Recherche pour le Développement (IRD), UMR232, Université de Montpellier; Montpellier, France 34394
3
National Laboratory of Genomics for Biodiversity, CINVEST AV-IPN; Km 9.6 Lib. Norte Carr. Irapuato-León;
Irapuato, Guanajuato, México 36821
In angiosperms, germline initiates from a somatic subepidermal cell that acquires an archeosporial cell fate and
then differentiates directly into the the megaspore mother cell (M M C). The MMC undergoes meiosis and from
the resulting four megaspores, the three most apical degenerate while the surviving functional one will
differentiate into the functional megaspore (FM ). After three rounds of mitotic divisions, the FM will give rise to
the mature megagametophyte or embryo sac that contains two gametes (the egg cell and the binucleated central
cell) and accessory cells (two synergids and a cluster of antipodal cells). Specification of the germline, requires
the orchestration of developmental programs and epigenetic mechanisms involved in the reprogramming and
protection of the genome. Paramutation at the b1 locus in maize is the most stable and penetrant example of
transgenerational epigenetic inheritance known to date in nature. M utations in the gene mediator of paramutation
1 (mop1) prevents paramutation and induce pleiotropic developmental phenotypes including reduced height,
feminization of tassels (tasselseed), alterations in flowering time, failure to develop ears and semi sterility. mop1
encodes an RNA-DEPENDENT RNA POLYM ERASE that regulates transposon activity as a component of the
major small RNA-directed epigenetic regulatory pathway in plants known as the RNA-directed DNA
methylation pathway (RdDM). In order to understand the role of RdDM during gamete development in maize,
we performed a systematic cytological analysis during megasporogenesis and megagametogenesis and profiled
global changes in gene expression in mop1-1 mutant plants. We found that mop1 is required for the specification
of the female germline and identified a NAC transcription factor that when mutated leads to the phenocopy of the
deffects observed during megasporogenesis in the mop1-1 mutant.
Funding acknowledgement: Agropolis fondation, Jeunes Equipes AIRD, Cuerpo Academico CA-UVER-234
P120
Movement of premiotic phased small-interfering RNAs (phasiRNAs) is essential
for male meiosis in maize
(submitted by Yang-Seok Lee <Y.Lee.6@warwick.ac.uk>)
Full Author List: Lee, Yang-Seok 1; Maple, Robert 1; Luo, Anding2; Sylvester, Ann W. 2; Birchler, James3; T amim,
Saleh 4; Meyers, Blake5; Gutierrez-Marcos, Jose F. 1
1
School fo Life Sciences, University of Warwick, Coventry, West Midlands, United Kingdom, CV4 7AL
2
Department of Molecular Biology, University of Wyoming, Department # 3944, 1000 E. University Ave., Laramie,
WY 82071
3
Biological Sciences, University of Missouri, 105 T ucker Hall, Columbia, MO 65211 -7400
4
Plant and Soil Sciences, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711
5
Donald Danforth Plant Science Center, 975 N. Warson RD., Room 384, St. Louis, MO 63132
M aize anthers accumulate a discrete group of 21- and 24-nt phased small-interfering RNAs (phasiRNAs).
However, the precise function of these RNAs is currently unknown. The production of phasiRNAs is thought to
be mediated by the slicing of long non-coding RNA precursors and initiated by discrete miRNAs. Pre-meiotic
21-nt phasiRNAs accumulate in the anther epidermis and are found in meiocytes later in development. We
hypothesized that 21-nt phasiRNAs migrate from the epidermis to inner tissues during anther development. To
test this hypothesis we have generated transgenic lines carrying viral proteins that sequester small non-coding
RNAs in the anther epidermis. Our data suggest that movement of premiotic phasiRNAs is essential for anther
meiosis in maize.
Funding acknowledgement: BBSRC
120
P121
Natural variation in the molecular circuitry underlying cell type specification
drives key plant architectural traits in maize
(submitted by Steffen Knauer <steffen.knauer@uni-tuebingen.de>)
Full Author List: Knauer, Steffen 1 5; Javelle, Marie1; Li, Lin 2; Li, Xianran 3; Wimalanathan, Kokulapalan 4; Ma, Xiaoli5;
Kumari, Sunita1; Leiboff, Samuel6; Ware, Doreen 1; Lawrence-Dill, Carolyn 4; Schnable, Patrick 7; Yu, Jianming3;
Muehlbauer, Gary 2; Scanlon, Michael6; T immermans, Marja 1 5
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
2
Department of Agronomy and Plant Genetics, University of Min nesota, Saint Paul, MN 55108, USA
3
Department Agronomy, Iowa State University, Ames, IA 50011, USA
4
Department of Genetics, Development and Cell Biology and Department of Agronomy, Iowa State University, Ames,
IA 50011, USA
5
Center for Plant Molecular Biology, University of T übingen, 72076 T übingen, Germany
6
Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
7
Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA
The shoot apical meristem (SAM ), a specialized stem cell niche at the growing shoot tip, integrates
developmental and environmental signals to direct the initiation and patterning of new organs such as leaves. Its
activity throughout the plant’s lifetime is tightly controlled. To gain insight into gene regulatory networks behind
stem cell maintenance and organogenesis, we generated a high-resolution gene expression atlas of 10 distinct
domains and cell types within the vegetative maize shoot apex using laser microdissection and RNA deep
sequencing. We found that ~10% of all transcribed genes are differentially expressed across these tissue types,
including a valuable collection of cell type specific genes. Interestingly, very few functional categories are
enriched among the differentially expressed genes, which we show reflects prominent sub-functionalization
within gene families. Through cluster analysis, we further identified expression signatures for the functional
domains within the SAM , the stem cell harboring central zone (CZ), the peripheral zone (PZ), and organizing
center (OC) located directly underneath the stem cells. Genes in these zones are in part conserved among maize
and Arabidopsis, but also reveal remarkable differences and novel gene functions in maize. M oreover, we found
that unique transcription factor (TF) signatures are predictive of meristematic and vascular cell fate. Analyses of
TF binding sites within promoter regions of stem cell specific genes predicts a hierarchical network in which the
combinatorial actions of diverse TF families underlie their spatially restrictive expression. Additionally, we
demonstrate that KNOTTED1, a key meristem determinant, acts mainly by inhibiting organogenesis and
differentiation within the SAM . Finally, we show that natural variation associated with import ant agronomical
traits in GWAS, maps preferentially to genes showing domain specific patterns of expression or the TFs that
drive this. Our findings thus indicate that gene regulatory networks acting in the SAM underlie adult plant
architecture and important agronomical traits.
Funding acknowledgement: National Science Foundation (NSF), DFG, Alexander von Humboldt Foundation
121
P122
nop genes promote pollen tube growth in the maize male gametophyte
(submitted by Matthew Warman <warmanma@oregonstate.edu>)
Full Author List: Warman, Matthew1 ; Fowler, John1
1
Oregon State University, Department of Botany & Plant Pathology, Corvallis, Oregon 97331
Pollen tube growth is fundamental to plant reproduction. GRMZM2G372877 and GRMZM2G470666, tentatively
designated nop1 and nop2, were identified as highly-expressed in mature pollen relative to other maize tissues
(Chettoor et al. 2014). These genes are orthologous to the rice no pollen (Osnop) gene (Jiang et al. 2005). Structurally,
proteins encoded by the nop genes possess both calcium and phosphoinositide binding domains. Our current data
support the hypothesis that nop genes have a role in pollen tube germination or growth, where they could help link
calcium and/or phosphoinositides, which have important roles in pollen tubes, to other cellular processes.
Independent lines with transposable element insertions in exons of either nop1 (Ds) or nop2 (Mu) were found to be
linked to gametophytically-expressed male-specific transmission defects (16.1% and 2.3% transmission, respectively).
Derivative nop1 alleles with non-frameshifted footprints were recovered in active Ac lines. T he nop1-d3 allele shows
an increased transmission rate when compared to mutant nop1 lines, proving that the transmission defect is due to loss
of nop1 function. A second mutant allele of nop2 was acquired from the Dooner collection of DsGFP-tagged insertions
(Li et al. 2013). T his insertion confirmed a male transmission defect is associated with reduced nop2 function.
Contrasting with the “no pollen” phenotype associated with a large deletion encompassing the Osnop gene, anthers and
pollen grains have no visible phenotype in single nop mutant maize plants; nor was an obvious phenotype observed in
pollen from nop1::Ds/+; nop2::Mu/+ plants. Using Inv9b to link nop1::Ds to the wx1 - phenotype allowed us to
differentiate wx1 - (nop1::Ds-linked) and Wx+ (nop1 +-linked) pollen in 1:1 segregating populations from heterozygous
plants. When germinated in vitro, nop1::Ds pollen tubes were significantly shorter than wild-type pollen tubes,
indicating that NOP1 promotes pollen tube growth and/or germination, and suggesting a possible explanation for the
nop1 male transmission defect.
Funding acknowledgement: National Science Foundation (NSF)
P123
Pursuing maize (Zea mays) tassel development by small RNA sequencing,
transcriptomics, and proteomics
(submitted by Karina van der Linde <karina.van-der-linde@ur.de>)
Full Author List: van der Linde, Karina 1 2; Bear Don’t Walk IV, Oliver 1; Morrow, Darren1 ; Mathioni, Sandra3 ; Kakrana, Atul3;
Fernandes, John1; Fiedler, Isabell2; Meyers, Blake3; Walbot, Virginia1
1
Department of Biology, Stanford University, Stanford, California, USA
2
Department of Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
3
Donald Danforth Plant Science Center, St. Louis, Missouri, USA
During their life cycle land plants generate new organs from distinct meristems, containing a set of undifferentiated
stem cells. In maize (Zea mays) tassel development, the inflorescence meristem (IM) initiates in parallel both branch
meristems (BM) with an indeterminate fate and spikelet pair meristems (SPM). SPMs subsequently divide into two
spikelet meristems (SM) and each of those produces two glumes and initiates the upper floral meristem (FM) and then
converts itself into the lower FM. Florets contain four concentric whorls that are formed sequentially from the FM.
First the palea and the lemma are initiated in the outer whorl, followed by the lodicule, then three stamens, and finally
three carpels. In maize tassels all the carpels abort while the stamens differentiate into a supporting filament and the
terminal anther. Within each anther 4 lobes are formed: these contain four distinct somatic cell types that are each
required to support the central, pre-meiotic archesporial cells.
T o determine the temporal progression of RNA, protein, and small RNA changes during tassel ontogeny, Agilent
microarray transcriptomes, mass spectrometry proteomes, and small RNA-sequencing data were collected at 4 stages of
early tassel development (0.5 cm, 1.0 cm, 1.5 cm, 2.0 cm). At the 0.5 cm and 1.0 cm stages tassels lack stamens, the 1.5
cm stage has stamens including anther primordia, and the 2.0 cm stage has anthers as large as 0.1 mm, prior to germinal
specification within lobes. T hese data are the foundation to define meristem- and anther-specific genes for further
functional study. Latest results from the data analysis and from gene-specific studies will be shown.
Funding acknowledgement: National Science Foundation (NSF), National Academy of Sc iences Leopoldina, Deutsche
Forschungsgemeinschaft through SFB 924
122
P124
Redundant roles of two paralogous INDETERMINATE DOMAIN (IDD)
transcription factors in maize development
(submitted by Max Braud <mbraud@danforthcenter.org>)
Full Author List: Braud, Max 1; Yang, Jiani1; Eveland, Andrea L 1
1
Donald Danforth Plant Science Center; St. Louis, MO, 63132
Functions of numerous genes controlling various aspects of maize growth and development have been
elucidated, however comprehensive knowledge of gene regulatory networks that fine-tune key developmental
processes remains limited. In maize, genome duplication resulted in functional redundancy among many gene
pairs, thus masking phenotypic outputs in genetic screens. In this work, we investigate the functions of two
paralogous INDETERMINATE DOMAIN (IDD) transcription factors (TFs), ZmIDD16 and ZmIDD18, in maize
development. These two TFs share 88% amino acid identity. Based on co-expression network analyses of early
tassel and ear development, Zmidd16 was prioritized as a candidate gene in controlling inflorescence branching:
i) its spatiotemporal expression across a panel of mutant backgrounds suggested a role in meristem determinacy,
and ii) it was bound and positively modulated by the RAM OSA1 (RA1) TF, which functions to suppress branch
outgrowth in maize inflorescences. Zmidd16 and Zmidd18 showed highly redundant gene expression profiles
during inflorescence development, but Zmidd18 was expressed consistently at lower levels and not bound by
RA1. Preliminary in situ hybridization analysis showed that Zmidd16 mRNAs localize to vascular tissues during
early inflorescence development and in spikelet pair meristems, consistent with its regulation by RA1. To
identify potential protein interacting partners of IDD16, we performed a yeast -two hybrid assay using a bait
library derived from maize inflorescence primordia. Among high-confidence interactors identified were members
of the Networked proteins, which are broadly thought to mediate actin interaction with plasma membranes. To
test genetic perturbation of Zmidd16 and/or Zmidd18 on phenotype, we used CRISPR/Cas9-based gene editing to
generate indels in coding sequences of both genes. T2 plants with homozygous edits in either paralog alone
showed subtle effects on phenotype, while disruption of both genes resulted in pleiotropic developmental defects
including severe dwarfism, increased tillering, short and broad leaves, sterile and branchless tassels, and antherear phenotypes.
Gene / Gene M odels described: IDD16, IDD18; GRM ZM2G074032, GRMZM2G465595
Funding acknowledgement: National Science Foundation (NSF)
P125
Relative abundance of Proteins to Multiple stresses suggests Cross-Tolerance
Mechanism in Soybean
(submitted by Ramesh Katam <ramesh.katam@famu.edu>)
Full Author List: Katam, Ramesh 1; Byount, T iffany 1
Florida A&M University T allahassee FL 32307
1
Water stress (WS) and high temperatures (HS) have a negative effect on soybean crop productivity. During WS,
soybean plants opt for survival through ion homeostasis and the conformations of proteins are perturbed as plant
cells lose water, while HS leads to difficulties in flowering and fruiting. Proteomic studies were conducted to
obtain insight into the effects of WS and HS on molecular and cellular functions. Two soybean cultivars (A:
Slow wilting and high yielding; and B: High protein with moderate yield potential) were exposed to different
heat and water stress conditions in plant growth chambers. Changes in the leaf protein composition were studied
using 2-DE complemented with M ALDI-TOF mass spectrometry. Thirty-nine proteins were differentially
expressed in response to WS and HS in both cultivars. Gene ontology analysis revealed majority of the
functional categories including photosynthesis, metabolism, transport, stress and defense, and glycolysis.
Expression of proteins was largely affected to WS in Cultivar A, while HS affected their expression in cultivar B
suggesting genetic variation for stress tolerance. Combined abiotic stresses (WS+HS) equally affected both
cultivars. RT-PCR studies and enzyme assays of selected genes suggest a positive correlation with protein
expression among the cultivars. Proteins involved in metabolism, glycolysis, photosynthesis, such as HSPs,
enolase, rubisco activase, were over expressed during WS+HS stress in both cultivars. Based on protein
interaction studies, we hypothesize the plant’s development of cross-stress tolerance.
123
P126
Responses to hypoxia and endoplasmic reticulum stress: relationships with
vitreousness of maize endosperm
(submitted by Didier Marion <didier.marion@inra.fr>)
Full Author List: Gayral, Mathieu1; Elmorjani, Khalil1; Dalgalarrondo, Michèle 1; Linossier, Laurent 2; Delluc,
Caroline3; Bakan, Bénédicte1; Marion, Didier 1
1
INRA, Biopolymers, Interactions, Assemblies, 44316 Nantes cedex 3, France
2
Limagrain Céréales Ingrédients, 63200 Riom, France
3
Limagrain Europe, 63270 Chappes, France
Endosperm vitreousness is an important quality trait of maize crops. To delineate the mechanisms controlling the
formation of endosperm texture, i.e. compactness of the starch/protein matrix, most studies have been focused on
opaque/floury mutants, never on conventional maize crops. Therefore, we analyzed protein and starch
depositions in the floury and vitreous regions of mature endosperms of conventional flint and dent maize inbred
lines. We disclosed biochemical gradients, with a continuous decrease of protein contents and an increase of
starch crystallinity (related to an increase of amylopectin/amylose ratio) from the periphery (subaleurone region)
to the center of endosperm. To grasp these gradients, we analyzed the transcriptome and specific metabolites of
developing central and peripheral endosperms (at 15 and 20DPA) that will become, later, the floury and vitreous
regions of mature seeds, respectively. The results revealed clearly that the formation of endosperm vitreousness
is associated with significant differences in the responses to two closely linked stress phenomena, hypoxia and
endoplasmic reticulum stress; hypoxia being probably the major stress affecting endosperm development.
Indeed, transcriptomic and metabolomic data indicated a strong regulation of energy metabolism in developing
endosperm. Genes involved in glycolysis and tricarboxylic acid cycle are up -regulated in the periphery, while
genes involved in alanine, sorbitol and fermentative metabolisms are up -regulated in the center of endosperm.
Besides hypoxia, the massive synthesis of proteins (mainly storage proteins, i.e. zeins) in the endoplasmic
reticulum elicits unfolded protein responses (UPR), as indicated by the splicing of bZip60 transcription factor.
UPR was differentially regulated between the center and periphery of the endosperms. Taking together, these
results suggested that regulation of energy metabolism and UPR allow the production of ATP needed for protein
synthesis and their folding in the endoplasmic reticulum, respectively. Spatial regulation of these mechanisms
within endosperm probably drives the compositional gradient, governing hence maize vitreousness
Funding acknowledgement: Fond Unique Interministériel
124
P127
RMR12 is a CHD3 nucleosome remodeler required for maintaining paramutations
and normal development
(submitted by Natalie Deans <deans.11@osu.edu>)
Full Author List: Deans, Natalie1 ; Giacopelli, Brian1 ; Hlavati, Daniel1 ; McCormic, Emily 1; Addo-Quaye, Charles2 ; Dilkes,
Brian 2 ; Hollick, Jay 1 3
1
Department of Molecular Genetics, The Ohio State University, Columbus, OH
2
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN
3
Center for Applied Plant Sciences and Center for RNA Biology, The Ohio State University, Columbus, OH
In maize, paramutations result in meiotically heritable changes in the regulation of certain alleles of purple plant1 1, a
gene encoding a transcription factor required for anthocyanin production 2. A strongly expressed Pl1-Rhoades allele is
suppressed in trans when combined with a transcriptionally and post -transcriptionally repressed Pl1-Rhoades allele,
and both alleles are transmitted in a repressed (denoted Pl´ ) state. At least sixteen loci whose functions are required to
maintain repression (rmr) of Pl´ have been identified by ethyl methanesulfonate mutagenesis 3. All known RMR
proteins mediate 24 nucleotide (24nt) RNA biogenesis4, 5, 6, 7, 8, and four are putative orthologs of Arabidopsis proteins
central to an RNA-directed DNA Methylation (RdDM) pathway facilitating repressive chromatin modifications. Here
we describe four recessive alleles defining the rmr12 locus. Unlike other rmr-type mutations found to date 4, 5, 7, 8, 9, 10,
rmr12 mutants display a unique set of defects, including male gametophyte dysfunction, that highlight a novel
mechanistic connection between paramutation and developmental gene control. We used positional cloning to discover
that rmr12 encodes a Chromodomain Helicase-DNA Binding3 (CHD3) protein whose presumed Arabidopsis ortholog,
PICKLE, alters nucleosome positions in vitro 11 and affects both development and chromatin modifications specified by
RdDM12, 13. Maize CHD3 represents the first RMR protein not having a predicted role in 24nt RNA biogenesis and thus
might facilitate paramutations by converting 24nt RNA effectors into meiotically -heritable nucleosome profiles.
1. Hollick et al. 1995 Genetics 141, 709. | 2. Cone et al. 1993 Plant Cell 5, 1795 | 3. Hollick and Chandler 2001 Genetics 157, 369 | 4. Erhard et
al. 2009 Science 323, 1201 | 5. Hale et al. 2007 PLoS Biol. 5, 2156 | 6. Nobuta et al. 2008 PNAS 105, 14958 | 7. Stonaker et al. 2009 PLoS
Genet. 5, e1000706. | 8. Barbour et al. 2012 Plant Cell 24, 1761 | 9. Dorweiler et al. 2000 Plant Cell 12, 2101. | 10. P arkinson et al. 2007 Dev.
Biol. 308, 462. | 11. Ho et al. 2013 Biochim. Biophys. Acta 1829, 199 | 12. Ogas et al. 1997 Science 277, 91 | 13. Yang et al. 2017 Genome
Biol. 18, 103
Gene / Gene Models described: rmr12/chd3a; Zm00001d045109
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture (USDA),
Syngenta
P128
Role of introns in the correct expression of the meiotic cyclin SOLO DANCERS
(SDS) of maize in A. thaliana
(submitted by Oscar Sanz Mora <osanz.osm@gmail.com>)
Full Author List: Sanz Mora, Oscar1 ; Brettschneider, Reinhold1 ; Schnittger, Arp1
University of Hamburg-Biozentrum Klein Flottbek, Hamburg, Germany, 22609
1
Meiosis, in contrast to mitosis, halves the nuclear DNA content. T his is important for sexual reproduction to maintain
genome size in the offspring. Moreover, meiosis accomplishes recombination between the parental homologous
chromosomes leading to new allelic combinations in the offspring. Despite the differences between meiosis and
mitosis, the progression through both cell division events appears t o be regulated by the same or highly related
regulators, such as cyclin-dependent kinases, cyclins and the anaphase-promoting complex/cyclosome, etc. One of the
meiosis specific cyclins is called SOLO DANCERS (SDS) and has been described before in A. thaliana. T here, SDS is
expressed specifically in male meiotic cells where it functions in homolog synapsis, recombination and bivalent
formation. While putative SDS homologs in Zea mays have already been discovered, their actual biochemical function
in the cell cycle remains unknown. Due to its agronomical relevance the regulation of meiosis in maize in general as
well as the recombinational process in particular should be studied. In this study rescue experiments with the genomic
sequence of one of the putative orthologues, ZmSDS57, were conducted in order to complement sds deficient
Arabidopsis thaliana mutants. In preliminary experiments it was found that this gene driven by the AtSDS promoter is
not able to rescue the mutant, whereas the same construct with the genomic ORF of AtSDS does. On the other hand,
the cDNA ORF of AtSDS did not show any sign of expression either. T hese observations can lead to the idea that the
introns harbored in the genomic SDS sequence can have an important role at the expression level. In order to confirm
this, several constructs exchanging and deleting introns have been designed. It is known that the first two introns are
more likely to contain regulatory elements. T herefore, the focus was put on that region of the sequence.
Gene / Gene Models described: solo dancers (SDS); GRMZM2G093157
125
P129
Search for genetic modifiers of knotted1
(submitted by Jack Satterlee <jws429@cornell.edu>)
Full Author List: Satterlee, Jack W 1; Leiboff, Samuel2 ; Qiao, Pengfei1 ; Timmermans, Marja C.P. 3; Schnable, Patrick S. 4 ;
Scanlon, Michael J. 1
1
Section of Plant Biology, Cornell University; Ithaca, New York, United States 14853
2
Plant Gene Expression Center, University of California Berkeley; Albany, California, United States 94710
3
Center for Plant Molecular Biology, University of Tübingen; Tübingen, Germany 72076
4
Plant Sciences Institute, Iowa St ate University; Ames, Iowa, United States 50010
Over two decades ago the maize gene knotted1 (kn1) was cloned, marking the discovery of the first homeodomain containing transcription factor in plants and a key regulator of shoot apical meristem (SAM) main tenance. T he
KNOT T ED1 protein is strongly expressed in the SAM as well as the subtending rib and inflorescence meristems where
it binds and modulates the expression of hundreds of genes. Despite its known contribution to SAM maintenance, the
penetrance of the shoot termination phenotype caused by the loss-of-function kn1-e1 allele varies dramatically between
inbred lines. While B73 plants homozygous for kn1-e1 exhibit a phenotypic penetrance of less than 5%, W23 plants are
severely affected, with 95% of individuals failing to maintain a SAM. Penetrance of kn1-e1 is thought to negatively
correlate with SAM size.
We sought to determine the genetic basis for this difference in phenotypic penetrance by performing laser capture
microdissection followed by RNA-Seq on the SAMs of normal B73, kn1-e1 B73, and normal W23 plants. Few genes
were differentially expressed between normal B73 and kn1-e1 B73 SAMs, suggesting that the transcriptional network
controlling SAM maintenance is robust to loss of kn1 function in this line. Meanwhile, the SAMs of W23 exhibited
differential expression of several thousand genes compared to those in B73. Included are genes bound and modulated
by kn1 as well as the closely related paralog gnarley1 (gn1), which was significantly upregulated in B73 compared to
W23. In addition, in a previously generated dataset, gn1 was more highly expressed in SAMs of inbreds with large and
medium compared to small SAM sizes. We therefore hypothesize that increased expression of gn1 in the SAM of B73
compensates for loss of kn1 function, which will be tested in future reverse genetic analysis.
Gene / Gene Models described: knotted1, gnarley1; GRMZM2G017087, GRMZM2G452178
Funding acknowledgement: National Science Foundation (NSF)
P130
Sex and violence: the classic maize mutant Tasselseed5 is encoded by a woundresponsive JA-inactivating enzyme
(submitted by China Lunde <lundec@berkeley.edu>)
Full Author List: Lunde, China 1; Leiboff, Samuel1 ; Kimberlin, Athen 2; Koo, Abraham2; Sarah, Hake1
Plant Gene Expression Center USDA-ARS and UC Berkeley, Albany, CA USA 94710
2
University of Missouri, Columbia, MO, USA 65211
1
Notable both for a long history and genotype-dependent expression, Tasselseed5 (Ts5) mutants have ectopic silks in the
tassel and ear row defects from failed lower floret abortion. Maize flowers of both the tassel and ear are initially perfect
but become staminant or pistillate by selective abortion of carpels in tassel florets and stamen in ear florets. Usi ng a
combination of fine-mapping and transcriptomics we found that Ts5 encodes a CYP94B3, known to convert the
bioactive jasmonate, JA-Ile, to less active 12OH-JA-Ile, as part of normal recovery from wounding or herbivory. Our
RNAseq analysis identified over 240 DE genes in 1cm tassels with putative functions that are consistent with the
predicted enzymatic role of CYP94B3. T he Ts5 gene had a logFC of 11.7 strongly implicating its ectopic upregulation
as causal to its observed tassel feminization. Ts5 tassel phenotypes are suppressed by exongenous JA application and
metabolite profiling for jasmonate derivitives in both developing tassels and wounded leaves, show enhanced
catabolysis of JA in Ts5 mutants. T hus, misexpression of Ts5 in inflorescences destroys monoecy by breaking down JA
-- which is required for carpel abortion in tassels and lower floret abortion in ears. Heterologous overexpression in both
a dicot (Arabidopsis) and monocot with perfect flowers (Brachypodium distachyon (L.) P.Beauv.) uncovered known
and novel JA-deficient phenotypes. T o explore natural modifiers of the Ts5 phenotype, we performed a QT L analysis
leveraging the fact that Ts5 is completely feminized in Mo17 and nearly fully suppressed in B73. One of 10 high confidence QT L interval contains tasselseed2 with which Ts5 displays epistasis (Irish et al. (1994) Dev Genet 15: 155 –
171), is also wound-inducible, and is misexpressed in Ts5 .
Gene / Gene Models described: Ts5; Zm00001d049201
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture (USDA)
126
P131
Single Cell Transcriptomic Analysis of the Developing Maize Embryo
(submitted by Jack Satterlee <jws429@cornell.edu>)
Full Author List: Satterlee, Jack W 1; Scanlon, Michael J1
Cornell University; Ithaca, New York, United States 14853
1
Single cell RNA-Seq (scRNA-Seq) has emerged as a technology to facilitate the high-throughput transcriptomic
analysis of individual cells. Numerous scRNA-Seq studies are reported in animals; however, the technology has
seen limited use in plants. Here we present preliminary single cell transcriptomic data generated from maize
embryos using the 10X Genomics Chromium platform. The maize embryo was selected as a study system owing
to its diversity of cell and tissue types, including the embryonic shoot and root apical meristems (SAM and
RAM , respectively). We aim to use this technology in combination with existing in situ hybridization and RNASeq data to examine the contributions of cell-type heterogeneity, signaling, and differentiation programs to SAM
patterning and development, and to resolve single-cell gene co-expression networks.
Analysis of the dataset identifies embryo-specific marker genes, including previously -described lowly-expressed
genes and transcripts accumulating in small cell populations. Expression analysis of characterized markers
enables assignment of cells back to their spatial positions in the embryo. A preponderance of cells expressing
epidermal cell marker genes were identified, suggesting biases in cell isolation. Nonetheless, marker gene
expression analysis and pseudotemporal ordering of cells using manifold learning reveals potentially pertinent
developmental biology. These findings include the identification of yab9 as a potential regulator of scutellum
development and dynamic changes in cell cycle genes over pseudotime that may be correlated with epidermal
cell proliferation rate and differentiation.
Future work will attempt to circumvent the unique challenges of unbiased cell-type isolation in plants by using
nuclei as a source of RNA for transcriptomic profiling, and utilizing higher cell/nuclei populations to enhance
statistical power.
Gene / Gene M odels described: yabby14, yabby9; GRM ZM2G005353, GRMZM2G074543
Funding acknowledgement: National Science Foundation (NSF)
P132
The genetic control of a new tassel seed mutant in maize
(submitted by Silvio Salvi <silvio.salvi@unibo.it>)
Full Author List: Salvi, Silvio 1; Bovina, Riccardo 1; Giuliani, Silvia1; Frascaroli, Elisabetta 1; T uberosa, Roberto 1; Landi,
Pierangelo 1
1
Department of Agricultural and Food Sciences, University of Bologna, viale Fanin 44, Bologna, Italy, 40127.
Unisexual maize flowers originate through selective abortion of female primordia in the tassel and of male
stamens in the ear from bisexual inflorescences. Tassel seed mutations are known to alter the usual sex fate
allowing carpel survival in the male inflorescence. Objective of the present research is to describe and map a
novel tassel seed phenotype shown by an inbred line, Rig7, identified among a set of lines derived from in vitro
regeneration. Genetic mapping was carried out using a B73 x Rig7 F 2 population (genotyped with 15K SNP
array) and by SNP-based bulk segregant analysis using two additional populations (BC 1 and F2). Both
approaches clearly indicated that the tassel seed phenotype is under the control of two loci mapping on
chromosomes 2 and 6. The locus on chromosome 2 showed remarkable dominant epistasis on the second locus
and was mapped near the known tassel seed gene ts1, in the pericentromeric region. The locus on chromosome 6
was mapped to a 130-kb region which included three genes based on B73 genome annotation. Candidate genes
are being tested by reverse genetics, comparison of allele sequences and by analysis of different hormones
concentration in young tassels.
127
P133
The role of boron in vegetative and reproductive development in maize
(submitted by Michaela Matthes <matthesm@missouri.edu>)
Full Author List: Matthes, Michaela 1; Robil, Janlo 1; T ran, T hu1; Kimble, Ashten 1; Durbak, Amanda1; McSteen, Paula1
1
Bond Life Sciences Center, Department of Biological Sciences, University of Missouri-Columbia, Columbia, MO
65211, USA
Boron deficiency is a common abiotic stress negatively affecting crop yield worldwide. We have identified the
tasselless1 (tls1) gene as the co-orthologue of the Arabidopsis boron importer NIP5;1. Since the tls1 mutant
cannot actively take up boron out of the soil, it is inherently boron deficient. By using this mutant, we found that
one of the earliest symptoms of boron deficiency is a reduction in meristem size. Depending on the boron
availability in the soil, this leads to vegetative and/or reproductive defects, which can all be rescued by boron
supplementation. In order to understand what causes the reduction in meristem size in tls1, we are studying the
involvement of boron in meristem maintenance pathways as well as in hormone pat hways regulated by cytokinin
and auxin. We are analyzing double mutants between tls1 and known meristem pathway mutants and with
mutants involved in auxin/cytokinin biosynthesis and signaling. These analyses are combined with confocal and
fluorescence microscopy of marker genes such as ZmWUSCHEL:RFP.
We also found, that the tassel phenotype of tls1 can be rescued by additional light in the greenhouse. We found
this effect to be correlated with increased transpiration, which indicates that passive boron transport is a major
boron source in maize, even under boron deficiency conditions. Our studies will aid in understanding the role of
boron in plant development and will ultimately lead to the development of higher yielding plants in marginal
soils.
Funding acknowledgement: United States Department of Agriculture (USDA)
P134
The role of CT2 in maize internode development
(submitted by Dave Stateczny <dave.stateczny@uni- hamburg.de>)
Full Author List: Stateczny, Dave1; Köhling, Vasco 1; Kluth, Jantjeline1; Oppenheimer, Jara 1; Bommert, Peter 1
1
Department of Developmental Biology, University of Hamburg, Germany
Heterotrimeric G proteins are membrane-associated molecular switches and are composed of the three subunits
Gα, -β and -γ. They transduce extracellular signals to induce specific cellular responses by activating
downstream effectors and are involved in a wide range of growth and developmental p rocesses in animals and
plants.
In maize COM PACT PLANT2 (CT2) was identified as the α-subunit. Compared to wild type the shoot apical
meristem of ct2 mutant plants is enlarged and internodes are shortened, indicating that CT2 influences cell
proliferation and elongation. These processes are orchestrated by the reorganization of microtubules. Although
CT2 does not bind directly to microtubules in vitro, the Gα subunit might influence their reorganization in vivo
via interacting proteins which bind both to microtubules and CT2. In initial IP/M S experiments with the CT2YFP reporter line we identified the Phospholipase Dα5 (ZmPLDα5) as a potential CT2 interacting protein.
Phospholipases have been shown to influence microtubule reorganization in Arabidopsis and additionally
AtPLDα1 physically interacts with Gα to accelerate GTP hydrolysis in vitro, indicating that AtPLDα1 is a
GTPase accelerating protein (GAP). In maize no GAPs are known so far, so these proteins could illuminate the
regulatory network of maize G protein signaling.
We investigated the possibility of the AtPLDα1 homolog ZmPLDα2 being the missing link between microtubule
reorganization and G protein signaling as well as being the missing GAP in maize. Förster Resonance Energy
Transfer (FRET) and co-immunoprecipitation (Co-IP) data indicate an interaction at the plasma membrane of
transiently transformed tobacco leaf cells. Additionally Loss-Of-Function (LOF) lines were identified to analyze
their genetic interaction.
Gene / Gene M odels described: compact plant2, phospholipase D2; GRM ZM2G064732, GRM ZM2G061969
Funding acknowledgement: German Research Foundation (DFG)
128
P135
The role of maize mutant Suppressor of sessile spikelets 2 (Sos2) in meristem
maintenance
(submitted by Katherine Guthrie <klgdn2@mail.missouri.edu>)
Full Author List: Guthrie, Katherine 1; McSteen, Paula1
University of Missouri - Columbia, 301 Bond Life Sciences Center, Columbia, MO, 65211
1
Plant development is driven by a group of undifferentiated stem cells, called meristems. During maize
reproductive development, the shoot apical meristem (SAM ), responsible for above ground growth, transitions
into an inflorescence meristem (IM ) which then produces a series of meristems along the periphery to give rise to
the male reproductive structure called the tassel. The female reproductive structures, or ears, arise similarly from
elongation of axillary meristems half-way down the stem. This developmental progression requires a fine balance
of stem cell proliferation and differentiation, referred to as meristem maintenance. M y research focuses on the
semi-dominant maize mutant Suppressor of sessile spikelets 2 (Sos2), which has defects in meristem maintenance
in all above ground meristem types, resulting in altered meristem size and timing of termination. Sos2
heterozygous plants have decreased branching in the tassel and suppression of spikelets, the short flower-bearing
branches, in the tassel and the ear. If a tassel is formed in Sos2 homozygotes, it is short and bifurcated and ears
are small and ball shaped. To determine the Sos2 gene function, I have analyzed double mutants of Sos2 with
CLAVATA pathway mutants, previously shown to play a role in meristem maintenance. In addition, fluorescent
microscopy of ZmWUSCHEL:RFP transgenic marker lines was used to characterize the stem cell niche of Sos2
mutants. The region was Sos2 maps on chromosome 10 has been sequenced and dosage analysis has been
performed to determine the gene responsible for the Sos2 phenotype and the type of dominance seen in Sos2
populations. Our results indicate that Sos2 plays a fundamental role in meristem maintenance throughout plant
development.
Funding acknowledgement: National Science Foundation (NSF)
P136
The role of ZmSCR1 and ZmSCR1h during maize leaf development
(submitted by Thomas Hughes <thomas.hughes@plants.ox.ac.uk>)
Full Author List: Hughes, T homas E. 1; Wu, Hao 2; Becraft, Philip W. 2; Langdale, Jane A. 1
1
Department of Plant Sciences; University of Oxford; South Parks Road; Oxford; UK; OX1 3RB
2
Genetics, Development & Cell Biology Department; Iowa State University; Ames; Iowa; USA; 50011
In most cases, the C4 photosynthetic pathway is underpinned by characteristic Kranz anatomy, with concentric
wreaths of bundle sheath (BS) and mesophyll (M ) cells surrounding closely spaced veins. It has been
hypothesised that the SHORTROOT/SCARECROW (SHR/SCR) transcription factors act to regulate Kranz
anatomy development in maize. In support of this, Zmscr1 and Zmshr1 mutants show perturbations in Kranz
formation. However, the phenotype exhibited in Zmscr1 mutants is relatively subtle, with many vascular bundles
appearing to develop normally. Here, we show that ZmSCR1 functions redundantly with the closely related
homeolog ZmSCR1h. Double mutant Zmscr1-1; Zmscr1h-1 plants exhibit a reduced growth phenotype not seen
in either of the single mutants, with drooping leaves caused by incomplete midrib extension. Furthermore,
Zmscr1-1; Zmscr1h-1 plants exhibit more severe perturbations in BS and M cell patterning than previously found
in Zmscr1 single mutants, as well as clear alterations in vein order formation. Expression of maize SHR orthologs
do not appear to be altered in the Zmscr1-1; Zmscr1h-1 background. We hypothesise that many of the observed
phenotypic perturbations may be caused by increased SHR movement in the absence of SCR. To test this, we
have generated SHR and SCR antibodies to enable protein accumulation to be compared. This study has
provided insight into how the SCR/SHR pathway acts to regulate Kranz anatomy development in maize.
Funding acknowledgement: Bill & M elinda Gates Foundation, Newton Abraham Studentship, Biotechnology
and Biological Sciences Research Council
129
P137
The scarecrow mutation enhances auxin-related leaf and inflorescence defects in
maize
(submitted by Janlo Robil <jmrobil@mail.mizzou.edu>)
Full Author List: Robil, Janlo M. 1; McSteen, Paula1
Division of Biological Sciences, University of Missouri, Columbia MO, U.S.A. 65211
1
Decades of research have underscored the role of auxin in the morphogenesis of plant organs. Auxin biosynthesis
and transport, have been known to steer early morphogenic events while numerous auxin signals and responses
have also been identified to fine-tune developmental processes from cell division to tissue differentiation. On the
other hand, non-hormone players such as transcription factors have been recognized as key components of
various developmental pathways. The connection between auxin and non-hormone regulators of plant
development still needs to be understood in detail. The transcription factor SCARECROW (SCR) was identified
as a key regulator of endodermis development in roots and more recently as a developmental switch for bundle
sheath differentiation in maize. The endodermis/bundle sheath, a high-capacity auxin conduit, has been
recognized as a critical spatial hub for regulation of root and shoot development. Here, we report genetic
evidence of possible connections between auxin and ZmSCR during leaf and inflorescence development in maize.
Double mutant analyses reveal enhancement of phenotypes attributed to defective auxin biosynthesis and
transport. These observations indicate a possible genetic interaction between auxin and a tissue-specific
transcription factor and demonstrate other ways in which auxin shapes organ development in maize.
Funding acknowledgement: The Fulbright Program
130
P138
Tissue- and cell-specific multi-omics analyses define a key molecular pathway of
lateral root initiation and its interaction with arbuscular mycorrhizal fungi in
maize
(submitted by Peng Yu <yupeng@uni-bonn.de>)
Full Author List: Yu, Peng1; Kortz, Annika 1; Gutjahr, Caroline2; T ian, T ian 4; Su, Zhen 4; Hamacher, Joachim 5; Li,
Chunjian 3; Hochholdinger, Frank 1
1
Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn;
Bonn, North Rhine-Westphalia, Germany, 53113
2
Plant Genetics, School of Life Science Weihenstephan, T echnical University of Munich; Freising, Bavaria, Germany,
85354
3
Department of Plant Nutrition, College of Resources and Enviro nmental Science, China Agricultural University;
Beijing, China, 100193
4
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural
University; Beijing, China, 100193
5
Department of Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn; Bonn,
North Rhine-Westphalia, Germany, 53115
Heterogeneity of xylem- and phloem-pole pericycle cells determines their competence for lateral root initiation.
Outgrowth of lateral roots from competent phloem-pole pericycle cells allows them to forage for soil resources.
Arbuscular mycorrhizal (AM ) fungi play an important role in triggering the developmental program of their host
roots. The present study aims to decipher the mechanisms of post -embryonic lateral root initiation and their
interaction with AM fungi in maize.
Systemic histological and histochemical analyses of the lateral root defective mutants lateral rootless 1 (lrt1) and
rootless with undetectable meristem 1 (rum1), revealed excessive cell wall lignification of phloem-pole pericycle
cells in these mutants. We surveyed the transcriptome signatures of xylem- and phloem-pole pericycle cells of
these mutants isolated during different stages of lateral root initiation by laser capture microdissection (LCM )based RNA-seq. We demonstrated that cell wall biogenesis and organization are key processes controlling
pericycle cell competence.
We further determined 12 inbred lines with disparate lateral root initiation frequency from the intermated B73by-M o17 (IBM ) population. In general, lines with few lateral (FL) roots displayed higher cell wall lignification
in pericycle cells. Comparative transcriptome profiling of manually dissected steles revealed that genes involved
in ubiquitination and phenylpropanoid biosynthesis were exclusively enriched in FL lines.
To explore the role of AM fungi on lateral root initiation, we demonstrated that AM fungi (Rhizophagus
irregularis) exclusively induce lateral root formation in FL lines and lrt1. Tissue-specific metabolome (GC-M S)
and proteome (iTRAQ) analyses of lrt1, demonstrated that AM fungi induce lateral root formation by interfering
with biosynthetesis of phenylpropanoid-related compounds. M oreover, the transcriptomes of isolated phloempole pericycle cells from AM -treated and non-AM -treated lrt1 plants showed diverse regulation of cell wallrelated genes. Taken together, these results highlight a novel role of phenylpropanoid-related cell wall
biosynthesis in lateral root initiation by interacting with AM fungi in maize.
Funding acknowledgement: Deutsche Forschungsgemeinschaft (DFG)
131
P139
Towards a comprehensive understanding of genetic architecture underlying
senescence
(submitted by Rajandeep Sekhon <sekhon@clemson.edu>)
Full Author List: Sekhon, Rajandeep 1; Saski, Christopher4 ; Beissinger, Timothy2 ; Bridges, William3 ; de Leon, Natalia5;
Kaeppler, Shawn 5
1
Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA, 29634
2
Institute for Translational Genomics, Clemson University, Clemson, SC, USA, 29634
3
USDA & Divisions of Plant and Biological Sciences, University of Missouri, Columbia MO, USA, 65211
4
Department of Mathematical Sciences, Clemson University, Clemson, SC, USA, 29634
5
Department of Agronomy, University of Wisconsin, Madison, WI, USA, 53706
Senescence is a very important agronomic trait due to its close association with photosynthetic assimilation,
partitioning of photoassimilate among reproductive and vegetative organs, and the ability of the plant to cope with
biotic and abiotic stress. Senescence represents a major shift in plant developmental program and is, therefore, under a
highly complex genetic regulation. Among a multitude of internal and external factors, senescence is also regulated by
source-sink cross-talk. For instance, we and others have shown that removal of primary sink leads to disruption of
carbohydrate partitioning among source and sinks, and triggers source-sink regulated senescence (SSRS). We are using
a systems genetics approach to dissect the genetic, physiological, and metabolic determinants of natural senescence and
SSRS. T hrough extensive multi-location and multi-year phenotyping a diversity panel and a bi-parental RIL
population, we have identified very strong associations and QT L underlying natural senescence and SSRS. Further
analyses of these associations revealed several novel genes underlying natural senescence and SSRS. QT L underlying
SSRS were confirmed by near-isogenic lines (NILs) and the QT L introgressions in NILs were reduced in size through
backcrossing. Remarkably, we identified several candidate genes underlying SSRS, however, none of these have been
implicated in carbohydrate partitioning, thus suggesting mechanistically unique regulation of SSRS. We are currently
performing transcriptomic and metabolic analyses to corroborate the associations and QT L. Experiments are also
undergoing to validate and further understand the role of candidate genes in natural senescence and SSRS, and th ose
results will be presented.
Funding acknowledgement: Department of Energy (DOE)
P140
Towards live imaging of meiosis in maize
(submitted by Martina Balboni <martina.balboni@uni-hamburg.de>)
Full Author List: Balboni, Martina1 ; Prusicki, Maria Ada1 ; Schnittger, Arp 1
1
University of Hamburg; Biozentrum Klein FLottbek; Hamburg, Germany, 22609
Meiosis is a specialized cell division, which reduces the genome by half through two consecutive chromosome
separation events. Meiosis is key to biological diversity since homologous chromosomes exchange DNA fragments in
the process of meiotic recombination, giving rise to novel combination of parental alleles. Due to this function, meiosis
is also central to plant breeding. Despite of its importance, many crucial steps in meiosis are not well understood. So
far, most studies of meiosis in plants have relied on classical genetic analyses and cytological observations of fixed
chromosome spreads. Although important and informative, these studies have limits in accurately examining the
dynamics of meiotic processes and investigating temporal and spatial aspects. Here, we present our set up of an
efficient live imaging system for maize meiosis that is based on a previously established protocol in our team to follow
meiosis in Arabidopsis.
T he method relies on transgenic lines producing fluorescently labeled proteins that highlight hallmarks of meiosis. We
selected different live imaging markers, by which specific aspects of meiosis are visualized. T hese include CENH3 (a
centromeric histone variant) as chromosome marker as well as DSY2 and ZYP1 as elements of the synaptonemal
complex to follow chromosome movement and pairing. Furthermore, AM1 and SDS as markers to monitor entrance
and progression through meiotic stages and COM1 and MUS81 to visualize recombination events. By themselves and
especially in combination, these different reporter lines will be a useful tool to reveal the dynamics of meiotic
chromosome behavior in vivo and define a time course of meiosis in maize.
Gene / Gene Models described: Am1; ASY3; CENH3; MUS81; SDS; COM1; Zyp1 ; GRMZM5G883855;
LOC103626703; GRMZM2G158526; GRMZM5G822970; GRMZM2G093157; GRMZM2G076617;
GRMZM2G143590
132
P141
Transcriptomic characterization of male sexual reproduction in maize
(submitted by Matthew Warman <warmanma@oregonstate.edu>)
Full Author List: Vejlupkova, Zuzana 1; Hokin, Sam 2; Panda, Kaushik 3; Warman, Matthew1; Cole, Rex A1; Slotkin, R.
Keith 3; Evans, Matthew MS2; Fowler, John E 1
1
Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
2
Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
3
Department of Molecular Genetics, T he Ohio State University, Columbus, OH 43210, USA
Sexual reproduction in plants involves developmental regulation of key cellular processes (e.g., pollen tube
growth, cell-cell signaling, fertilization). Recent results demonstrate that plant genomes undergo large scale
alteration of gene expression and epigenetic modifications as plants undergo meiosis to produce haploid
gametophytes for the next generation. We have undertaken a transcriptomic study of male sexual development in
maize to investigate these regulatory events.
We developed methods to isolate and sequence mRNA and small RNA from the same tissue sample at four
developmental stages, with four biological replicates for each stage: tassel primordia, microspores, mature
pollen, and sperm cells. PCA analysis of the datasets indicate that replicates from each tissue have low variance,
enabling statistical confirmation of any observed differential expression of genes/transposable elements between
tissues. We additionally show that our mature pollen sequencing datasets resemble previously sequenced highquality datasets. Gene ontogeny analysis of mRNA transcripts highlights contrasting cellular processes in mature
pollen, consistent with the distinct roles of the sperm cells and the vegetative cell in reproduction. To better
assess dynamic transposable element regulation in maize male reproductive tissues, we developed a
bioinformatic tool to easily visualize and identify differentially expressed transposable elements in these
samples.
Intriguingly, genes that are highly -expressed in either mature pollen or sperm cells are associated with fewer
transposable element insertions in exons in sequenced populations (UniformMu, Photosynthetic M utant Library),
relative to highly-expressed seedling genes. This is consistent with the idea that deleterious mutations in genes
important for either pollen or sperm cell function are subject to relatively higher purifying selection, likely due to
the haploid nature of these stages.
Funding acknowledgement: National Science Foundation (NSF)
P142
Transient interaction analysis of the Zea mays (L.) CT2 and PLDα1 proteins in
Nicotiana benthamiana (L.)
(submitted by Vasco Köhling <vasco.koehling@gmx.de >)
Full Author List: Köhling, Vasco 1; Stateczny, Dave1; Oppenheimer, Jara1; Kluth, Jantjeline1; Bommert, Peter 1
Universität Hamburg; Biozentrum Klein Flottbek; Hamburg; Hamburg;Germany; 22609
1
Heterotrimeric G protein signaling is involved in a variety of growth and developmental processes in animals and
plants. These membrane-associated complexes consist of the three subunits Gα, -β and -γ. The number of
subunits differs from animals to plants. Plants usually have one canonical α-, one β- and three to six γ-subunits.
In maize COM PACT PLANT2 (CT2) has been identified as the α subunit of the heterotrimeric complex.
The regulation of G protein signaling differs in plants as well. There are no G Protein Coupled Receptors
(GPCRs) in plants. In addition, maize, like many other grasses, lacks the REGULATOR OF G PROTEIN
SIGNALING (RGS).
In Arabidopsis it has been demonstrated that Phospholipase AtPLDα1 interacts with Gα (GPA1) via a conserved
DRY motif that is also required for the interaction of multiple GPCRs with Gα subunits in animal systems.
Furthermore it has been shown that AtPLDα1 can act as a GTPase accelerating protein (GAP) on AtGPA1 in
vitro.
As we identified maize PHOSPHOLIPASE Dα5 (ZmPLDα5) in previous CT2-YFP IP/M S experiments as a CT2
interacting protein, we continued to investigate the interaction between CT2 and ZmPLDα1, the likely maize
ortholog of AtPLDα1 using Förster Resonance Energy Transfer (FRET) and co-immunoprecipitation (Co-IP)
experiments. Our results indicate an interaction of ZmPLDα1 and CT2 at the plasma membrane, which is
dependent of the DRY motif. This interaction might expand the regulatory network of maize G protein signaling.
Gene / Gene M odels described: compact plant2, phospholipase D1; GRM ZM2G064732, GRM ZM2G054559
Funding acknowledgement: German Research Foundation (DFG)
133
P143
AFD1 and DSY2 are both required for chromosomal localization of ASY1 and
meiotic double-strand break formation in maize
(submitted by Ding Hua Lee <dinghua@gate.sinica.edu.tw>)
Full Author List: Lee, Ding Hua 1; Ronceret, Arnaud2; Wang, Chung-Ju Rachel1 3
1
Institute of Plant and Microbial Biology, Academia Sinica, T aipei 11529, T aiwan
2
UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVEST AV Irapuato, Km 9.6 Libramiento Norte
Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
3
Biotechnology Center, National Chung-Hsing University, T aichung 40249, T aiwan
M eiosis is a specific type of cell division required for generating haploid gametes. It contains single round of
DNA replication, followed by two rounds of chromosome segregation. M eiotic recombination initiated by
double-strand breaks (DSBs) are essential for homologous pairing and the proper segregation of homologues at
metaphase I. Synapsis, a process of synaptonemal complex (SC) formation between newly paired homologous
chromosomes, regulates meiotic recombination. Despite the importance of SC proteins in meiosis, relatively little
is known about their genetics and molecular biology in plants. In maize, the known SC proteins include axial
element components ASY1 and AFD1, and the central element component ZYP1. Previously, we had identified
DESYNAPTIC2 (DSY2) as an axial element protein and showed that DSY2 is required for normal level of DSBs
and SC formation. In this study, we found that proper localization of DSY2 and ASY1 depends on AFD1. In
contrast to a linear pattern of both DSY2 and ASY1 in the wild-type, DSY2 and ASY1 form short stretches in the
afd1-1 mutant. On the other hand, ASY1 shows a weaker but linear signal in dsy2, indicating that DSY2 is
required for the proper recruitment of ASY1. Interaction between DSY2 and ASY1 was confirmed by both yeasttwo hybrid and immunoprecipitations of anti-DSY2 and anti-ASY1. The double mutant lacking both Dsy2 and
Afd1 shows a synergistic phenotype that ASY1 signals appear diffused and unable to load on chromosome. In
addition, the number of γH2AX and RAD51 foci is totally abolished in dsy2 afd1 double mutant, indicating that
chromosome axes are required for DSB formation and DSB repair, respectively. Taken together, these results
suggest that AFD1 serves as a basic foundation of chromosome axis that facilitate the recruitment of DSY2 and
ASY1, and the chromosome axes formed by these proteins are required for recruitment of DSB formation
factors.
P144
Analysis of ten meiotic mutants of maize
(submitted by Arnaud Ronceret <ronceret@ibt.unam.mx>)
Full Author List: Ronceret, Arnaud1
Instituto de Biotecnologia -UNAM; Cuernavaca, Morelos, Mexico C.P. 62210
1
M aize is an excellent model to study meiosis thanks to excellent cytology and a large collection of meiotic
mutants (Cande et al., 2009). We are analyzing five mutants affected in meiotic prophase I and recombination
(spo11-1 (cloned), as1, dsy9902, dsy9905, and meiN2415) and five mutants that have defects in the condensation
of meiotic chromosomes (afd1 (cloned), elongate1, ms43, sticky and M ei025). Our detailed analyzes of
molecular cytogenetics will allow to concentrate on several aspects of the early meiotic recombination process
and the chromosomal condensation that occurs during the progression of prophase I of meiosis. We are also
investigating how meiotic recombination coordinates with the progression of chromosome conformation by
studying an essential part of the collection of the maize meiotic mutants. This project allowed to save (repropagate) ancient seeds of eight of these mutants (except M ei025 and sticky). We are mapping and trying to
clone the corresponding eight genes. We are also analyzing them with new cytogenetic and proteomic tools. An
applied aspect of this research in progress is to valorate this collection of mutants with the aim of introducing a
clonal reproduction in maize. The possibility of manipulation of maize sexuality to maintain heterosis (vigor of
the hybrids) was revived by the development of transgenic lines of Arabidopsis capable of clonal reproduction
similar to apomixis (M arimuthu et al., 2011) (Ronceret and Vielle-Calzada 2015) and the recent clonation of the
haploid inducer stock6 (Kelliher et al. 2017, Gilles et al 2017, Liu et al. 2017). We have initiated crosses between
non-transgenic meiotic mutants to produce an 'apomeiotic' maize, the first step for the generation of maize seeds
with a clonal reproduction that can maintain heterosis.
Funding acknowledgement: UNAM -PAPIIT
134
P145
Dynamics of meiotic spindle assembly in Zea mays
(submitted by Natalie Nannas <njnannas@hamilton.edu>)
Full Author List: Nannas, Natalie J. 1; Weiss, Jodi D. 1; Dawe, R. Kelly 2
1
Hamilton College, Department of Biology; Clinton, New York, USA 13323
2
University of Georgia, Department of Genetics, Department of Plant Biology; Athens, Georgia, USA 30602
The success of an organism is contingent upon its ability to faithfully pass on its genetic material. Chromosomes
must be correctly segregated between dividing cells, a process that is particularly critical in the meiotic divisions
that generate an organism’s gametes. The machinery used to pull chromosomes apart is the spindle, a bipolar,
microtubule-based structure. M ale maize meiocytes lack many of the features that govern the assembly,
organization and positioning of the spindle, so we investigated the dynamics of the spindle assembly process in
wild-type meiotic cells. Using fluorescently-tagged lines, spindle assembly was observed in meiosis I and II via
live microscopy. We found that meiotic spindle assembly is characterized by the following steps: collapse of the
nuclear envelope with associated microtubules, a re-organization of these microtubules into a bipolar shape,
lengthening of the spindle and focusing of the poles. Cells frequently formed tripolar or multipolar spindles;
approximately half of all assembly events initially formed a tripolar spindle. Tripolar spindles were re-organized
into correctly shaped bipolar spindles during prometaphase chromosome congression. Spindle also frequently
failed to fully focus their poles before transitioning from metaphase to anaphase. The frequency of substantial
errors in assembly and their subsequent correction before anaphase suggests an active and essential role for the
spindle assembly checkpoint in the progression of meiosis. However, the initiation of chromosome segregation in
the presence of unfocused poles suggests a leniency of the checkpoint that allows progression despite minor
errors.
Funding acknowledgement: National Science Foundation (NSF)
P146
Frequency of abnormal chromosome 10 in tropical landraces of Zea mays
(submitted by Jodi Weiss <jdweiss@hamilton.edu>)
Full Author List: Weiss, Jodi D. 1; Nannas, Natalie J. 1; Dawe, R. Kelly 2
1
Hamilton College; Clinton, Department of Biology; Clinton, New York, US 13323
2
University of Georgia; Department of Genetics, Department of Plant Biology; Athens, Georgia, US 30602
Abnormal chromosome 10 (Ab10) is a selfish maize chromosome that promotes its own inheritance to future
progeny over normal chromosomes. Extensive genetic analysis of this abnormal meiotic drive system has been
carried out mainly on agricultural and research landraces of North America and M exico. The presence of Ab10,
however, has not been widely studied in tropical maize landraces. We investigated the frequency of abnormal
chromosome 10 in a variety of Zea mays tropical landraces from five South American countries. Only two of 43
tropical landraces tested positive for the presence of Ab10. Of the two positive landraces, 67% of Peruvian
individuals, and 60% of Venezuelan individuals contained Ab10. Currently, three types of Ab10 exist and are
determined by their cytological structure. Fluorescence in-situ hybridization (FISH) revealed that the Peruvian
population carries Ab10 variant type-III, which is the most prevalent type. In addition, geographic observations
revealed that both Ab10 positive landraces were cultivated from regions at average altitudes of 120m and 115m.
These findings support previous research reporting high occurrences of abnormal chromosome 10 within
populations found at lower altitudes.
Funding acknowledgement: National Science Foundation (NSF)
135
P147
Meiotic crossovers in maize: the interfering and non-interfering recombination
pathways have different landscapes
(submitted by Olivier Martin <olivier.c.martin@inra.fr>)
Full Author List: Basu Roy, Sayantani1; Falque, Matthieu2; Martin, Olivier C. 2
1
Institute for Human Genetics, UCSF School of Medicine; San Francisco, CA, USA 94117
2
GQE– Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisT ech, Université Paris-Saclay; Gif-sur-Yvette, France
91190
The formation of crossovers in meiosis ensures a proper segregation of homologous chromosomes, but it also
shuffles the allelic combinations, generating in each product a mosaic of the homologous pairs. Thus crossovers
are the physical cause of recombination while providing the variation upon which natural and artificial selection
operate. In maize, the majority of crossovers come from the interfering pathway, while the remaining 15% or so
of the crossovers come from the non-interfering pathway (Falque et al., Plant Cell 2009). Direct observations in
tomato have revealed that these two pathways have different recombination landscapes, with crossovers in the
peri-centromeric regions coming mainly from the non-interfering pathway (Anderson et al., PNAS 2014).
Unfortunately similar experiments to identify the pathway via which each observed crossover was formed have
not been performed in any other plant species. Hence to understand the properties of the two recombination
landscapes in maize, we resort to data analysis and modeling.
Our first approach relies on a test within a novel statistical framework. By performing a model-independent
analysis of maize data (Anderson et al., Genetics 2003), we are able to reject the hypothesis that crossover
interference operates homogeneously in genetic coordinate space and thus points to having different shapes of
landscapes for each pathway, as is known to be the case in tomato. Our second approach, based on modeling,
allows the two pathways to have different recombination landscapes and takes the crossovers of the first to be
generated by the so-called Gamma model. By fitting the crossover data (not knowing whether a crossover was
formed as a result of the interfering or non-interfering pathway), we infer the two separate landscapes in maize
for each of the 10 chromosomes. The trends arising in these predictions are then compared with what is known in
tomato.
P148
Visualizing plastid sequences present on the B Chromosome of maize
(submitted by Mohamed El-Walid <mze99d@mail.missouri.edu>)
Full Author List: El-Walid, Mohamed1; Cody, Jon 1; Baum, April1; Birchler, James1; Newton, Kathleen 1
1
Division of Biological Sciences, University of Missouri, Columbia, MO, USA 65211
In maize, B chromosomes are extra chromosomes that exist in association with the normal chromosomal set and
are not essential for the survival of the organism. Through mitotic drive, a two-part accumulation mechanism
during pollen maturation, B chromosomes are maintained in populations and can be present in variable numbers.
The exact origin of the B chromosome is uncertain; however, previous research has determined its structure to be
mostly heterochromatic, containing a collection of repetitive sequences from nuclear and organellar genomes.
Using fluorescent in situ hybridization (FISH), we have shown the presence of mitochondrial DNA on B
chromosomes. Sequence analysis suggests that plastid DNA sequences are also present on B chromosomes. This
research focuses on using FISH analysis to visualize plastid sequences present on the B chromosome of maize.
Funding acknowledgement: National Science Foundation (NSF)
136
P149
Doing genetics research in the classroom: CRISPR-Cas9 and cold stress in plants
(submitted by Irina Makarevitch <imakarevitch01@hamline.edu>)
Full Author List: Makarevitch, Irina 1; Hillmann, Katie1; Permentine, Chris1
1
Hamline University; 1536 Hewitt Ave, Saint Paul, MN, US 55449
Integration of authentic research experiences is crucial to providing all students with equal access to research
opportunities. To engage students in plant genetics research, we developed a laboratory series guiding students
through the process of creating CRISPR-Cas9 vectors and producing mutant Arabidopsis plants. Despite being a
relatively new technology, CRISPR (Clustered regularly -interspaced short palindromic repeats)/Cas9 has proven
to be a revolutionary, efficient, and precise mechanism for editing genomes through targeted mutagenesis and it
could be used as an effective draw for students’ interest in genetic and biotechnology. In our system, the students
can choose the genes that they would like to knock out or the target genes could be drawn from research projects
that involve testing the effects of mutations in candidate genes. We developed all learning materials using the
protocols from Voytas Lab (Čermák et al., 2017) and tested them on Arabidopsis genes homologous to maize
genes involved in cold stress response, as well as several Arabidopsis genes with well characterized phenotypes
as controls. The vectors produced by students were analyzed by restriction digests, colony PCR, and sequencing,
demonstrating the success of vector assembly. The T0 plants were transformed with T-DNA transformation
vectors for all five selected genes and T1 transformed seeds were selected. The results of the phenotypic screens
show the success of CRISPR-Cas9 protocols we implemented and the suitability of this approach to a regular
laboratory course. The results of student learning assessment indicate the effectiveness of our approach.
Funding acknowledgement: National Science Foundation (NSF)
P150
Evaluation of genetic progress in grain and silage corn afforded by the renewal
of varieties in France over the past 30 years
(submitted by Josiane Lorgeou <j.lorgeou@arvalis.fr>)
Full Author List: Lorgeou, Josiane 1; Martin, Bruno 1; Audigeos, Delphine1; Mangel, Nathalie1; Piraux, François1
Arvalis - Institut du Végétal; France
1
Genetic improvement made on different grain corn traits over the past 50 years in France has been the subject of
several studies based on specific trials comparing varieties, which have marked the history of maize since the
1950s (Derieux et al., 1987; Welcker et al., 2011). Annual yield gain results align with the estimations obtained
in the United States (Duvick et al., 2005). Therefore, regular updating of the references for each earliness group
in grain corn and corn harvested as silage (Baldy et al., 2017) is important to (i) evaluate selection dynamism in
each earliness group, (ii) show farmers the effect of genetic progress in the evolution of agricultural yields in a
context where the increase in national average yield has slowed since the 2000s, (iii) determine the expected
levels of progress for different variety selection criteria, particularly in the context of discussions on variety
registration rules. The results database of the last 30 years from the Arvalis – Institut du Végétal maize variety
evaluation network (10 to 35 validated trials/year according to the variety earliness group) represents valuable
material for proposing, with the help of statistical fitting for incomplete data series, an assessment of annual
genetic progress in yield, earliness and lodging. This poster describes the methodology and assessment of genetic
improvement of the varieties offered annually to farmers in France.
137
P151
Fifty years of mirrored in situ and ex situ conservation of Mexican maize
landraces: socioeconomic dynamics and genomic diversity
(submitted by Francis Denisse McLean Rodriguez <f.mcleanrodriguez@sssup.it>)
Full Author List: McLean Rodriguez, Francis Denisse 1; Camacho Villa, T ania Carolina 2; Costich, Denise3;
Almekinders, Conny 4; Dell'Acqua, Matteo 1; Pè, Mario Enrico 1
1
Institute of Life Sciences, Sant’Anna School of Advanced Studies; Pisa, Italy, 56127
2
Socio-Economics Program, International Maize and Wheat Improvement Center (CIMMYT ); El Batán, T excoco,
Mexico, 56237
3
CIMMYT Germplasm Bank, International Maize and Wheat Improvement Center (CIMMYT ); El Batán, T excoco,
Mexico, 56237
4
Department of Social Sciences, Wageningen University; Wageningen, T he Netherlands, 8130
Although in situ and ex situ strategies for genetic resource conservation are considered complementary, the
evidence available on the topic and specifically on maize is indirect. Our objective is to make a straightforward
comparison of how the diversity of M exican maize landraces has been conserved in genebanks and in farmers’
fields over the last 50 years. To do so, we focus on a set of 93 accessions of maize traditional varieties collected
in 1967 from 66 families from the state of M orelos, M exico and stored at the CIM M YT Maize Germplasm Bank.
Passport information from each accession included its common name, pictures of five representative ears, village
where the sample was collected, name of the farmer who donated the sample and number of collected ears. With
this information we traced back the same farmer families 50 years later, in 2017, and collected new samples from
the accessions that had been conserved in situ. Thirteen families had conserved 14 accessions under constant
cultivation during the 50-year period. We collected 11 of these accessions and assembled 11 ex situ and in situ
accession pairs for genetic characterization and comparison. DNA from these populations was genotyped using
double restriction site associated DNA markers (ddRAD). We opted for a mixed approach in which both single
plants (10 individuals per accession) and pooled samples (2-3 pools of 30 individuals per accession) were
compared. Through in depth interviews we also documented the history of loss or conservation of these maize
traditional varieties among the families who donated the samples in 1967. By bringing genetic and
socioeconomic approaches together our aim is to assemble a comprehensive picture of how variation in these
maize populations has evolved over time and to shed light on which could be the most appropriate strategies for
their conservation.
Funding acknowledgement: Sant’Anna School of Advanced Studies, Department of Social Sciences Wageningen
University
138
P152
Learning how to rescue a landrace: A study of the giant maize, Jala, and the
community who grows it
(submitted by Denise Costich <d.costich@cgiar.org>)
Full Author List: Costich, Denise E. 1; Vidal Martinez, Victor A. 2; Camacho-Villa, T . Carolina1; Zavala Espinosa,
Cristian 1; Gore, Michael A. 3; Bernau, Vivian 4; Flores, Luis Armando 5; Waybright, Aaron 1
1
International Center for Maize and Wheat Improvement (CIMMYT ); T excoco, Mexico
2
Santiago Ixcuintla Experimental Station - National Institute of Forestry, Agricultural and Livestock Research
(INIFAP); Santiago Ixcuintla, Nayarit, Mexico
3
Cornell University; Ithaca, New York, USA
4
T he Ohio State University, Columbus, Ohio, USA
5
T echnological University of the Coast, T epic, Nayarit, Mexico
M aize landraces are famous for their high degree of local adaptation and specialization, resulting from many
cycles of selection by the communities who grow them. One of the most famous examples is the giant maize,
“Jala,” named after the valley where it grows in the central western state of Nayarit in M exico. Even though this
variety has distinctive agronomic and culinary attributes that are expressed and valued mainly at the local level,
there has been a reduction of the total metapopulation size, from millions of plants grown in large, contiguous
land holdings in the 1950s, to relatively few (<100) small, isolated individual smallholder farmer plots since the
1980s. In 2017, we carried out a field trial near the village of Jala, evaluating Jala landrace collections from four
local farmers versus 14 historical materials conserved in the CIM M YT Germplasm Bank. In addition, we
conducted a socioeconomic survey to understand Jala maize dynamics, replicating a survey carried out in 2001
by Rice (2004; 2007). This multi-disciplinary approach is helping us to identify the main biological (genetic and
agronomic) and socioeconomic factors that affect Jala maize conservation. The field trial clearly identified which
of the historical collections could provide useful germplasm for a future breeding program. Socioeconomic
results indicate that although Jala maize is multi-purpose, displaying a variety of culinary uses, as well as
providing quality forage for livestock, the main reason the farmers keep conserving it is tradition. This tradition
has been reinforced by an annual local contest that rewards the producers of the largest ears of Jala maize.
However, these first findings also indicate that a more holistic and aggressive strategy of conservation is needed
to truly rescue the Jala maize landrace from the current trend toward its eventual disappearance from the Jala
Valley.
Funding acknowledgement: CGIAR and Global Crop Diversity Trust; USAID Linkage Program
139
P153
The maize collection of CIMMYT’s germplasm bank: Promoting the
conservation, use and study of diversity
(submitted by Denise Costich <d.costich@cgiar.org>)
Full Author List: Costich, Denise E. 1; Zavala Espinosa, Cristian 1
International Center for Maize and Wheat Improvement (CIMMYT ), Texcoco, Mexico
1
This is an exciting time for the M aize and Wheat Germplasm Bank at CIM M YT. DNA sequence data are now
available for diversity analyses of the collections, from our colleagues in the Seeds of Discovery Project. The
implementation of the GRIN Global database management system is nearing completion. Our germplasm is
being used for gene discovery projects for emerging diseases, such as M aize Lethal Necrosis (M LN) and Tarspot
Complex. The CIM M YT Maize Lines (CM L) collection has never been better documented, both phenotypically
and genetically. Innovations in seed processing and regeneration that focus on enhancing the maintenance of
genetic diversity and maximizing efficiency, are currently being tested. We are building a new screenhouse
dedicated to the regeneration of wild relatives. Strengthening our relationship with the USDA M aize Collection
in Ames, Iowa has accelerated many of these improvements. We continue to participate in research on
community-centered landrace conservation and the development of community seedbank networks, in
partnership with the M asAgro Program. In order to provide the maize genetics community with a more detailed
understanding of the germplasm we hold in trust for humanity, a diversity tree analysis of the collection will be
presented. Another activity underway to promote use by breeders and researchers includes the identification of
subsets with special types of associated data, such as kernel characteristics or disease resistances. This is part of
an effort throughout all CGIAR genebanks to connect decades of characterization data with the seed accessions,
to promote gene discovery and related genetic research. We acknowledge the strong sup port from the Global
Crop Diversity Trust, as well as its unwavering leadership in promoting and giving direction to our mission
through the CGIAR Genebank Platform.
Funding acknowledgement: CGIAR and Global Crop Diversity Trust
140
P154
NSF Plant Transformation Workshop
(submitted by Hyeyoung Lee <leehye@missouri.edu>)
Full Author List: Lee, Hyeyoung1
1
Plant T ransformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, MO 65211.
Plant transformation has been a bottleneck in advancing plant functional genomics study and genome editing.
Transformation of recalcitrant cereal crop species has been challenging. The National Science Foundation - Plant
Genome Research Program sponsors this training workshop. The goal of this workshop is to provide attendees
with hands-on experience in Agrobacterium-mediated transformation of cereal crop species. Attendees will have
the opportunity to walkthrough advanced protocols for transformation of cereal crops with focus on three
recalcitrant cereal species; including Zea mays inbred lines, Sorghum bicolor public genotype, and
Brachypodium distachyon public genotype. Trainees will have the opportunity to learn how to utilize plant
morphorgenic regulator genes to transform B73 as well as the best practice for cereal transformation. In addition,
the workshop will offer two lectures and host a discussion forum. The first lecture will focus on the mechanism
of plant somatic embryogenesis whereas the second lecture will center on how to establish and implement cereal
transformation systems. The Plant Transformation Core Facility at University of M issouri, Columbia, M O, USA,
will host this workshop from July 30 to August 3, 2018. For workshop pre-registration (free), please visit Plant
Transformation Core Facility website at https://plantsciences.missouri.edu/muptcf/ workshop and for any
workshop update. Seats are limited. Pre-registration is required by June 20, 2018 to secure y our spot and
facilitate our workshop organization. Please contact Dr. Zhanyuan J. Zhang (zhangzh@missouri.edu) for any
workshop related questions.
Funding acknowledgement: National Science Foundation (NSF)
141
P155
Maize annotation jamboree on last B73 RefGen_V4 assembly
(submitted by Cristina Marco <marco@cshl.edu>)
Full Author List: Marco, Cristina F. 1; T ello-Ruiz, Marcela1; Hsu, Fei-man 2; Wu, Hao 3; Wimalanathan, Kokulapalan 3;
Zhan, Jungpeng4; Stitzer, Michelle5; Qiao, Pengfei6; Wasikowski, Rachael7; Khangura, Rajdeep 8; Sapkota, Sirjan 9;
Brenton, Zach 9; Okoro, Michael1 10; Munoz-T orres, Monica11; Hilgert, Uwe12; Williams, Jason 1; Ware, Doreen 1;
Micklos, Dave1
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
2
Graduate School of Frontier Sciences, the University of T okyo, Chiba 277-8561, Japan
3
Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011
4
School of Plant Sciences, University of Arizona, T ucson, Arizona 85721
5
Department of Plant Sciences, University of California, Davis, CA 95616, USA
6
Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
7
Department of Biological Sciences, University of T oledo, T oledo, OH 43560
8
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
9
Institute for T ranslational Genomics, Clemson University, Clemson, SC, USA
10
Center of Genomics and Systems Biology, New York University, New York, NY 10003
11
Phoenix Bioinformatics, Redwood City, CA 94063, USA
12
Bios5 institute, University of Arizona, T ucson, Arizona 85721
The first genomic Annotation Jamboree for the current reference M aize B73 (B73, RefGen_V4) was held on
December 4-5, 2017 at Cold Spring Harbor Laboratory (CSHL). Sponsored by the NSF-funded M aizeCODE
(IOS-1445025) and Gramene (IOS-1127112) projects, the Jamboree developed a model for how graduate
students can be involved in improvement of M aize gene models. This event was a proof-of-concept for similar
future efforts for improving annotations in M aize inbreeds, sorghum, and other important crops, as well as for
inclusion of undergraduates. This event brought together participants from seven US and one International
institution (University of Tokyo). 10 graduate students and one postdoctoral fellow participated in this two-day
event.
Students grouped in pairs checked the accuracy of five M aize gene families: PIN, GH3, ABC, TCP and ORC.
From these gene families, ‘suspicious’ M AKER-P-generated annotations were identified based on their
annotation edit distance (AED) and quality indexes (QI2). Working independently on the same set of models,
students found that 19% of the genes they looked at needed manual annotation including setting exon boundaries,
identification of non-canonical splice sites, missing exons or missing UTRs. From the genes that were tagged
with the AED and QI2 parameters, the primary gene model was corrected in approximately 70% of them and the
other 30% represented multiple isoforms which were difficult to curat e. Further tests are being performed to
determine if this method might be used to better predict gene models for manual curation and develop workflows
to automatize the process.
We describe conclusions, approaches, and identified improvements that will ult imately be fed back to
M aizeGDB curators as updates.
Funding acknowledgement: National Science Foundation (NSF)
142
P156
A candidate gene approach to identify markers associated to Fusarium Kernel
Rot resistance in maize
(submitted by Lorenzo Stagnati <lorenzo.stagnati@unicatt.it>)
Full Author List: Stagnati, Lorenzo 1; Soffritti, Giovanna1; Battilani, Paola1; Lanubile, Alessandra1; Busconi, Matteo 1;
Marocco, Adriano 1
1
Department of Sust ainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, 29100 Italy
Fusarium verticillioides is a major maize pathogen and it is associated with various symptoms of Fusarium ear
rot on maize. Resistance during seed germination is part of the plant-pathogen interaction but this aspect has
been poorly investigated. The best way to contrast this disease is the development of immune maize genotypes.
Several genes are reported as important for disease resistance, but their role against F. verticillioides is still not
understood. Point mutations, small insertions and deletions are responsible for the evolution of resistance genes
within a species. In this work, the presence of sequence polymorphisms in maize R genes, encoding NBS-LRR
proteins, and in Fusarium induced genes, identified by a RNAsequencing experiment, were analyzed in resistant
and susceptible lines. Then, the detected polymorphisms were used to genotype a panel of 267 lines with
phenotypic data for F. verticillioides resistance obtained using a rolled towel assay.
For R genes, 171 SNPs and 11 INDEL and for RNAseq-derived genes 104 SNPs and 11 INDEL were found in
38 and 17 genes, respectively. Forty polymorphisms were selected to genotype the panel of 267 maize inbred
lines. Genotypes were correlated to phenotypic data and four markers were associated to five different
phenotypic traits. All markers significantly associated with phenotypes were present in genes with a clear
function in disease resistance. These findings will contribute to understanding the maize-F. verticillioides
pathosystem interaction.
Funding acknowledgement: Doctoral School on the Agro-Food System (Agrisystem) of Università Cattolica del
Sacro Cuore (Italy), European Union’s Horizon 2020 Grant Agreement No. 678781 (M ycoKey)
P157
A Novel Mating Design Provides High Power to Detect Epistasis in Maize
(submitted by Husain Agha <hiagha@mail.missouri.edu>)
Full Author List: Agha, Husain I 1; T urner, Sarah D2; Guill, Katherine E 3; Beissinger, T im 1 2 3
Division of Plant Sciences, University of Missouri, Columbia, MO, USA
2
Division of Biological Sciences, University of Missouri, Columbia, MO, USA
3
United States Department of Agriculture, Agriculture Research Division, Columbia, MO, USA
1
Quantitative phenotypes are determined by a myriad of genes functioning in concert within an organism. The
phenomenon of two or more of these genes interacting to influence a phenotype, known as epistasis, is critical
for understanding genetic architecture. However, the complexity of epistasis makes it hard to detect. From a
computational standpoint, searching all pairwise interactions in a dense marker panel is a daunting task. From a
statistical standpoint, appropriately accounting for multiple-testing corrections can make this nearly impossible.
Here, we describe a crossing scheme that can be used to develop Epistasis M apping Populations (EMPs), which
leverage search space reduction to powerfully detect epistasis. Our strategy employs near isogenic lines (NILs)
crossed in a simplified half-diallel mating scheme and backcrossed to the recurrent parent. Ultimately, a
collection of triplets can be formed that allows the straightforward evaluation of whether or not introgressions in
the founding NILs interact epistatically. The efficacy of this approach to detect epistasis was evaluated using
both simulations and a field trial. We simulated an EM P based on B73 and M o17 and compared its power to
detect epistasis to that observed in the commonly -studied Intermated B73 x M o17 (IBM ) population. Results
from field trialing in the summer of 2017 using two replications in two locations suggest that epistasis may be
widespread for several maize traits, including days to anthesis, days to silking, plant height, ear height, and ear
number, but barely impact additional traits including node number. Our analysis using simulated and real maize
EM P populations demonstrates that this approach can be powerful for detecting epistasis in maize.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
143
P158
A RNA-Seq atlas on the founder lines of the MAGIC population “BALANCE”, a
supplementary tool for gene discovery
(submitted by Clement Buet <clement.buet@biogemma.com>)
Full Author List: Maillard, Morgan1 ; Bosio, Mickael1 ; Leveugle, Magalie1; Duborjal, Herve1; Lopez, Jeremy 1; Doridant,
Ingrid1 ; Lafarge, Stephane1 ; Praud, Sebastien1
1
BIOGEMMA, Centre de Recherche, Route d'Ennezat, Chappes 63720, France
LD mapping in the BALANCE panel (derived from the BALANCE population) offers a sufficient resolution to reduce
traits associated genomic regions to several putative causal genes. Access to expression data is an additional step to
understand which gene(s) could explain phenotypic variations. In our strategy to aggregate complementary layers of
information around our BALANCE panel, a significant sampling experiment was conducted in greenhouse on the
founder lines in order to answer several questions: Are genes differentially expressed among founder lines, tissues or
developmental stages? Is gene expression affected by an abiotic stress? Can we detect splicing variants or PAV? Eight
hundred plants from testcross progenies were grown into 2 water regimes. More than 1000 samples were collected at 6
developmental stages in 3 different tissues (leaf, silk, kernels) under well-watered and water deficit situation. T o date,
transcripts of 93 leaves samples, collected at 0/5/15 days after anthesis in optimal and stress conditions, were
sequenced and analyzed. After raw data processing (read normalization and alignment on B73 V2 sequence), 23 749
genes were considered as expressed among which 5 253 were differentially expressed. Clustering of leaf samples
results shows an obvious separation between well-watered and water deficit samples. A weighted gene co-expression
network analysis (WGCNA) was used to identify highly co -expressed genes involved in drought -stress responses.
Gene-ontology enrichment, differentially expressed genes mapping and cross-network comparison (with Arabidopsis
and Maize co-expression networks from literature) were then performed to select a stress related module of genes. A
list of 351 candidate genes with high connectivity parameter (hub genes) were selected for further evaluation,
especially by LD mapping.
P159
Agronomic trials characterization and clustering using water and nitrogen stress
indices simulated with a crop model
(submitted by Matthieu Bogard <m.bogard@arvalis.fr>)
Full Author List: Bogard, Matthieu1 ; Dubreuil, Pierre2 ; Bauland, Cyril3; Soenen, Baptiste1 ; Giauffret, Catherine4; Lorgeou,
Josiane1
1
Arvalis institut du végétal; 3-5 rue Joseph et Marie Hackin; Paris; France 75016
2
Biogemma; Centre de Recherche de Chappes; route d'Ennezat; Chappes; France 63720
3
INRA; Ferme de Moulon, Gif-sur-Yvette; France 91190
4
INRA; Chaussée Brunehaut, Estrées-Mons; France 80200
Evaluation of cultivars performances, either during the breeding process or the post-registration phase, are largely
based on multi-environment trials (MET) consisting in testing genetic material over a broad range of genotype x
management x environment (location and year). Analysis of these data allows estimating the average performances of
cultivars or lines across different agroclimatic scenarios. T hese MET s are also commonly used in plant genetics
research to identify quantitative trait loci (QT L) involved in plant performances. A significant part of the phenotypic
variation explained by those QT L comes from QT L×E interactions which often involve different responses of
genotypes to biotic or abiotic stresses. Despite some of the environmental factors can be controlled in a field trial with
proper crop management options (sowing date, fertilization, irrigation), a large number of other factors are out of
control (climatic conditions) and the chosen management options may sometimes fail. T herefore, it is often difficult to
determine what really happened in terms of the dynamics of the limiting factors that occurred in a trial. Here, we
present the a posteriori characterization of the MET carried out on a dent panel in the Amaizing project. T his panel was
tested over eight locations in France during two years and under different crop managements (optimal condition, low
nitrogen, early sowing, rainfed). We used the CHN crop model to calculate high temperature, nitrogen and water stress
indicators based on on-site meteorological records, soil characteristics and crop management inf ormation. T his led to
revisit trial classification due to unexpected water or nitrogen stress. T rials were grouped based on the dynamics of
these stresses. QT L×E interactions within groups are expected to be lower. T his may improve our understanding of the
QT L×E interactions and finally provide knowledge to breeders on specific adaptation QT L related to high temperature,
nitrogen and water stress tolerance.
Funding acknowledgement: Agence Nationale de la Recherche (ANR)
144
P160
AMAIZING, a project on Maize Integrative Genomics supported by the French
program “Investments for the Future”
(submitted by Alain Charcosset <alain.charcosset@inra.fr>)
Full Author List: Charcosset, Alain 1; Joets, Johann 1; Vitte, Clémentine1; Moreau, Laurence 1; Giauffret, Catherine 2;
Rogowsky, Peter 3; T ardieu, François4; Flament, Pascal5; Praud, Sébastien 6; Gaillard, Antoine7; Lorgeou, Josiane8;
Renard, Agathe9; Nodet, Claire9
1
INRA; UMR Génétique Quantitative et Evolution - Le Moulon; Ferme du Moulon, Gif-Sur-Yvette, F91190, France.
2
INRA; UMR Agroressources et Impacts environnementaux; 180 rue Pierre-Gilles de Gennes, Barenton-Bugny,
F02000, France.
3
INRA; UMR Reproduction et Développement des Plantes – ENS de Lyon; 46 Allée d'Italie; Lyon, F69364, France
4
INRA; UMR Écophysiologie des Plantes sous Stress environnementaux; 2 Place Viala; Montpellier, F34060, France
5
Limagrain Europe; rue Georges Gerschwin; Riom, F63204, France.
6
Biogemma; 8 Rue des Frères Lumière;Clermont -Ferrand, F63028, France.
7
Maïsadour Semences; BP. 27; Mont de Marsan, F40001, France.
8
Arvalis; Station Expérimentale; Boigneville, F91720, France.
9
INRA T Ransfert; 3 rue de Pondichéry, Paris, F75015, France
M aize is cultivated annually on 3 M ha in France (23 M ha in Europe). In addition to grain and silage for animal
feeding, France produces hybrid seed on 58 000 ha. The AM AIZING project (https://amaizing.fr/en/) was started
in 2011 with the support of the French National Research Agency (ANR) and will end in 2020. In view of
breeding next generations of varieties, it aims at increasing knowledge on maize (epi)genomic diversity, genetics
of adaptation to abiotic constraints (cold, drought, limited nitrogen supply) and heterosis, and to develop genetic
and (eco)physiological modelling.
The project groups 24 partners with complementary expertise: 15 public research laboratories at universities or
national research organizations, 7 seed companies, a biotechnology company, a technical institute and seed
certification organism. It is organized in 9 workpackages, led by the authors of this poster. The experimental
workpackages target (posters at M GC 2018 indicated):
- Characterization of maize genomic and epigenomic variation, its effect on gene expression and contribution to
European maize adaptation (WP3; P7, P29, P147, P254)
- Optimized genetic resources, genotyping and statistical approaches for GWAS mapping and genomic selection
(WP4; P176, P177, P185, P194, P197, P199)
- Genome-wide analysis of environmental adaptation (WP5), based on hybrid diversity panels evaluation for
proteomics (P191), metabolomics, platform phenotyping (P100, P103, P239), multi-location field trials
characterized for environmental data (P159),
- Functional validation and fine characterization of main loci detected for yield and adaptive traits (WP6, P239)
- M odelling and integrative approaches: environmental adaptation, ecophysiological modelling in view of genetic
gain analysis and prediction (WP7; P79, P100, P103)
- Application in breeding programs and variety evaluation (WP8).
These scientific workpackages are supported by transversal workpackages dedicated to management (WP1),
bioinformatics (WP2, see P232) and communication (WP9). Information on project structure and results can be
found at https://amaizing.fr/en/
Funding acknowledgement: INRA, ANR‐10‐ BTBR‐01 (Amaizing), France Agrimer
145
P161
Analyses of genetic variation ass ociated to deep planting resistance in maize
revealed genes controlling development, growth, and adaptation to soil conditions
(submitted by Jorge Nieto-Sotelo <jorge.nieto@ib.unam.mx>)
Full Author List: Nieto-Sotelo, Jorge1 ; Vázquez-Marcial, Leopoldo 1 ; Vallejo-Reyna, Miguel A. 2 ; Figueroa-Maya, Alejandra1;
Martínez-Nava, Alejandro1 ; Cruz, Alberto 1; Alonso, Raymundo1 ; Villa, Juan M. 1 ; Ávila, Alma X. 1; Rojas, Claudia I. 1 ;
Aguilar, Cristina1 ; Rangel, Luz M. 1 ; Zhang, Xuecai3; Sawers, Ruairidh 4 ; Cassab, Gladys I. 5
1
Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico 04510
2
Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Mexico City, Mexico 04010
3
Centro Internacional de Mejoramiento de Maíz y T rigo (CIMMYT), Apdo. Postal 6 -641, Mexico City, Mexico 06600
4
LANGEBIO Cinvestav, Irapuato, Gto., Mexico 36821
5
Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor., Mexico 62210
Crop adaptation to drought and high temperature depends not only on genetic and phenetic traits and their interaction
with the physical, chemical, and biological environments, but also to humans through their interaction with agricultural
management practices. Few studies have focused in understanding the extent at which selection by agricultural
management modifies the phenotype and genotype of crop populations and much less how all of these leads to stress
adaptation. T o better understand these interactions we studied deep planting resistance in inbred maize lines, hybrids,
and native landraces of Mexico. Deep planting is used in semiarid regions of the Mixteca Alta, T rans-Mexican
Volcanic Belt, and the US southwest to take advantage o f residual soil humidity. Analyses of a large panel of Mexican
landraces uncovered two developmental patterns that accounted for deep planting resistance: long mesocotyls without
plumular growth or short mesocotyls with rupture of the coleoptile by the plumule. We found a strong correlation
between growth and developmental patterns with planting depth (deep versus shallow) practiced by the donating
farmer, supporting the idea that deep planting selected in favor of long mesocotyls and against rupture of the coleoptile
by the plumule prior to seedling emergence. GWAS of mesocotyl length variation under deep planting revealed a
variety of transcription factors and small molecule transporters associated to photomorphogenesis and adaptation to soil
conditions below 20 cm depth. GWAS of plumular growth variation under deep planting identified transcription factors
involved in morphogenesis, cell differentiation, and regulation of growth, in addition to kinase receptors, metabolic
enzymes, and transporters. Some of these markers were validated by QT L, resequencing, and transcriptome analyses.
T hese molecular markers will be fundamental to understand the evolution of traits relevant to climate change
adaptation that were selected during domestication and/or improvement by traditional and sustainable agricultural
methods
Funding acknowledgement: CONACYT -Mexico, PAPIIT -UNAM-Mexico
P162
BALANCE, a powerful MAGIC population for the identification of genetic
determinants involved in the variation of traits of interest in maize
(submitted by Clément Buet <clement.buet@biogemma.com>)
Full Author List: Buet, Clement1; Dubreuil, Pierre1; Tixier, Marie-Helene1; Praud, Sebastien 1
1
BIOGEMMA, Centre de Recherche, Route d'Ennezat, Chappes 63720, France
LD mapping has become a method of choice to identify genomic regions involved in the variation of traits of interest in
various species. T o overcome the problem of genetic structure in association panel, BIOGEMMA has developed a
MAGIC population from 16 historical lines representative of the genetic diversity used for hybrid production in
temperate regions. T his MAGIC population was used to produce a panel of ~400 DH lines: the BALANCE panel. For
LD mapping, this panel has the advantages of a typical diversity panel (large genetic diversity, rather low LD) without
the main handicaps (strong genetic structure and heterogeneit y of parentage relatedness). Simulations of phenotypes
showed that the panel had enough power to detect QT Ls explaining 5% of the phenotypic variation of a quantitative
traits; that is 2 times higher than that in a panel of elite lines and slightly higher than that in a maize diversity panel. T o
reap all the benefits of this panel for gene discovery, BIOGEMMA capitalizes on many “omics” aspects, aggregating
complementary layers of information in an integrative strategy. For several years, the BALANCE panel has been
extensively phenotyped for agronomic traits under water deficit (more than 20 field trials). T he panel is also being
phenotyped with innovative tools (UAV, root phenotyping platforms) for physiological traits. Moreover, the 16 founder
lines were sequenced and several millions of SNPs were identified and imputed on the entire panel. Finally, a
transcriptomic experiment was conducted on the founder lines (more than 1000 samples) to identify genes differentially
expressed under well-watered and water deficit situation. T his experiment provided candidate genes and enabled the
development of a gene atlas. Phenotypical, transcriptomic and genomic aspects are detailed in three different posters.
146
P163
Changes in carotenoid and tocopherol content in maize grain during cold storage
(submitted by Violeta Andjelkovic <avioleta@mrizp.rs>)
Full Author List: Andjelkovic, Violeta1; Mesarovic, Jelena1; Kravic, Natalija1 ; Babic, Vojka1; Mladenovic Drinic, Snezana 1
1
Maize Research Institute Zemun Polje, Slobodana Bajica 1, 11185 Belgrade, Serbia
Carotenoids are yellow, orange, or red plant pigments, the second most abundant pigment in nature. T hey are found in
most plant organs and tissues, although are not visible in green tissues, due to presence of chlorophylls. In dormant
grains, an non-photosynthetic tissue, carotenoids are located in plastids, improving integrity of membranes, preventing
degradation of nutrients, and protecting against free radicals during seed aging. T hey comprehend two chemicaly
similar groups of carotene and xanthophyllus. Lutein and zeaxantin are the most abundant carotenoids in maize,
followed by smaller amounts of ß-carotene. T he aim of present work is comparison of five maize landraces differing in
carotenoids and tocopherols content in grain, after cold storage in gene bank, for 5, and 30 years, as well as in samples
after their field regeneration. ß-carotene content in the oldest samples decreased in range of 81.57 -91.86% compared to
newly regenerated samples, while lutein+zeaxantin content reduction was in range of 66.66 -83.28%. Considering
tocopherol content, the greatest lowering was evident for α-tocopherol (52.9%), folowed by 37.23% decrease in ß+γ
content. T he smallest changes were in δ-tocopherol content of the oldest seeds, but five-years old samples had smaller
content in newelly regenerated seeds. T he greatest decrease of about 5 0% was evident after five years of cold storage in
carotenoid content, followed by slowlier reduction with seed ageing. T he similar trend was observed for tocopherol
content. Carotenoids of heterotrophic organs and seeds are with larger diversity compared to those involved in
photosynthesis, and are less investigated. T heir protective function and decelerating againg, together with increased
importance in biofortification breeding programs, gave higher importance to maize landraces stored in genebank,
towards achivement of target nutritional content in maize grain.
Funding acknowledgement: Ministry of Education, Science and T echnological Development of the Republic of Serbia
(T R-31068)
P164
Co-regulation of ZCN8 and ZCN12 underlies Maize flowering variability
(submitted by Lucio Conti <lucio.conti@unimi.it>)
Full Author List: Castelletti, Sara 1 ; Coupel Ledru, Aude2 ; T onelli, Chiara1 ; Tardieu, François2 ; Welcker, Claude2 ; Conti,
Lucio 1
1
Dipartimento di Bioscienze, Universita' degli studi di Milano
2
Laboratoire d'écophysiologie des Plantes sous Stress Environnementaux, INRA Montpellier
When to flower is a critical decision affecting maize productivity for its connection to the different local cropping
environments. Still very little is known about the mechanisms regulating flowering time in maize and how their genetic
variability accounts for the different phenology observed. T he florigen genes, encoding a systemic flowering signal, are
critical promoters of the floral transition. We will present expression and functional data supporting the contribution of
two maize florigen genes - ZCN8 and 12 - in the maize flowering time diversity. From a panel of 320 temperate maize
lines grown in a phenotyping greenhouse we could produce quantitative, tissue-specific and temporal information of
different florigen genes expression which could be related to the flowering phenology. Our results demonstrate a robust
negative correlation between ZCN8 transcript levels and time to flowering. Moreover, variability in ZCN8 expression
can be confidently related to flowering time under field conditions. ZCN8 eQT Ls regions overlap with flowering time
QT Ls detected under both greenhouse and field conditions, suggesting that differences in ZCN8 levels contribute to
modulate flowering.
Our dataset offers opportunities to evaluate the role of other ZCN8 -like genes to flowering. Differences in the
accumulation of ZCN12 are determined by a major effect eQT L, mapping in the first exon of ZCN12 itself. Molecular
markers allowed us to distinguish two ZCN12 allelic variants, one of which transcriptionally active, and whose
accumulation is negatively correlated with flowering time. Strikingly, expression of this allele version across our lines
closely follows that of ZCN8, indicating a common regulatory mechanism. Modelling studies support the existence of a
two tiers florigen system in maize, whereby accumulation of ZCN8 promotes the activation of ZCN12. Our data
suggest that different combinations of ZCN8 and ZCN12 expression underpin developmental variability which could
enable further flexibility of maize cultivation to different environments.
Gene / Gene Models described: ZCN8 ZCN12; GRMZM2G179264 GRMZM2G103666
Funding acknowledgement: Ceres initiative of Fondazione Cariplo and Agropolis Fondation
147
P165
Computer-vision into the biology of fungal-leaf interactions in maize
(submitted by Randall Wisser <rjw@udel.edu>)
Full Author List: Wisser, Randall1; Saponaro, Philip2 ; Treible, Wayne2; Kolagunda, Abhishek2 ; Chaya, Timothy1 3 ; Yang,
Qin 4 ; Wiesner-Hanks, Tyr 5; Balint-Kurti, Peter 4 6; Caplan, Jeffrey1 2 7 ; Holland, James6 8; Kambhamettu, Chandra2; Lauter,
Nick 9 10 ; Nelson, Rebecca5
1
Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA 19716
2
Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA 19716
3
Department of Biological Sciences; University of Delaware; Newark, DE, USA 19716
4
Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA 27695
5
School of Integrative Plant Science, Cornell University, Ithaca, NY, USA, 14853
6
Plant Sciences Research Unit, USDA-ARS; Raleigh, NC, USA 27695
7
Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA 19711
8
Department of Crop Science; North Carolina State University; Raleigh, NC, USA 27695
9
Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA 50011
10
Interdepartmental Genetics Graduate Program; Iowa State University; Ames, IA, USA 50011
Quantitative disease resistance (QDR) is a sustainable solution for disease management in crop production systems, but
the biology of QDR is only beginning to be understood. Using whole plant, field-scale studies and multiple genetic
methods, our team has identified genes and elucidated the molecular genetic basis of QDR to fungal pathogens of
maize, including Cochliobolus heterostrophus and Setosphaeria turcica. Highlights of these genetic studies will be
presented. T o understand QDR at the tissue-level, a semi-automated 3D macroscopic microscopy platform was
developed and used to microscopically image multi-millimeter areas of pathogen infected leaf tissue. Using this image
data, the U-Net convolutional neural network was adapted to computationally segment cells of the host leaf and
mycelial networks of the pathogen. T his process generates comp lex, cell-level 3D morphology data, which we are
currently analyzing (and figuring out suitable methods for analysis). Specifically, we are extracting high level plant pathogen information such as features of the neighborhood of host cells and stomata surr ounding fungal penetration
events, as well as fungal infection network sizes and shapes. Macroscopic microscopy was also complemented with
higher-resolution images captured by multi-photon confocal microscopy in order to distinguish specific aspects of
fungal-leaf interactions. We find that infections by Cochliobolus heterostrophus have a similar depth of penetration
into the leaf tissue of maize lines with contrasting levels of resistance, but the infection networks are differentiated by
their spread within the subepidermal space. T he two pathogens show very different infection strategies that produce
macroscopically visible lesions which are either congruent or incongruent with the localization of the pathogen.
T ogether, our work is providing unique insight into fungal pathogenesis on maize while contributing to the
advancement of cellular phenomics in plants. T he latest results from this work will be presented.
Funding acknowledgement: National Science Foundation (NSF)
P166
Construction of maize grain moisture content related near-isogenic lines for
developing SNP molecular marker
(submitted by Junjie Zou <zoujunjie@caas.cn>)
Full Author List: Zou, Junjie 1 ; Xu, Miaoyun1 ; Wang, Lei1
1
Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese
Academy of Agricultural Sciences, Beijing 100081, China
Maize is an important food crop, and is also used as an ideal material for plant genetics and functional genome
research. With the completion of the maize genome sequence, studies on maize functional genomics become more and
more widely. T he near-isogenic lines (NILs) are the important materials for the construction of molecular genetic maps,
QT L location and molecular markers-assisted breeding. Maize species Zhengdan 958 (Zheng 58 x Chang 7 -2) and
Xianyu 335 (PH6WC x PH4CV) are widely cultivated in China, showing differences on growth period, plant
architecture, grain filling rate, grain dehydration rate, etc. Here, we create Zheng 58 NILs and Chang 7-2 NILs by
introducing PH6WC and PH4CV background. T hese NILs were obtained by consecutive selective backcrosses and
then selfing. T here were highly significant differences in growth period, flowering date, plant height, grain filling rate,
grain dehydration rate, etc among these 600 NILs. Genotypes of these NILs were identified by using maize 55 K SNP
array. And genome wide association study (GWAS) was used to detect genetic factors for governing grain moisture
content (GMC), grain filling rate (GFR) and grain drying rate (GDR). And SNP molecular markers will be developed
for molecular marker-assisted selection breeding.
148
P167
Creation of subgroup specific haplotype blocks and libraries
(submitted by Torsten Pook <torsten.pook@uni-goettingen.de>)
Full Author List: Pook, T orsten1; Schlather, Martin 2; de los Campos, Gustavo 3; Schön, Chris-Carolin 4; Simianer,
Henner 1
1
University of Goettingen, Department of Animal Sciences, Center for Integrated Breeding Research, Animal
Breeding and Genetics Group; Germany; D-37075 Goettingen
2
University of Mannheim, Stochastic and Its Applications Group; Germany; D-68131 Mannheim
3
Michigan State University, Department of Epidemiology and Biostatistics; USA; 48824 East Lansing
4
T echnical University of Munich, Plant Breeding, T UM School of Life Science Weihenstephan; D -85354 Freising;
Germany
Over the years defining haplotype blocks has been shown to be a very useful tool in genomic approaches. Fields
of application range from the detection for regions under positive selection to all sorts of statistical application
that make use of variable reduction. In contrast to traditional methods we do not use a population-wide measure
(linkage disequilibrium, LD) but instead screen subgroups of haplotypes for common variants and thereby focus
on linkage. We define a haplotype block as a sequence of alleles and only those haplotypes with a similar
sequence are considered to be part of a block. Because of this, blocks can overlap and not every position has to
be part of a block. Out of these haplotype blocks we construct a haplotype library representing a large proportion
of genetic variability with a limited number of blocks. Depending on the application, different optimization goals
of the haplotype library (e.g., the identification of shared segments between different breeds) are possible. Our
methods are implemented in the so far unpublished R-package HaploBlocker. By applying this method we
reduce a dataset comprising of 313 DH-lines in a European Landrace (75k SNPs, chromosome 1) to 370
haplotype blocks with an average length of 2’015 SNPs that represent 93.7% of the dataset. In contrast blocks
derived via HaploView have an average length of 89 SNPs – this difference becomes even more severe when
comparing the block length of a dataset with two landraces (1’705 SNPs vs. 24 SNPs) since LD is heavily
reduced in more diverse panels whereas linkage can still be detected similarly. By using haplotype blocks instead
of SNPs, local epistasis interactions can be modelled naturally and the typical p>>n-problem in genetic datasets
can be reduced, which enables the application of a wide variety of new methods for further analysis.
Funding acknowledgement: Federal M inistry of Education and Research (BM BF; project: M AZE;
http://www.europeanmaize.net/)
149
P168
Deployment of a novel phenotypic platform based on biomechanical engineering
principles provides novel insights into stalk lodging in maize
(submitted by Arlyn Ackerman <arlyna@clemson.edu>)
Full Author List: Ackerman, Arlyn 1; Sekhon, Rajandeep 1; Daniel, Robertson 2; Douglas, Cook 3
Clemson University, Clemson, SC, USA 29634
2
University of Idaho, Moscow, ID, USA 83844
3
Brigham Young University, Provo, UT , USA 84602
1
Stalk lodging in maize poses an important production challenge worldwide. While these losses are preventable
through genetic improvement of stalk lodging resistance (SLR), such efforts have been impeded by the lack of a
robust phenotyping method. Traditionally used testing methods like lodging incidence count and rind penetrance
resistance are prone to inconsistent testing parameters, heavy environmental influence, and one-dimensional
analysis. M any intermediate phenotypes contribute to SLR that are not accounted for in the currently available
phenotyping methods. We have employed a novel phenotyping platform, developed with extensive insight from
structural engineering that evaluates the ability of an individual maize stalk to bend before failure (bending
strength). Additionally, we identified key intermediate traits putatively underlying SLR and recorded these traits
to obtain insights into their relative impact on SLR. Testing materials included a diversity panel, divergently
selected high and low rind penetrance resistance (RPR) populations, and hybrids from the G2F initiative,
collectively spanning over 500 genotypes. Deployment of the new platform was successful in providing a variety
of both accurate and consistent measurements for a multitude of intermediate traits related to SLR. This data
revealed interesting relationships among the intermediate traits and provided novel insights into the structural
and anatomical features contributing to SLR. Importantly, we show that simultaneous measurements of multiple
structural features by the new platform provide a comprehensive picture of SLR compared to traditional methods
like RPR. GWAS analysis on the diversity panel identified serval novel associations for bending strength and the
intermediate traits. Importantly, many of the associations were shared between multiple traits demonstrating
shared genetic regulation of these traits. We demonstrate that the platform is very effective in providing a reliable
estimation of SLR both for phenotypic selection and for generating mechanistic insights into the genetic
regulation of SLR in maize.
Funding acknowledgement: United States Department of Agriculture (USDA)
P169
Design Thinking and Data Mining in Plant Breeding
(submitted by Jianming Yu <jmyu@iastate.edu>)
Full Author List: Yu, Jianming1; Guo, T ingting1; Li, Xianran 1
Iowa State University, Department of Agronomy, Ames, Iowa, USA, 50011
1
Plant breeding is enhanced by integrating different scientific innovations and enabling tools. One major
challenge that comes with the wide adoption of genomics and biotechnologies is to rethink and redesign the
breeding programs at different stages and different scales. The essence of this new wave of breeding
methodology research is to effectively identify and exploit genotype to phenotype relationship so that desirable
cultivars are continuously and efficiently developed. Design thinking is a human-centered mindset and problemsolving methodology that is being widely adopted to address complex problems. Data mining, successful in
many other areas, provides technical solutions to address this question, particularly when findings are integrated
into the designing process. Enhanced by design thinking and data mining, genomics-assisted prediction may
reshape the plant breeding pipeline by enabling the efficient exploration of the enormous inference space of
genetic combinations, environment combinations, and performance dynamics. We propose three essential
components to streamline the breeding in the post-genomic era: better product creation (BPC), knowledge
discovery from data (KDD), and optimal program design (OPD).
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA), Department of Energy (DOE)
150
P170
Development of a new high throughput 105K presence/absence variation genotyping
array for quantitative genetic studies
(submitted by Clement Mabire <clement.mabire@inra.fr>)
Full Author List: Mabire, Clément2; Duarte, Jorge1; Darracq, Aude1 ; Piranni, Ali3 ; Rimbert, Hélène1 ; Madur, Delphine2; Vitte,
Clémentine2; Rivière, Nathalie1; Combes, Valérie2; Joets, Johann 2; Pichon, Jean-Philippe1 ; Nicolas, Stéphane2
1
Biogemma - Upstream Genomics Group, route d’Ennezat, CS 90126, Chappes 63720, France
2
Génétique Quantitative et Evolution - Le Moulon, INRA - Université Paris-Sud - CNRS - AgroParisTech, Ferme du Moulon,
F-91190, Gif-sur-Yvette, France
3
Affymetrix - 3420 Central Expy, Santa Clara, CA, 95051, USA
Structural variation are pervasive in plants. In the last decades, thousands of copy number variations (CNV) have
been discovered among the maize genome, notably Presence/absence variation (PAV) of some genomic
sequences.
We developed a new genotyping array to genotype PAV in a large set of individuals in order to explore their
contribution to genetic diversity and trait variation in maize.
First we discovered 120,178 PAV from the resequencing data of 3 inbred lines (F2, C103, PH207) compared to
the B73 reference genome. Second, we designed 26 million probes in order to be able to genotype PAV
breakpoints as well as PAV internal sequence. Among them 662,772 were selected and used to design an
Affymetrix Axiom array. These probes make it possible to genotype 105,927 PAV sequences from 35bp to
127kbp long. Among these PAV, 25% are deletions and 75% are insertions regarding to the reference genome of
B73. We genotyped these PAV on a collection of 480 lines representative of maize genetic diversity. A new
Affymetrix pipeline was developed to call presence or absence of a genomic sequence from fluorescence
intensity and contrast between probes. We evaluated the quality of the calling by comparing the expected allele
from resequencing data of the 4 lines used for PAV discovery to the observed one from the array. We showed
that 72% of the probes gave consistent results. PAV genotyping was used to analyze the genetic diversity within
a core panel of 20 inbred lines. We showed that PAV well separated these lines according to their genetic group
origin.
These results illustrate the ability of our high throughput genotyping PAV array to genotype accurately a large
number of PAV and their breakpoints on a large and diverse set of maize inbred lines.
Funding acknowledgement: French National Research Agency, Amaizing Project, CNV-M aize Project
P171
Development of late temperate maternal haploid inducers
(submitted by Rahime Cengiz <rahime.cengiz@tarim.gov.tr>)
Full Author List: Cengiz, Rahime1 ; Esmeray, Mesut1
Maize Research Institute, Breeding and Genetics Department, Arifiye, Sakarya, 54580, Turkey
1
In recent years, in vivo doubled haploid technique has been widely used on advanced maize breeding programs.
Obtaining doubled haploids by in vivo maternal haploid technique shorten time of breeding and increase the
efficiency of maize breeding. According to literatures, inducer lines are not available the large number in the
world. In our country, maize breeders in both public and p rivate sectors have to buy inducer lines from abroad
for implementing in vivo maternal haploid technique. M ost of inducer lines were used in in vivo haploid
technique have adapted of the temperate zone. These inducer lines are earlier (FAO 400-450), short plant height,
poor pollen yield than our maize materials and in terms of their other morphological characteristics are weaker.
The breeding programs have been initiated in order to transfer from early inducer lines haploid induction features
and R1-nj marker to local inbred maize lines on M aize Research Institute (M RI) in 2011. Crosses were made
between three local inbred lines from M RI as female parents and inducer lines RWS, RWK-76 and inducer
hybrid RWSxRWK-76 as pollinators. F2 populations were obtained in consequence of selected criterias such as
anthocyanin coloration, tassel length, branch number, plant height, days to flowering and embryo-endosperm
colorfulness. F3 generations were planted by ear-to-row and were selected according to late flowering, good
plant vigor, high pollen yield. At the same time, every generation were crossed with liguleless line as female and
were determined haploid induction rate of candidate inducer lines on F3-F7. The morphological and genetic
similarity was examined between the candidate inducer lines and RWS, RWK-76 donor lines.
Funding acknowledgement: National Science Foundation (NSF), The Scientific and Technological Research
Council of Turkey
151
P172
Developmental and morphological changes associated to flowering time shifts
produced during divergent selection experiments in maize : developmental
transitions and architecture
(submitted by Adrienne Ressayre <adrienne.ressayre@u-psud.fr>)
Full Author List: Ressayre, Adrienne 1; Marchadier, Elodie1; Tenaillon, Maud1 ; Dillmann, Christine1
1
Génétique Quantitative et Evolution – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay ;
Gif-sur-Yvette, France, 91190
An original plant material resulting from two Divergent Selection Experiments (DSEs) for flowering time of maize was
developped over the last 20 years. Within two maize inbred lines, Early- and Late-flowering populations, subsequently
structured into families within populations were formed. Comparisons between Early and Late populations or between
Early or Late families within each DSE allow to study the effects of flowering time shif ts in the same genetic
background.
A strong response to selection was observed over the 20 generations and results indicate that this response is due to a
variety of changes affecting different aspects of the life cycle. T o better understand these changes, we set up field
experiments to describe plant growth and development for different families issued from the DSEs. We observed that
differences between Early and Late progenitors concerned timing of transitions, phyllochron, and the delay between the
end of leaf emergence and blooming, while organs’ growth rates were much less variable. Marked differences in
developmental timings were associated with large morphological changes. Changes in the duration of developmental
phases impact both plant architecture (leaf number and shape) and the duration of organ growth, and can explain
changes in morphology like leaf length.
When comparing Early populations together, or Late populations together, we found that a delay in flowering time can
result from changes eit her in the length of juvenile phase, the time of floral transition or the length of the reproductive
phase. Phenotypic convergence for flowering time was therefore achieved through different developmental routes.
Funding acknowledgement: INRA, CNRS, Labex BASC
P173
Developmental and morphological changes associated to flowering time shifts
produced during divergent selection experiments in maize : phyllochron
(submitted by Christine Dillmann <christine.dillmann@inra.fr>)
Full Author List: Marchadier, Elodie 1; Ressayre, Adrienne1; Tenaillon, Maud1 ; Dillmann, Christine1
Génétique Quantitative et Evolution – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay ;
Gif-sur-Yvette, France, 91190
1
An original plant material resulting from two Divergent Selection Experiments (DSEs) for flowering time of maize was
developped over the last 20 years. Within two maize inbred lines, Early- and Late-flowering populations, subsequently
structured into families within populations were formed. Comparisons between Early and Late populations or between
Early or Late families within each DSE allow to study the effects of flowering time shifts in the same genetic
background.
A strong response to selection was observed over the 20 generations and results indicate that this response is due to a
variety of changes affecting different aspects of the life cycle. T o better understand these changes, we set up field
experiments to describe plant growth and development for different families issued from the DSEs (phyllochron,
growth rates, plant architecture, developmental transitions). We observed that differences between Early and Late
progenitors concern timing of transitions, phyllochron, and the delay between the end of leaf emergence and blooming,
while organs’ growth rates were much less variable. Comparisons of the different families suggest tha t phenotypic
convergence for flowering time between Early or between Late progenitors is achieved through different
developmental routes.
T his poster focuses on changes observed in leaf emergence rates (phyllochron) for Early and Late genotypes. We found
that average values of leaf or collar emergence rates exhibited few differences between genotypes, but strong year
effects. Observed flowering time shifts were therefore not associated with major changes in the phyllochron. Analysis
of temporal variation of departures to average values throughout the season revealed the same non linear patterns for all
genotypes, indicating that phyllochron was not constant through time. We discuss the role of different environmental
factors in the temporal changes of plant growth rates.
Funding acknowledgement: INRA, CNRS, Labex BASC
152
P174
Dissecting the genetics of cold tolerance in maize
(submitted by Pedro Revilla <previlla@mbg.csic.es>)
Full Author List: Revilla, Pedro 1; Alvarez-Iglesias, Lorena1; Yi, Qiang1; Romay, Maria Cinta 2; Ordas, Bernardo 1;
Malvar, Rosa Ana1
1
Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain
2
Institute for Genomic Diversity, Cornell University, Ithaca, NY14853, USA.
Cold tolerance is a complex trait that limits adaptation of maize in temperate areas. The available literature
shows that cold tolerance is regulated by large number of QTLs with small effects and weak consistence across
genotypes. However, previous studies have involved a limited number of genotypes with narrow genetic
diversity, and scarce genetic recombination mapping populations. We investigated the genetics underlying cold
tolerance in a multi-parent advanced generation inter-cross (M AGIC) population genotyped using genotyping by
sequencing (GBS) with near one million SNPs. This M AGIC population consisted on recombinant inbred lines
(RILs) released from a synthetic population (EPS21) obtained from Spanish, Italian, and French flints, and two
non-Reid Corn Belt inbred lines. A set of 406 RILs was evaluated in a growth chamber under cold and control
conditions, as well as in the field at early and late sowing dates. Our results showed no evidence for any single
large-effect quantitative trait loci (QTLs); however, a region on chromosome 2 had a dense concentration of
significant QTLs for fluorescence (Fv/Fm) that were consistent in growth chamber and early field sowing.
Besides, we identified numerous additional small-effect QTLs for cold tolerance-related traits in growth chamber
(64 QTLs) and early field sowing (61 QTLs). The large number of markers involved, the small effects explained
by each QTL, and the difficulties on collecting phenotypic data, encourage the implementation of genomic
selection programs to improve cold tolerance in maize.
P175
Dissecting the role of lncRNA during maze domestication
(submitted by Yaoyao Wu <yyw_cau@163.com>)
Full Author List: Wu, Yaoyao 1; Wang, Xufeng1; Chen, Qiuyue1; T ian, Feng1
National Maize Improvement Center, China Agricultural University, Beijing, China 100193
1
Long non-coding RNA (lncRNA) plays important roles in various biological processes and contributes to plant
adaptation. To dissect the role of lncRNA during maize domestication, we analyzed the genome-wide cis and
trans regulatory difference between maize and teosinte using RNA-seq data of F1 hybrids and parents for leaf,
ear, stem tissues. We identified 1055, 1153 and 1156 cis-regulated lncRNAs, and 1365, 1753 and 1030 transregulated lncRNAs for leaf, ear and seed tissues, respectively. For more than 70% of cis-regulated lncRNAs,
maize allele is more highly expressed than teosinte allele, suggesting domestication more frequently favors up regulated lncRNAs. Furthermore, we found that cis-regulated lncRNAs tended to be neighbor of genes showing
expression divergence between maize and teosinte especially for genes under selection. These results indicated
that the regulatory differences in lncRNA might play an important role in driving the transcriptome divergence
during maize domestication.
Funding acknowledgement: the National Natural Science Foundation of China
153
P176
Diversity analysis within a collection of 1191 flint maize inbred lines using
genotyping-by-sequencing
(submitted by Brigitte Gouesnard <brigitte.gouesnard@inra.fr>)
Full Author List: Gouesnard, Brigitte 1; Negro, Sandra2; Laffray, Amélie2; Glaubitz, Jeff 3; Melchinger, Albrecht 4;
Revilla, Pedro 5; Moreno-Gonzalez, Jesus6; Madur, Delphine2; Combes, Valérie2; T ollon-Cordet, Christine 1; Laborde,
Jacques7; Kermarrec, Dominique 8; Bauland, Cyril2; Moreau, Laurence 2; Charcosset, Alain 2; Nicolas, Stéphane2
1
AGAP, INRA, Montpellier, France
2
Génétique Quantitative et Évolution - le Moulon, INRA, Gif-sur-Yvette, France
3
Buckler Lab for maize Genetics and Diversity, Cornell University, Ithaca, USA
4
Seed Science, and Population Genetics, University of Hohenheim, Stuttgart, Germany
5
Misión Biológica de Galicia, CSIC, Pontevedra, Spain
6
Mabegondo Agricultural Research Centre, CIAM-INGACAL, A Coruña, Spain
7
Unité Expérimentale du Maïs, INRA, St Martin de Hinx, France
8
Unité Expérimentale Ressources Génétiques Végétales en Conditions Océaniques (UERGCO), INRA, Ploudaniel,
France
Genotyping-by-sequencing (GBS) is a highly cost-effective procedure that permits the analysis of large
collections of inbred lines. We used it to characterize diversity in 1191 maize flint inbred lines from the INRA
collection, the European Cornfed-Flint association panel, and flint lines recently derived from landraces. We
analyzed the properties of GBS data obtained with different imputation met hods, by comparison with a 50K SNP
array. We identified 7 ancestral groups within the Flint collection (five typically flint: Northern Flint, Italy,
Pyrenees-Galicia, Argentina, Lacaune, and also Dent and Pop corn) that are in agreement with breeding
knowledge. This analysis highlighted that many lines are issued from crosses between different flint ancestral
groups (admixture). Approximately 200 lines also appear to be issued from crosses with dent germplasm aiming
at the improvement of flint germplasm. We performed association studies on different agronomic traits, revealing
SNPs associated with cob color, kernel color, and male flowering time variation. We analyzed the relationship
between the haplotype diversity and the trait variation at some strong association peaks.
Funding acknowledgement: French National Research Agency (Amaizing, ANR-10-BTBR-03)
154
P177
Diversity of maize landraces from south-west of France: origin and morphological
differentiation analyzes
(submitted by Yacine Diaw <yacine.diaw@supagro.fr>)
Full Author List: Diaw, Yacine 1 2 ; Tollon, Christine3; Zanetto, Anne3; Charcosset, Alain4 ; David, Jacques1 ; Ronfort, Joëlle3;
Gouesnard, Brigitte3
1
Montpellier SupAgro, UMR AGAP, 2 place Viala, 34060 Montpellier, France
2
ISRA du Sénégal
3
INRA, UMR AGAP, 2 place Viala, 34060 Montpellier, France
4
INRA, UMR Génétique quantitative et évolution, Ferme du Moulon, 91190 Gif/Yvette, France
In south-west of France, maize landraces had evolved under environmental condition and human management since
17th century and until the arrival of the hybrids in1960s. In the sixties, these landraces have been conserved ex situ at
the maize biological resource center (INRA, Mauguio, France).
Previous genetic studies of a sample of this collection allowed identifying a distinct genetic group named PyreneesGalicia. T his group has been hypothesized to come from an hybridization between the Northern Flint group and the
Caribbean group
In this study, we analysed a broader sample of the INRA collection in order to determine their genetic structure and to
describe their morphological diversity.
Firstly, we analysed genetic diversity of 194 maize landraces from south -west of France with the 50K SNPs array and
using a bulk DNA sample of 15 plants. A non-supervised admixture analysis was performed by adding 148 American
and European landraces. T his analysis shown that there were 8 genetic groups. In fact, two separate genetic groups
were identified in South-west of France, one in the West ern part and one in the Eastern part.
Secondly, we assessed morphological differentiation between the two genetic groups found in south -west of France,
using a principal component analysis and an analysis of variance on 15 traits. Landraces located in West part of southwestern France are earlier with bigger kernels and ears with a lower number of rows than landraces located in East part.
Finally, we performed a principal coordinate analysis (PCoA) on 194 maize landraces from south -west of France. We
showed that landraces were distributed continuously along the first component of PCoA analysis. T his component was
correlated with geographical coordinates of the landrace collection sites, highlighting a longitudinal gradient and a
latitudinal gradient.
Funding acknowledgement: ANR France : Amaizing, WAAPP (ISRA Senegal)
P178
Does subspecific variation correspond to genetic or cytotypic variation in the
widespread taxon Phlox speciosa (Polemoniaceae)?
(submitted by Estefania Aguilar-Gutierrez <Estefania55@mail.fresnostate.edu>)
Full Author List: Aguilar Gutierrez, Estefania 1; Waselkov, Katherine1
1
California State University, Fresno; Fresno, CA, 93740
Phlox speciosa, or showy phlox, ranges from the Sierra Nevada of California into the Coast and Cascade Ranges of the
Pacific Northwest (to British Columbia), and into the Rocky Mountains in Idaho and western Montana. It grows at low
to middle elevations (100-2400 m), in rocky, wooded slopes and sagebrush habitat, and is easily distinguishable from
congeneric taxa by its upright habit, showy flowers, and short length of the style relative to the stigmas. Several
subspecies and varieties were identified by previous taxonomists (originally Edgar Wherry in 1955), based on the
obvious morphological variation in the group, but this variation does not correspond well to geography, and the current
Flora of North America taxonomic treatment has suspended the recognition of subspecific taxa in P. speciosa pending
genetic and cytotypic investigation. We are exploring the genetic diversity and connectivity of 25 populations from
across the range of this species, to test the hypothesis that the observed patterns of morphological and ecological
differentiation between populations are due to genetic discontinuity rather than simply phenotypic plasticity. Field
sampling of leaf tissue (20 plants per population) was guided by our study of previously collected herbarium
specimens. T hus far, our flow cytometry results show little cytotypic variation in the species: out of 21 populations
sampled to date, all proved to be diploid (2n = 14) except one tetraploid population. We can conclude that the
phenotypic and habitat variability that P. speciosa exhibits is not due to ploidy -level differences leading to intraspecific
reproductive isolation. T his finding has provided the basis for our exploration of genetic connectivity between
populations using codominant genotyping data from seven microsatellite markers designed specifically for western
North American Phlox species. T his research will inform important evolutionary questions about species limits and
subspecific variation in the genus Phlox.
Funding acknowledgement: Maize Genetics Network Enhancement via T ravel (MaGNET )
155
P179
eQTL mapping and genome wide association study for maize leaf traits using
markers derived by RNA sequencing of two RIL populations
(submitted by Matteo Dell'Acqua <m.dellacqua@santannapisa.it>)
Full Author List: Miculan, Mara 1; Nelissen, Hilde2 3; Dell’Acqua, Matteo 1; Marroni, Fabio 4; Pè, Mario E 1; Inzè, Dirk2 3
Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
2
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
3
VIB Center for Plant Systems Biology, Ghent, Belgium
4
Institute of Applied Genomics (IGA), Udine, Italy
1
T he capacity to generate high throughput sequencing data on genetic plant materials revolutionized the characterization
of complex traits. Recently, the use of expression quantitative trait loci (eQT L) approach emerged as an effective tool
for identifying genomic regions affecting gene regulation. Concurrently, genome wide association studies (GWAS)
became a powerful tool to identify the genetic contribution to phenotypic outcomes. eQT L ana lysis combined with
GWAS may provide a detailed picture of the process by which genetic variants affect complex traits. In this study we
focus on 200 RILs derived from two maize populations: a B73xH99 cross and the multiparental MAGIC maize. We
analyzed RNAseq data produced in proliferative leaf tissues in each of the 200 RILs to derive a variant callset for
downstream analysis. T he bioinformatics pipeline for variants discovery in RNAseq data followed the GAT K best
practices. After a stringent filtering for marker quality, we obtained several hundred thousand genome-wide SNPs.
When compared to sparse molecular markers previously developed on the RIL populations, these SNPs proved solid in
describing the RILs genetic makeup. T he RILs were phenotyped for ten leaf traits describing the dynamics of seedling
growth. We integrate the genomic, transcriptomic and phenotypic information in eQT L and GWAS approaches to
identify candidate genes for early leaf traits in maize. A preliminary eQT L mapping identified more t han 30,000
significant cis and trans eQT L. When used in a GWAS approach, the RNA-derived SNPs reported highly significant
associations with the leaf traits. Linkage disequilibrium decay was used to group the several thousand marker -trait
associations in approximately 30 QT L currently under characterization. So far, only a limited number of studies have
integrated eQT L data and GWAS to investigated the plant growth mechanisms. Our approach will refine the
identification of candidate genes in QT L and allow to prioritize loci relevant for breeding for early vigor.
Funding acknowledgement: European Research Council (European Research Council grant agreement number
[339341-AMAIZE]11, Ghent University, Scuola Superiore Sant’Anna
P180
Evaluation of functional stay-green in maize inbred lines and their relationship with
agronomic traits
(submitted by Marlon Caicedo <mcaicedo@mbg.csic.es>)
Full Author List: Caicedo, Marlon1 ; Malvar, Rosa Ana1; Revilla, Pedro 1; Ordás, Bernardo 1
1
Misión Biológica de Galicia, Spanish National Research Council (CSIC), 36080 Apartado 28, Pontevedra, Spain.
T he time and rate of senescence in maize affects the duration of photosynthetic activity and the remobilization of
nutrients from leaves to grain which has an impact on biomass and grain yield. Various types of late senescence or
stay-green have been proposed which can be reduced t o two types: functional, when the photosynthesis is active while
the plant is green, and cosmetic, when photosynthesis is not working out in spite of the green color of the leaves. Little
information has been published about the types of stay-green in inbred lines of temperate maize. We evaluated the
functional stay-green of 197 lines developed in different public and private breeding programs. Many of the lines were
included in the study because they had visual stay-green according to personal information of breeders or information
found in the certification of the lines. Other lines were included because of their relevance in maize breeding, for
example B73, PH207, Mo17, etc. We found the reduction in chlorophyll content was always accompanied by a
decrease in photosynthetic rate, although, some lines retained small amounts of chlorophyll after losing its
photosynthetic activity. Therefore, we concluded that the predominant way of stay -green in inbred lines of temperate
maize is functional. T here was variat ion in the duration of photosynthetic activity between the inbred lines. Some lines
had active photosynthesis as late as 75 days after flowering, while many others did not. T he lines with late
photosynthesis had on average the highest grain yield and biomass yield, but also the highest grain filling duration and
the highest grain moisture. We conclude that the functional stay -green is favorable for grain yield, but at the cost of
increase the grain moisture.
Funding acknowledgement: Plan Nacional de I+D. Spain, Feder UE
156
P181
Exploring the genetic basis of cell wall traits upon contrasted water regimes in
maize
(submitted by Laetitia Virlouvet <laetitia.virlouvet@inra.fr>)
Full Author List: Virlouvet, Laetit ia1; Griveau, Yves1; Jacquemot, Marie-Pierre1; Beaubiat, Sébastion 1; Madur,
Delphine3; Falque, Matthieu3; Bauland, Cyril3; Combes, Valérie3; Sartre, Pascal2; Malavieille, Serge2; Baldy, Aurélie1;
Legay, Sylvain 1; El Hage, Fadi1; Cloarec, Gladys1; Moreau, Laurence3; Barrière, Yves4; Coursol, Sylvie1; Méchin,
Valérie1; Reymond, Matthieu1
1
Institut Jean-Pierre Bourgin, INRA, AgroParisT ech, CNRS, Université Paris-Saclay, RD10, F-78026 Versailles
Cedex, France
2
Unité expérimentale Diascope, INRA, Chemin de Mezouls, Domaine expérimental de Melgueil, 34130 Mauguio,
France
3
Génétique Quantitative et Évolution - Le Moulon, INRA, Université Paris Sud, CNRS, AgroParisT ech, Ferme du
Moulon, 91190 Gif-sur-Yvette, France
4
Unité de Génétique et d’Amélioration des Plant es Fourragères, INRA, le Chêne, route de Saintes,, F-86600 Lusignan,
France
Cell wall digestibility and composition are the major targets for improving both feeding value and industrial
valorizations (such as bioethanol) from lignocellulosic biomass. Biomass production should also reach expected
yields under environmental-friendly practices. It was brought back that the variations of the biomass quality and
composition are not only impacted by genetic, but also by environmental factors, such as water stress episodes.
To guide breeding of maize and other dedicated C4 species for biomass production, we evaluated a F271 x
Cm484 recombinant inbred population under non-irrigated and irrigated conditions during three consecutive
years near in M ontpellier (South of France). We quantified over 1,300 harvested stover samples using dedicated
near-infrared spectroscopy equations established with calibrated samples harvested under both water regime
conditions. We showed that biomass digestibility and composition varied between irrigated and non-irrigated
scenarios. Using a genotyping-by-sequencing approach, we then built a dense genetic map with 1,000 single
nucleotide polymorphism (SNP) markers and performed single-marker analyses to identify constitutive
quantitative trait loci (QTLs) across years and conditions, and responsive QTLs using the interaction effect
between the marker and the treatment. Overall, we identified 16 clusters of constitutive QTLs and 5 clusters of
responsive QTLs, of which only one did not co-localized with constitutive QTLs. These results showed that colocalization between traits were different depending on the QTLs, underlying different strategies for breeding.
Funding acknowledgement: Biomasse For the Future (ANR-11-BTBR-0006-BFF) funded by the French National
Research Agency under an Investment for the Future program (ANR-11-IDEX-0003-02); the LabEx Saclay Plant
Sciences-SPS (ANR-10-LABX-0040-SPS)
157
P182
Fine mapping of metabolite -QTLs for extracellular surface lipid accumulation on
maize silks
(submitted by Tes Posekany <posekany@iastate.edu>)
Full Author List: Posekany, Tes1 2 3 ; Hockemeyer, Katelyn 2; King, Kyle3 4; Loneman, Derek5 ; Hattery, Travis5; Lopez,
Miriam 2 3 4 ; Nikolau, Basil J1 6 ; Yandeau-Nelson, Marna D1 2 5; Lauter, Nick1 2 3 4
1
Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, Iowa 50011
2
Young Engineers and Scientists Program, Iowa State University, Ames, Iowa 50011
3
Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
4
USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, Iowa 50011
5
Department of Genetics, Development & Cell Biology, Iowa State University, Ames, Iowa 50011
6
Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011
Upon emergence from the husk leaves, maize silks are exposed to numerous environmental stresses (e.g., UV radiation,
insect damage, and desiccation). Like most other aerial plant surfaces, the maize silk has a cuticle infused with and
coated by extracellular surface lipids (SLs) that act as an environmental barrier. T he silk SL metabolome includes at
least 50 metabolites that are primarily linear hydrocarbons, fatty acids, and aldehydes ranging in chain lengths from 16
to 35 carbon atoms. T o identify the genomic loci controlling the biosynthesis of these metabolites, we performed
metabolite-quantitative trait locus (mQT L) mapping using the intermated B73xMo17 recombinant inbred line
(IBMRIL) population, which harbors considerable variation in the silk SL metabolome. Surface lipids were extracted
from emerged silks at three days post -silk emergence and subsequently identified and quantified using gas
chromatography-mass spectrometry (GC-MS) or GC-flame ionization detection (GC-FID). mQT L analysis of
constituent traits, metabolite-class traits, and relative composition traits identified >500 mQT Ls that modulate the
abundance and composition of the silk SL metabolome, with some mQT Ls detected in more than one environment. A
more complete characterization of the genetic network has been pursued through inclusion of traits that are precursor
(fatty acids), proposed intermediate (aldehydes), and end-product (hydrocarbons) lipids. T o connect this genetic
network to the predicted biochemical network for hydrocarbon biosynthesis, identification of causal genetic
polymorphisms or the ability to discriminate among competing candidate gene hypotheses is required. Here we report
our progress in dissecting two genomic loci that are particularly influential in shaping the silk SL metabolome. Fine
mapping results are reported from three complementary breeding and analysis approaches: isogenic dual testcross,
heterozygous inbred family and bi-parental introgression, each of which are used to interrogate potentially informative
recombination events.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture (USDA)
P183
Flowering time stability in doubled haploid lines derived from exotic maize
(submitted by Adam Vanous <adamv@iastate.edu>)
Full Author List: Vanous, Adam1 ; Guo, T ingting1 ; Li, Xianran 1; Peters, David W 2; Lübberstedt, Thomas1; Yu, Jianming1 ;
Gardner, Candice2
1
Dep. of Agronomy, Iowa State Univ., Ames IA, USA 50011
2
USDA-ARS, Ames, IA, USA 50011
Variation in flowering time phenotypes across maize germplasm is effected by a combination of the plant’s genotype,
environment, and genotype-by-environment interaction. When adapting exotic germplasm to the United States Corn Belt, the plant’s genotype is the crucial hindrance as it controls fundamental adaptation traits such as photoperiod
sensitivity and overall flowering time. T he unknown effect of the new environment on the germplasm’s genotype
exacerbates this issue. T he phenotypic plasticity created is ill-defined if moving specific exotic germplasm over large
latitudinal distances and for the adapted variants being created. Reduced plasticity, or stability, is desired for the
adapted variants as it allows for a more rapid implementation into breeding programs throughout the Corn -Belt. Herein,
doubled haploid lines derived from exotic maize, developed in a joint venture between the USDA Germplasm
Enhancement of Maize project and Iowa State University and adapted through backcrossing exotic germplasm to elite,
adapted lines, are studied for flowering time stability. Reaction norms are used to visualize patterns across multiple
environments and to quantify stability. Genome-wide association studies are used to further explore and dissect genes
and pathways. Knowledge gained will be implemented for adapting additional exotic germplasm.
Funding acknowledgement: United States Department of Agriculture (USDA)
158
P184
From the sequencing of 16 MAGIC population founders to a 8 million SNP
resource on the BALANCE panel
(submitted by Clement Buet <clement.buet@biogemma.com>)
Full Author List: Sounac, Nicolas1; Decousset, Laurent 1; Buet, Clement 1; Dubreuil, Pierre1; T ixier, Marie-Helene1;
Desplat, Nelly 1; Leveugle, Magalie1; Duborjal, Herve 1; Pichon, Jean-Philippe1; Praud, Sebastien 1
1
BIOGEMMA, Centre de Recherche, Route d'Ennezat, Chappes 63720, France
Association studies have become a method of choice to identify genomic regions involved in the variation of
traits of interest, especially in maize. BIOGEM M A has created a panel of DH lines from a M AGIC population
developped from 16 founder lines. This panel has suitable properties to map QTL at a high resolution provided
that a wealth of markers evenly spaced across the genome is available. To significantly increase the number of
markers in the DH lines:
- the founder lines were fully sequenced through Illumina HiSeq technology with a 15X mean coverage
(mapping on B73 RefGenV2),
- DH lines together with the founder lines were genotyped with the Axiom maize 600K chip and the genome of
each DH line was reconstructed as a mosaic of the founders’ genomes using statistical methods imported from
mouse studies,
- the founder sequence data were projected onto the each DH genome using a home-made R program.
M ore than 12 million of SNP were detected from the sequence data among which 8 million were selected using
different selection criteria (allelic segregation, IBD, LD). This extensive genotyping dataset represents a
powerful genetic resource to decipher genetic bases of complex traits especially when combined with all the
other “omics’ layers aggregated in this panel.
P185
Genetic and molecular basis of maize hybrid vigor: genome wide association
studies in factorial hybrid designs
(submitted by Julie Fievet <julie.fievet@inra.fr>)
Full Author List: Fabien, Laporte 1; Julie B., Fievet 1; Alain, Charcosset 1; T ristan, Mary-Huard1 2
1
UMR320 GQE - Le Moulon, INRA/Univ. Paris-Sud/CNRS/AgroParisT ech, Ferme du moulon, F-91190 Gif-surYvette
2
UMR518 MIA-Paris, AgroParisT ech/INRA, 16 rue Claude Bernard, F-75231 Paris Cedex 05
A common strategy to detect QTL for hybrid performance is to cross a population of inbred lines from one
heterotic group to a same common parent derived from the other heterotic group, referred as "tester". In the
context of linkage based mapping, the use of a tester raises important issues such as dependency of the results
according to the tester and buffered genetic variation. Also, analyzing two genetic groups calls for two
experiments. Giraud et al. (2017, Genetics) have therefore advocated the study of both heterotic groups at a same
time.
During the PIA/ANR Amaizing project, we assembled a panel of hybrids between the two complementary
groups largely used for maize production in northern Europe. Around 300 dent and 3oo flint lines were crossed
according to an incomplete factorial design to produce 348 hybrids. The hybrids were evaluated in 8
environments for yield components and phenology. Lines were genotyped using 600K SNP markers chip.
M issing data were imputed using Beagle and markers with a minor allele frequency lower than 4% were
discarded. Following a classical approach (Technow et al., 2014), the data were analyzed by decomposition into
the general combining ability (GCA) of each group and the specific combining ability (SCA) between groups
(Sprague & Tatum, 1942). The results showed that the contribution of GCA is largely more important than that
of SCA. The QTL detection implied to take into account the relatedness within and between the two parental
populations. Different hypotheses for the QTL effects were tested (additive, interaction and global marker
effects) either environment by environment and for all the environments taken together. The results indicated that
i) the associations that are detected differ according to effects included in the model and ii) the number of QTLs
detected in the multiple environment context is higher than in individual environments, confirming the interest of
such multi-environment analysis.
Funding acknowledgement: French National Research Agency (Amaizing, ANR-10-BTBR-03)
159
P186
Genetic architecture of complex traits in a maize-teosinte population
(submitted by Renyu Zhang <zhangrenyu@live.com>)
Full Author List: Zhang, Renyu1; Yang, Ning2; Zhang, Xuan 1; Cai, Lichun 1; Li, Xiaowei1; Chen, Wenkang1; Li,
Weiya1; Guo, Ce1; Yan, Jianbing2; Li, Jiansheng1; Yang, Xiaohong1
1
National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China
Agricultural University, Beijing 100193, China
2
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
Domestication and improvement have profoundly altered wild species to meet human needs. M aize has
undergone a striking transformation from the wild progenitor, Zea mays ssp. parviglumis, resulting in great
morphological differences. In this study, a M o17-mexicana BC2F5 population of 191 families was developed to
dissect the genetic architecture of 18 divergent morphological traits, including 2 plant, 3 flowering, 6 ear, 2 tassel
and 5 seed traits. Totally, 109 individual QTLs, which were clustered into 67 loci, were identified for 18 traits,
with each QTL explaining 3.4%-29.4% of phenotypic variation. For each trait, the number of identified QTL
ranged from 3 to 12, and the totally explained phenotypic variation ranged from 28.0% to 77.8%. In addition, we
identified 4 pairs of epistatic QTL, accounting for a small proportion of phenotypic variation for 4 detected traits.
These findings indicate that the additive effects play more important roles than epistatic effects in the genetic
architecture of the divergent morphological traits in the maize-teosinte population. Among 109 identified QTLs,
55 and 28 QTLs underwent domestication and improvement, respectively. A QTL-trait network constructed
based on the identified individual QTL revealed 66 QTLs with pleiotropy effect, which has the same positive or
negative additive effects for two or more traits. Our results provide useful information for future research on the
genetic basis of these traits.
Funding acknowledgement: National Science Foundation of China (NSFC)
P187
Genetic dissection of plant height and flowering using two Stiff Stalk multiparent advanced generation intercross populations of maize
(submitted by Kathryn Michel <kathryn.michel@wisc.edu>)
Full Author List: Michel, Kathryn 1; Vaillancourt, Brieanne2; Buell, C. Robin 2; Broman, Karl W. 3; de Leon, Natalia1;
Kaeppler, Shawn 1
1
Department of Agronomy and DOE Great Lakes Bioenergy Research Center; University of Wisconsin; Madison, WI
53706
2
Department of Plant Biology and DOE Great Lakes Bioenergy Research Center; Michigan State University; East
Lansing, MI 48824
3
Department of Biostatistics & Medical Informatics; University of Wisconsin; Madison, WI 53706
M ulti-parent advanced generation intercross (M AGIC) populations can be used to elucidate the genetic control of
complex traits in plants. Two M AGIC populations were developed at the University of Wisconsin from six
inbred parents (PHJ40, PHB47, LH145, NKH8431, B84, and B73) belonging to the Stiff Stalk heterotic pool.
Parents were crossed in all possible F1 combinations, and following balanced intermating of the F1 progeny, the
populations underwent additional intermating before doubled haploid (DH) generation. Version 1 (V1) of the
population had two generations and Version 2 (V2) had four generations of random intermating. The goal of this
project is to compare the level of variation present in the two populations and to determine differences in map
size and power to detect genotype-phenotype association in these M AGIC populations. Approximately 360 V1
and 430 V2 DH lines were grown along with the six parents as checks in two field replicates in 2016 and 2017 in
Wisconsin. Growing degree days (GDD) until anthesis and silking was evaluated on a whole-plot basis, while
three representative plants were evaluated for plant height, ear height, and cob color. Across both years, V1 had
an average plant height of 188 cm, SD 19.5 cm, while V2 had an average plant height of 182 cm, SD 21.3 cm.
V1 had later anthesis with an average of 1366 GDD, SD 60.1 GDD, while V2 had an average of 1354 GDD, SD
57.8 GDD. V1 also had later silking with an average of 1382 GDD, SD 65.1 GDD, while V2 had 1375 GDD, SD
62.6 GDD. A genetic map was developed using R/qtl2 (kbroman.org/qtl2) and markers scored from exome
capture sequencing. Outcomes from this research will further our understanding of the utility of different
structures of M AGIC populations for QTL detection.
Funding acknowledgement: United States Department of Agriculture (USDA) Hatch, Department of Energy
(DOE) Great Lakes Bioenergy Research Center, in-kind support by AgReliant Genetics
160
P188
Genetic distance in relation with specific combining abilities and heterosis for
vegetative traits in maize
(submitted by Nikola Grcic <ngrcic@mrizp.rs>)
Full Author List: Grcic, Nikola 1; Delic, Nenad1; Stevanovic, Milan 1; Mladenovic-Drinic, Snezana1; Andjelkovic,
Violeta1; Bozinovic, Sofija 1; Pavlov, Jovan 1
1
Maize research institute Zemun Polje; Zemun; Belgrade; Serbia; 11000
Prediction of maize hybrids performances based on the genetic distance between their parents has long been an
important path in the implementation of molecular marker technology in maize breeding programs. In this study
genetic distance assessment of six maize inbred lines was done using 21 SSR primers. In the analysis, 92 alleles
were detected with a mean of 4.38 per locus. Genetic distance (GD) determined using Simple matching
coefficient (SM ) between inbred lines ranged from 0.11 to 0.549. Using UPGM A clustering method a
dendrogram was constructed in wich inbred lines were separated into two main cluster, one containing 2 inbred
lines, and the other one with 4 inbreds. The bigger cluster furthermore was divided into two smaller subclusters.
This classification was in accordance with known pedigree data of analysed genotypes. Six investigated inbred
lines were furthermore crossed according to an incomplete diallel design forming 15 hybrid combinations. These
genotypes were tested in field trials on 3 locations together with inbred lines per se. In this study maize
vegetative traits: plant height and leaf number per plant were analyzed. Statistically significant specific
combining abilities (SCA) and high parent heterosis (HPH) were calculated for both traits. Spearman’s rank
correlation coefficient between genetic distance and SCA for plant height and leaf number was positive and
statistically significant while the correlation between high parent heterosis and genetic distance although positive
was not significant.
Funding acknowledgement: The ministry of Education, Science and Technological development of the Republic
of Serbia (project TR-31068)
P189
Genetic variation for early development and cold tolerance in DH libraries from
maize landraces
(submitted by Eva Bauer <e.bauer@tum.de>)
Full Author List: Bauer, Eva 1; Hoelker, Armin C. 1; Mayer, Manfred1; Presterl, T homas2; Ordas, Bernardo 3; Brauner,
Pedro C.4; Ouzunova, Milena2; Melchinger, Albrecht E. 4; Schön, Chris-Carolin 1
1
Plant Breeding, T UM School of Life Sciences Weihenstephan, T echnical University of Munich, 85354 Freising,
Germany
2
Maize Breeding, KWS SAAT SE, 37574 Einbeck, Germany
3
Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 36 080 Pontevedra, Spain
4
Plant Breeding, University of Hohenheim, 70593 Stuttgart, Germany
Due to the high sensitivity of current maize varieties to cold stress in early development, farmers bear the risk of
yield losses because of cold periods in late spring. Improving cold tolerance in maize could reduce this risk and
would allow earlier sowing dates. The European maize landraces are considered as “gold reserve” of genetic
variation for many quantitative traits. Strategies for efficiently utilizing this resource are currently evolving. In
our study, we aim to detect relevant regions for the expression of cold tolerance through genome-wide
association studies (GWAS). Further, we examine the practicability of whole-genome based prediction of
genotypic values in material derived from landraces with a focus on cold tolerance related traits. We applied invivo doubled-haploid (DH) induction to three selected landrace populations and produced libraries of about 1000
DH lines. The complete set of DH lines was genotyped using the 600k Affymetrix® Axiom® M aize array. In
2017, all lines were phenotyped for early vigor, early plant height, flowering time, final plant height and other
agronomic traits in six diverse environments in Germany and Spain.
In GWAS, we identified genomic regions significantly associated with cold tolerance related traits on
chromosomes 1 and 10, respectively. Cross-validated genomic predictions yielded intermediate to high
predictive abilities for cold tolerance traits within landrace populations (0.48 to 0.60). In predictions across
landrace populations, predictive abilities were close to zero. We will use these resources to identify novel
candidate genes and to assist breeding for cold tolerance in elite germplasm.
Funding acknowledgement: German M inistry of Education and Research (BM BF; Grant ID 031B0195)
161
P190
Genome wide association studies for kernel starch and protein content in the
Wisconsin diversity (WiDiv) maize association panel
(submitted by Jose Varela <jvarela@wisc.edu>)
Full Author List: Varela, Jose I 1; Reboucas, Joao R2; Haase, Nicholas1 3; Combs, David K2; Kaeppler, Shawn M 1; de
Leon, Natalia1
1
Department of Agronomy, University of Wisconsin -Madison, 1575 Linden Drive, Madison, WI, U.S.A, 53706
2
Department of Dairy Science, University of Wisconsin -Madison, 1675 Observatory Drive, Madison, WI, U.S.A,
53706
3
DuPont Pioneer, 19456 MN HWY 22, Mankato, MN, U.S.A, 56001
In maize forage production, the kernel is a major contributor of energy , therefore improved grain starch content
and bioavailability for digestion are important plant breeding objectives. Endosperm texture affects starch
degradation rates in ruminants. The range extends from loosely packed (floury) to densely packed (vitreous)
starch granules types. This condition is associated with the amount and type of proteins found in the matrix that
surrounds the starch granules. The main storage proteins in the endosperm are prolamins, also known as zeins.
The main objective of this study is to explore the natural variability of kernel starch and protein content of the
maize Wisconsin Diversity (WiDiV) association panel and identify region of the genome associated with these
traits. This population is genotyped with 899,784 RNA-seq based single nucleotide polymorphism (SNP)
markers. Open pollinated plants were grown in a randomized complete block design with two replicates in
Arlington, WI in the summer of 2013 at a density of approximately 65,000 plants/ha. Ears from three
representative plants per plot were collected after plants had reached physiological maturity. Kernels from the set
of three ears from 561 of the WiDiv lines were scanned using Near Infrared Transmittance (NIT) to obtain grain
starch and protein percentage. Significant variation was found for starch (40% to 75% of grain biomass) and total
protein (6% to 13.5% of grain biomass) content among genotypes. Repeatabilities of 0.85 and 0.9 were observed
for starch and protein content, respectively. We found one significant SNP on the long arm of chromosome 1
associated with kernel starch content. No significant associations were found for total protein content.
Investigating regions of the genome associated with starch and protein content could open new opportunities to
understand the contribution of these regions to grain quality in the context of forage maize.
Funding acknowledgement: United States Department of Agriculture (USDA)
162
P191
Genome wide association study for protein expression under normal and water
deficit conditions in maize leaves
(submitted by Mélisande Blein-Nicolas <melisande.blein-nicolas@inra.fr>)
Full Author List: Blein-Nicolas, Mélisande1; Negro, Sandra1; Balliau, T hierry 1; Corti, Hélène1; T ardieu, François2;
Welcker, Claude2; Nicolas, Stéphane 1; Charcosset, Alain 1; Zivy, Michel1
1
GQE - Le Moulon, INRA, Univ Paris-Sud, CNRS, AgroParisT ech, Université Paris-Saclay, F-91190, Gif-sur-Yvette,
France
2
INRA, UMR759, Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060
Montpellier Cedex 1, France
M aize is one of the main crops worldwide, but its yield can be severely affected by drought. Drought tolerance in
maize is genotype-dependent, indicating that this trait can be genetically improved. This study aimed to identify
genetic determinants of drought tolerance by using genome wide association study (GWAS) to identify QTLs for
protein abundance (pQTLs) that colocalize with QTL for ecophysiological traits. A panel of 251 maize
genotypes was grown in the high-throughput phenotyping platform PhenoArch (M ontpellier) under water deficit
(WW) and well-watered (WD) conditions and in two replicates. Several ecophysiological parameters were
measured during plant growth and analyzed elsewhere (Alvarez Prado et al., Plant Cell Environ. 2017; 1-13). At
the pre-flowering stage, 1004 samples were taken on the last ligulated leaf and analyzed by shotgun proteomics.
A total of 1950 proteins were quantified. M ost of them showed significant abundance variations in response to
water deficit and to genotype. In particular, drought responsive proteins, like dehydrins, were highly induced
under WD, while proteins of energy metabolism were down-regulated. GWAS was performed on 3900
molecular phenotypes (=1950 proteins x 2 conditions). 29004 pQTLs were detected for 3758 (96.4%) molecular
phenotypes, confirming the high genetic variability of protein abundances. Local pQTLs, located <1M pb from
the protein encoding gene, had much stronger effect than distant pQTL (19.3 % vs 5.5 % of explained variance
on average). M ore than 30 cases of pQTL/QTL colocalizations involving ecophysiological traits such as water
use or transpiration were detected, mostly in WD. Several candidate genes potentially controlling both the
abundance of a protein and a phenotypic trait were identified. Altogether, these results show the potential of
high-throughput quantitative proteomics to decipher the determinisms of protein abundance regulation and to
discover candidate genes and proteins potentially involved in the variation of plant phenotypic traits.
Funding acknowledgement: Agence Nationale de la Recherche (ANR), FranceAgrimer
P192
Genome-Wide association of biomass digestibility in the Wisconsin diversity panel
(submitted by Jonas Rodriguez <jrodriguez36@wisc.edu>)
Full Author List: Rodriguez, Jonas1; Heckwolf, Marlies1; Kaeppler, Shawn 1; de Leon, Natalia1
1
Department of Agronomy, University of Wisconsin - Madison, Madison, WI, USA
M aize stover comprises all the non-grain portions of the plant and accounts for approximately half the total
biomass yield. The stalk contributes most to stover biomass, and due primarily to secondary cell wall formation
during growth and development, it is recalcitrant to biological degradation. In the context of forage production
for ruminant nutrition and biofuel production, compositional attributes which reduce recalcitrance are of interest.
In this experiment, we collected the second lowermost stalk internode of ~4700 plants 45 days after flowering
and evaluated them for compositional characteristics by near infrared spectroscopy (NIRs). These plants
represent 667 diverse inbred lines from the Wisconsin Diversity (WiDiv) association panel, which were
evaluated in a replicated field trial across two years. Prediction equations were developed for neutral detergent
fiber (NDF) and acid detergent fiber (ADF) of stalk internodes. NDF represents total cell wall concentration
(hemicellulose, cellulose, lignin) while ADF encompasses cellulose and lignin. Prediction accuracies for NDF
and ADF using NIR were 0.95 and 0.94, respectively. Hemicellulose content was calculated from the percentage
of total cell wall constituents. Significant genetic variation for hemicellulose was observed for the collection of
lines, with values ranging from 16.9 to 36.1% of the dry matter. Hemicellulose was used to conduct a genome
wide association analysis using 899,784 SNPs generated by RNA-sequencing. This study demonstrates the utility
of the WiDiv association panel coupled with a dense marker set, to identify genomic regions associated with
biomass digestibility and more efficiently aid the development of superior forage maize varieties.
Funding acknowledgement: National Science Foundation (NSF)
163
P193
Genome-wide mapping of kernel color in maize (Zea Mays L.) reveals
associations with isoprenoid and carotenoid biosynthesis genes and carotenoid
degradation genes
(submitted by Torbert Rocheford <torbert@purdue.edu>)
Full Author List: Owens, Brenda 1; Mathew, Deepu1 2; T iede, T yler 1; Hernandez, Maria Mateos1; Diepenbrock,
Christine3; Gore, Michael3; Rocheford, T orbert 1
1
Purdue University, West Lafayette, IN 47907 USA
2
Kerala Agricultural University, KAU Post, T hrissur, Kerala - 680 656, INDIA
3
Cornell University, Ithaca, NY 14853 USA
Rapid development of biofortified crop varieties with improved levels of provitaminA and total carotenoids
would benefit from a greater understanding of relevant and useful genetic variation in the carotenoid and
isoprenoid biosynthetic pathways, and carotenoid degradation enzymes. Higher levels of provitamin A (proVA)
and total carotenoids in grains, roots, tubers and fruits are frequently accompanied by an increase in orange color.
Orange color in maize endosperm is being used successfully with consumers in Africa to differentiate the higher
proVA varieties. Genetic loci affecting maize kernel color were revealed through genome-wide association study
(GWAS) in a large association panel. Variation in the dxs2 and psy1 genes, both expressed in maize endosperm
and the first committed steps in the plastidic synthesis of isoprenoids and carotenoids, respectively, were
significantly associated with quantitative measures of kernel color determined by colorimeter analysis. The lcyE
gene, which affects partitioning between the α- and β-branches of the carotenoid pathway, and zep1, which
affects flux out of the β-branch of the carotenoid pathway, were also associated with color values in GWAS.
Because the β-branch carotenoids are more orange in color than more yellow α-branch carotenoids, a relative
increase in β-carotenoids relative to α-carotenoids will alter color. This shift is desirable because the major
proVA compounds present in maize, β-carotene and β-cryptoxanthin are part of the β-branch. The performance
of isoprenoid and carotenoid pathway analysis revealed an association with color of dmes2, a gene involved in
isoprenoid synthesis. Our results show that there are commonalities between t he genes influencing color revealed
in this study and genes influencing levels of proVA and total carotenoids reported in other studies. These results
establish colorimeter as a quantitative means of relating color to total carotenoids.
Funding acknowledgement: National Science Foundation (NSF), HarvestPlus
164
P194
Genome-wide SNP genotyping of DNA pools identifies original landraces to
enrich maize breeding pools
(submitted by Stéphane Nicolas <stephane.nicolas@inra.fr>)
Full Author List: Nicolas, Stéphane D 2; Arca, Mariangela2; Mary-Huard, T ristan 2; Le Paslier, Marie-Christine3;
Bauland, Cyril2; Combes, Valérie2; Madur, Delphine 2; Gouesnard, Brigitte1; Charcosset, Alain 2
1
Génétique Quantitative et Evolution - Le Moulon, INRA - Université Paris-Sud - CNRS - AgroParisT ech; Ferme du
Moulon, Gif-sur-Yvette, France, F-91190
2
Amélioration Génétique et Adaptation des Plantes méditéranéennes et T ropicales, CIRAD - INRA - SupAgro
Montpellier; 2 place Viala, Montpellier, France, F-34060
3
Etude du Polymorphisme des Génomes Végétaux, INRA, CEA Institut de Génomique, Centre National de
Génotypage, 2 rue Gaston Crémieux, Evry, France, F-91057
M aize landraces germplasm have a very large genetic diversity that is still poorly characterized and exploited in
plant breeding programs. We studied the effect of both human selection and environmental adaptation on
genome-wide diversity of landraces with a focus on landraces-hybrid transition in order to identify interesting
source of genetic diversity to enlarge modern breeding pools. We developed a high-throughput, cheap and labor
saving DNA pooling approach based on 50K SNP maize Illumina array and estimated thereby allelic frequencies
of 23412 SNP in 156 landraces representing worldwide maize diversity. We compared the diversity of this
collection at genome-wide scale level with that of a panel of 336 inbred lines. Our new approach: (i) gives
accurate allelic frequencies estimation that are reproducible across laboratories, (ii) p rotects both against false
detection of allele presence within landraces and against ascertainment bias. M odified Roger's genetic Distance
estimated from 23412 SNP and 17 SSR on same DNA pool are highly correlated, which validates our approach.
Accordingly, structuration analysis based on SNP gives consistent results with SSR for higher levels of
structuration but gives a slightly different pictures for more advanced structuration levels, suggesting that SNP
and SSR could capture differently recent evolution. Gene diversity of landraces varies strongly along the genome
and according to geographic origins. We identified 376 SNP under diversifying selection unraveling a selective
footprints in Tga1/Su1 regions. While some maize landraces were closely related to several inbred lines and
strongly contributed to modern breeding pools as Reid Yellow Dent or Lancaster Surecrop, some other have no
related inbred lines and seem to have poorly contributed. We identified limited diversity loss or selective sweep
between landraces and inbred lines, excepted in centromeric regions. For these regions, original landraces could
be interesting to enlarge genetic diversity of modern breeding pools.
Gene / Gene M odels described: Tga1 (teosinte glume architecture1), Su1 (Sugary1); GRM ZM2G101511,
GRM ZM2G138060
Funding acknowledgement: Agence Nationale de la Recherche (ANR), Association pour l'étude du mais
(Promais)
165
P195
Genomic prediction within and among doubled-haploid libraries from maize
landraces
(submitted by Albrecht E. Melchinger <melchinger@uni-hohenheim.de>)
Full Author List: C. Brauner, Pedro 1; Müller, Dominik 1; Schopp, Pascal1; Böhm, Juliane1; Bauer, Eva2; Schön, ChrisCarolin 2; Melchinger, Albrecht E. 1
1
Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart,
Germany
2
T UM School of Life Sciences Weihenstephan, T echnical University of Munich, 85354 Freising, Germany
Thousands of maize landraces are stored in seed banks worldwide. Doubled-haploid libraries (DHL) produced
from landraces allow to harness their rich genetic diversity for future breeding. We investigated the prospects of
genomic prediction (GP) for line per se performance in DHL from six European landraces (CG, GB, RT, SF, SM
and WA) and 53 elite flint (EF) lines by comparing four scenarios: GP within libraries (1L) as well as
incrementing training set (TS) size, between pairs of libraries (LwL), and among combined libraries, either
including (LwCLi) or excluding (LwCLe) lines from the TS that belong to the same DHL as the prediction set.
GP was performed using the GBLUP model and we report the prediction accuracy (ρ) averaged across seven
agronomic traits.
We will compare the different validation scenarios to investigate if GP can benefit from the information of
several landraces. Factors affecting ρ will be evaluated, such as training set size, linkage disequilibrium (LD) and
expected degree of relatedness between genotypes. The expenditures to create DHL are high, thus, we will give
recommendations regarding which factors to focus on when using GP to harness the genetic variability of
landraces.
Literature: http://www.europeanmaize.net/
Funding acknowledgement: BM BF - Projektträger Jülich - Förderkennzeichen 031B0195 F
P196
Genomic regions associated with Goss’s Wilt resistance in the commercial maize
germplasm pool.
(submitted by Dustin MacLean <dmacle02@uoguelph.ca>)
Full Author List: MacLean, Dustin 1; Lee, Elizabeth 1
1
University of Guelph; 50 Stone Road E; Guelph, Ontario, Canada, N1G2W1
Goss's Wilt (Clavibacter michiganensis subsp. nebraskensis) is a bacterial disease of maize (Zea mays) that
manifests itself predominately as a leaf blight. Recently, it has spread from the high plains of the United States
and is considered an emerging threat to Ontario. Fungicides are ineffective at controlling Goss’s Wilt; however,
development of resistant hybrids may be an option for mitigating yield losses. Current varieties grown in Canada
appear to have little or limited resistance to this pathogen. Resistance is thought to be quantitative and controlled
by 9-11 QTLs, making it more difficult to select for compared to single gene resistance. The objective of this
study is to use in silico mapping using a North Carolina Design II mating scheme to identify genomic regions
associated with Goss’s wilt resistance in 20 stiff stalk and 30 non-stiff stalk inbred lines from the modern
Canadian commercial germplasm pool and 600 hybrids derived from inbred crosses. QTL mapping will be
conducted on the hybrids and molecular markers will be developed. The proposed research will result in the
identification of genomic regions in the modern commercial germplasm pool utilized by breeding companies,
thereby facilitating rapid utilization of resistant material in commercial maize breeding programs.
166
P197
Genomic selection efficiency and a priori estimation of accuracy in a structured
dent maize panel
(submitted by Simon Rio <simon.rio@inra.fr>)
Full Author List: Rio, Simon 1; Mary-Huard, T ristan 1 2; Moreau, Laurence 1; Charcosset, Alain 1
1
UMR Génétique Quantitative et Evolution, Ferme du Moulon, Gif-sur-Yvette, France, 91120
2
UMR Mathématiques et Informatique Appliquées, AgroParisT ech, 16 rue Claude Bernard, Paris, France, 75005
Key message: Population structure affects genomic selection efficiency as well as the ability to anticipate
accuracy using standard GBLUP.
Genomic selection refers to the use of a prediction model calibrated on a set of individuals to predict the genetic
value of new individuals using marker data. Prediction models usually assume that the individuals used to
calibrate the prediction model belong to the same population as those to be predicted. M ost of the a priori
indicators of precision, such as the Coefficient of Determination (CD), were derived from those same models.
But genetic structure is a common feature in plant species and it may impact genomic selection efficiency as well
as the ability to anticipate prediction accuracy. We investigated the impact of genetic structure in a dent maize
panel (“Amaizing Dent”) using different scenarios including within or across group predictions. For a given
training set size, the best accuracies were achieved when predicting individuals using a model calibrated on the
same genetic group. Nevertheless diverse training panels representing all subgroups also appeared efficient and
should be recommended when the target population is not yet determined. Alternative prediction models, taking
genetic structure explicitly into account, did not allow us to improve the prediction accuracy compared to
GBLUP. We also investigated the ability of different indicators of precision to anticipate accuracy in the
structure based scenarios. There was a global encouraging trend of the CD to differentiate scenarios, although
there were specific combinations of target populations and traits where the efficiency of this indicator proved to
be null.
Funding acknowledgement: French National Institute for Agricultural Research (INRA) , Amaizing Project
167
P198
Genomic signatures of local adaptation unveil association with present
phenotypic variation in teosintes
(submitted by Natalia Martinez-Ainsworth <natalia.martinez@inra.fr>)
Full Author List: Martinez-Ainsworth, Natalia1; Fustier, Margaux-Alison 1; Corti, Hélène1; Rousselet, Agnès1; Falque,
Matthieu1; Venon, Anthony 1; Dumas, Fabrice1; de Meaux, Juliette2; Dittberner, Hannes2; Aguirre-Liguori, Jonas3;
Montes, Salvador 4; Eguiarte, Luis3; Yves Vigouroux, Yves5; Manicacci, Domenica 1; T enaillon, Maud1
1
Génétique Quantitative et Evolution – Le Moulon, INRA - Université Paris-Sud - CNRS - AgroParisT ech, Université
Paris-Saclay, 91190 Gif-sur-Yvette, France
2
Institute of Botany, University of Cologne Biocenter, 47b Cologne, Germany
3
Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México , 04510
Ciudad de México, Mexico
4
Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, 38010 Celaya,
Mexico
5
Institut de Recherche pour le développement (IRD), UMR Diversité, Adaptation et Développement des plantes
(DIADE), 34394 Montpellier, France
Teosintes are maize’s wild relatives and can be found in a vast range of environmental conditions. During maize
domestication and posterior breeding, a substantial amount of genetic variation was lost through consecutive
bottlenecks. Contemporary wild teosinte populations harbor rich genetic variation, some of which is expected to
be adaptive. Teosintes display pronounced population structure and phenotypic differences, which adds to their
attractiveness for the study of local adaptation and underlying adaptive variation. We have chosen to study the
two subspecies closest to maize (Zea mays ssp. parviglumis and ssp. mexicana) that are found only in M exico
and occupy different environmental niches. From a sampling of 37 populations along two altitudinal gradients,
we sequenced the genomes of 6 environmentally extreme populations. Following a reverse ecology approach,
genomic data was screened for Single Nucleotide Polymorphisms (SNPs) with high differentiation between
lowlands and highlands and/or displaying strong correlation with environmental variables. The resulting 218
candidate SNPs were further genotyped on all 37 populations as well as on an association mapping panel
composed of 11 of the 37 populations. This panel was grown in a two-year two-location common garden
experiment at mid-altitude where plants were scored for 18 phenotypic traits. After accounting for neutral genetic
structure by genotyping 35 microsatellite markers, we found that ~50% of our candidates are associated to at
least one trait. We also observed that candidate selection methods have a considerable influence in delivering
significant associations. Traits such as female and male flowering time and the number of lateral branches,
presented an enrichment of associated SNPs and followed a phenotypic distribution consistent with spatially
varying selection. Throughout this research we have successfully applied population genomic methods to
uncover genetic variants with a phenotypic link that are segregating in natural populations.
168
P199
Genotyping-by-sequencing highlights original diversity patterns within a
European collection of 1191 maize flint lines, as compared to the maize USDA
genebank
(submitted by Brigitte Gouesnard <brigitte.gouesnard@inra.fr>)
Full Author List: Gouesnard, Brigitte 1; Negro, Sandra2; Laffray, Amélie2; Glaubitz, Jeff 3; Melchinger, Albrecht 4;
Revilla, Pedro 5; Moreno-Gonzalez, Jesus6; Madur, Delphine2; Combes, Valérie2; T ollon-Cordet, Christine 1; Laborde,
Jacques7; Kermarrec, Dominique 8; Bauland, Cyril2; Moreau, Laurence 2; Nicolas, Stéphane 2; Charcosset, Alain 2
1
AGAP, INRA, Montpellier, France
2
Génétique Quantitative et Évolution - le Moulon, INRA, Gif-sur-Yvette, France
3
Buckler Lab for maize Genetics and Diversity, Cornell University, Ithaca, USA
4
Seed Science, and Population Genetics, University of Hohenheim, Stuttgart, Germany
5
Misión Biológica de Galicia, CSIC, Pontevedra, Spain
6
Mabegondo Agricultural Research Centre, CIAM-INGACAL, A Coruña, Spain
7
Unité Expérimentale du Maïs, INRA, St Martin de Hinx, France
8
Unité Expérimentale Ressources Génétiques Végétales en Conditions Océaniques (UERGCO), I NRA, Ploudaniel,
France
Comparing and identifying interesting sources of genetic diversity that have been maintained by different
genebanks and understanding the global organization of this genetic diversity is an important issue for prebreeding. We aimed at evaluating how genotyping-by-sequencing (GBS) technologies can address these both
issues. We used GBS to compare the genetic diversity of 1191 European Flint lines maintained by INRA and
other European institutes (see Gouesnard et al., this meeting) with the USDA collection (Romay et al., 2013,
Genome Biology).
We first examined the similarity of 68 inbred lines with a same variety name between the two collections, and
observed that IBS ranged from 0.775 to 0.997 (with a mean of 0.941). It indicated that GBS can be used for
comparing collections and identifying redundancy and illegitimate accessions between genebanks. Based on
principal coordinate analysis and structure analysis on 4001 lines, we showed the distinctiveness of flint
materials compared to the USDA collection. The structuration analysis in 12 groups confirmed the influence of
some historical founder lines in the genetic organization of the dent group (B73, A632, Oh43, M o17, W182E,
PH207 and Wf9). Flint lines were structured in 3 groups (a Sweet-Northern Flint group, an Italian-Argentinan
group and a European group formed by Pyrenees Galicia and Lacaune groups). The Tropical and Pop corn
groups were distinct. We identified several selective sweeps between Dent, Flint and Tropical inbred lines that
co-localized with SNPs associated with flowering time variation identified by association mapping. It suggests
that these genomic regions played an important role in adaptation to higher lattitude. The joint analysis of
collections by GBS offers opportunities for a global diversity analysis of maize inbred lines.
Funding acknowledgement: French National Research Agency (Amaizing, ANR-10-BTBR-03)
P200
Germplasm enhancement using former plant variety protected inbreds
(submitted by Torbert Rocheford <torbert@purdue.edu>)
Full Author List: Beckett, T ravis1; Mohammaddi, Mohsen 1; Rocheford, T orbert 1
1
Purdue University, West Lafayette, IN 47907 USA
Inbreds with expired Plant Variety Protection (PVP) certificates can be a cost -effective source
of elite germplasm. When developing new inbreds, the best breeding populations have both the highest mean and
the highest variance. Publications exist on genomic prediction of virtual breeding populations, but none have
used maize hybrid testcross data as the
training set. We predict the mean (μ) and variance (VG) of simulated breeding populations, and Identify the best
parents to use in a breeding cross for inbred development. We present a phenogram of diversity of maize exPVP
inbreds. We also present various quantitative genetic analyses using exPVP germplasm for identification of loci
associated with grain yield, and various prediction studies.
Funding acknowledgement: Dow AgroSciences
169
P201
Grain yield and stability parameters of ZP maize hybrids grown in Serbia in the
2014-2017 period
(submitted by Milan stevanović <mstevanovic@mrizp.rs>)
Full Author List: Stevanović, Milan 1; Čamdžija, Zoran1; Pavlov, Jovan 1; Delić, Nenad1 ; Mladenović Drinić, Snežana 1 ; Grčić,
Nikola1 ; Tolimir, Miodrag1
1
Maize Research Institute
In Serbia, maize is annually sown on approximately 1 million hectares. Since Serbia is a significant producer of maize,
a special attention has been paid to studies of new maize hybrids. Due to this reason, each year, the experts of the
Maize Research Institute, Zemun Polje perform production trials of hybrids most distributed in the market. T he aim of
such trials is to obtain a detail insight not only into potential and quality of each hybrid, but also into their stability a nd
regional distribution in the Serbian market. T en commercial ZP hybrids of FAO 300 -600 were tested in this study. T he
trial was carried out in 152 locations in the 2014-2017 period in the following mode: 50, 42, 42 and 18 locations in
2014, 2015, 2016, 2017, respectively. The average maize grain yields were recorded in 2014 and 2015, while 2016 was
a high yield year. Drought in 2017 resulted in the yield reduction. Yield stability was estimated by the method
developed by Eberhart and Russel (1966). T he average four-year yield recorded in all 152 locations amounted to 8.639
t ha-1. T he lowest (8.106 t ha-1), i.e. the highest (9.306 t ha-1) yield was detected in the hybrid ZP 341, i.e. ZP 606,
respectively. T he highest yield stability was recorded in the hybrid ZP 427 (bi=0.967). T he top yielding hybrid ZP 606
also expressed high stability (bi=1.054), as well as the hybrid ZP 666 (bi=1.054). T he hybrid ZP 341 (bi=0.897) was
the most unstable hybrid, showing significantly better adaptation to poorer growing conditions. Hybrid ZP 560
(bi=1.102) was also unstable, but was better adapted to favourable growing conditions. Based on four -year results it can
be concluded that medium early and medium late hybrids (FAO 400 -600) may be recommended for the production of
commercial maize in the region of Serbia.
P202
GWAS for resistance to mediterranean corn borer and agronomic traits in a
MAGIC population of maize
(submitted by Rosa Ana Malvar <rmalvar@mbg.csic.es>)
Full Author List: Malvar, Rosa Ana1 ; Jimenez-Galindo, José Cruz1 2; Butrón, Ana1; Santiago, Rogelio 3; Ordás, Bernardo 1
Misión Biológica de Galicia, Spanish National Research Council (CSIC), 36080 Apartado 28, Pontevedra, Spain.
2
National Institute of Forestry, Agriculture and Livestock Research (INIFAP), Ave. Hidalgo 1213, Cd. Cuauhtémoc,
Chihuahua, México, 31500
3
Agrobiología Ambiental. Calidad de Suelos y Plantas (Universidad de Vigo), Unidad Asociada a la Misión Biológica de
Galicia (CSIC), Spain
1
Understanding of the genetic basis of quantitative traits such as resistance to pest and yield are necessary to optimize
the breeding programs to simultaneously improve both characters. Genome Wide Association Studies (GWAS) are
useful tools to achieve this goal, especially when the mapping population is a Multi-Parent Advanced Generation
Intercross (MAGIC) population. A MAGIC population of 672 recombinant inbred lines (RIL) was gener ated after
inter-mating for six generations a synthetic variety composed of eight genetically diverse founder lines. T his MAGIC
population have been genotyped by genotyping based on the sequence (GBS) and evaluated for resistance to attack by
the Mediterranean Corn Borer (MCB, Sesamia nonagrioides) and for yield, plant height and silking. We found seven
QT L and six candidate genes for grain resistance, forty -eight QT L and sixty candidate genes for plant height, thirty four QT L and forty-nine candidate genes for silking time, five QT L and nine genes for tunnel length, and finally fifteen
QT L and twenty-four candidate genes for grain yield. We expect that tunnel length produced by MCB larvae attack and
plant height also increase when yield is improved due to t he genetic correlation between these traits. T he intermediate
role of plant height on the undesirable genetic relationship between yield and resistance was highlighted suggesting that
tradeoff between plant growth and resistance could mediate that undesirable relationship. MAGIC population was
useful to discover genomic regions involved in MCB resistance with greater precision than those determined using
more structured populations,. T he GRMZM2G178190 (Zm00001d048129) gene related to the natural resistance could
intervene in the ear resistance and the GRMZM2G057140 (Zm00001d043286) gene that is related to the regeneration
of the cell wall could be related to stem resistance to corn borer attacks. A genetic improvement program can be
designed with the 5 QT L detected for tunnel length using markers-assisted selection to decrease the tunnel length
without neglecting QT L for grain yield, thus improving both traits.
Funding acknowledgement: Plan Nacional I+D. Spain, Feder EU
170
P203
GWAS of inflorescence architecture in maize
(submitted by Torbert Rocheford <torbert@purdue.edu>)
Full Author List: Owens, Brenda 1; Mathew, Deepu1 2; Mateos, Maria1; Rocheford, T orbert 1
Purdue University, West Lafayette, IN, 47907 USA
2
Kerala Agricultural University, KAU Post, T hrissur, Kerala - 680 656 | INDIA |
1
A number of genes have been shown to be involved in the differentiation of male and female maize
inflorescences in both mutant characterizations and in bi-parental populations. Fine-mapped regions of QTL for
inflorescence traits identified in the maize NAM population did not contain the genes previously assumed to
underlie the QTL. This result suggests that previously unknown variation may have a significant contribution
variation in inflorescence traits. This conclusion was further tested in Genome-wide association study of 21
tassel and ear traits measured in 2302 lines of the Ames association panel. A low number of significant
associations were detected and these did not coincide with genes previously established to affect inflorescence
architecture. Nevertheless association analysis resulted in a significant SNP identified in the coding region of
Zm00001d052355, a WRKY77 transcription factor and Zm00001d046642, a GDSL esterase/lipase. While these
genes have not been shown to affect inflorescence, they are likely to affect development and can be considered
new inflorescence candidate genes. Together these results suggest that a potentially large number of genes of
small effect, including the new candidates revealed in this study, influence inflorescence architecture on a
population wide basis.
Funding acknowledgement: National Science Foundation (NSF)
P204
Hydrotropism: an important root trait for drought and heat avoidance in maize
(submitted by Gladys Cassab <gladys@ibt.unam.mx>)
Full Author List: Cassab, Gladys I 1; Martínez-Guadarrama, Jesús J1; Eapen, Delfeena 1; Medina-Andrés, Rigoberto 1;
Sáenz-Rodríguez, Mery N1; Lledías, Fernando 1; Peñaloza, Maximiliano 1; Hernández-Montes, Georgina3; Hurtado, Juan
M1; Bueno-Hernández, Brandon 1; Nieto-Sotelo, Jorge2
1
Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de
México,Av. Universidad 2001, Cuernavaca, Mor. 62210, México.
2
Red de Apoyo a la Investigación Coordinación de la Investigación Científica Instituto Nacional de Ciencias Médica s
y Nutrición Salvador Zubirán, Edificio de Radio-Oncología, 2o piso Vasco de Quiroga 15, Sección XVI, T lalpan 14000
Ciudad de México, México.
3
Laboratorio de Fisiología Molecular, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de
México, Circuito Zona Deportiva s/n, Ciudad Universitaria, Ciudad de Mexico, 04510, México.
Roots of higher plants change their growth direction in response to moisture, avoiding drought and gaining
maximum advantage for development. This response is termed hydrotropism. There have been few studies of
root hydrotropism in grasses, particularly in maize. We developed a laboratory bioassay for testing hydrotropic
response in primary roots maize elite DTM A hybrids and several maize landraces. The hydrotropic response was
classified as robust or weak according to the angle of curvature, having a weak response those roots with less
than 40o, and a robust response those roots with more than 40 o.We recently showed the benefit of intensive
phenotyping of hydrotropism in primary roots since maize plants that display a robust hydrotropic response grew
better under drought and partial lateral irrigation, indicating that a selection for robust hydrotropism might be a
promising breeding strategy to improve drought avoidance in maize. Robust root hydrotropic response in maize
correlated with other root specific traits such as: increased lateral root branching, decrease in above ground
crown roots, decreased formation of root cortical aerenchyma, increased cortical cell file number, and decreased
cortical cell size. This indicates that the utility of the root hydrotropic response phene or trait depend on
interactions with other root traits (phenes) in integrated phenotypes. GWAS of robust and weak hydrotropic
response revealed a variety of transcription factors, proteasome enzymes, several kinases, ethylene signaling,
transporters and proteins with DUF. M ost of these molecular markers were validated by QTL and re-sequencing.
The power of genomic selection will be enhanced by including phenomic information for understanding maize
domestication and adaptation to changes in climate.
Funding acknowledgement: DEGAPA, UNAM IG200515, CONACYT PN 247732
171
P205
Identification of haploid immature embryos by their morphological difference in
maize
(submitted by Yu Zhong <zhongyu306@cau.edu.cn>)
Full Author List: Zhong, Yu1; Chen, Chen 1; Liu, Chenxu1; T ian, Xiaolong1; Li, Jinlong1; Chen, Shaojiang1
National Maize Improvement Center of China, China Agricultural University, Beijing, China 100193
1
The doubled haploid (DH) breeding technology is being applied extensively and deeply in modern maize
breeding and genetic research. Rapid and reliable identification of haploid is a key step to DH breeding
technology but current systems were suitable for the selection of mature kernels. Here, we describe a new
method for discrimination of haploid from diploid immature embryos based on their morphological difference. In
our preliminary study, one inbred line and two hybrids were induced by three inducers with different oil content
to confirm the morphological differences between the haploid and heterozygous diploid and find out the period
of the biggest differences. The length, width and area of the heterozygous diploid immature embryos were
significantly bigger than that of haploids, with the biggest differences during 16-18 days after pollination, which
mainly showed the difference at the width and area. Compared with low oil inducer, the differences between the
haploid and the heterozygous diploid immature embryos, which generated from high oil inducer, were more
significant. Based on the difference of immature embryo shape of haploids and heterozygous kernels, haploid
embryos could be discriminated effectively, and it worked better when based on both the width and area of
immature embryos. In order to test the efficiency of the method for heterogeneous source materials, ten source
germplasms, including inbred lines and the commercial hybrids, were pollinated by the same inducers above. We
determined that the accuracy of haploid identification is influenced by the parent materials and the high oil
inducer was superior to that of the low oil inducer. Under the premise to ensure the haploid number, 47.0%75.8% of diploid could be rapidly eliminated before double treatment. In conclusion, this new method could
extend the application and increase the efficiency of the double haploid technology in maize.
Funding acknowledgement: the National Key Research and Development Program of China
(2016YFD0101200), M odern M aize Industry Technology System (CARS-02-09)
P206
Inbreeding depression in wild maize populations (Zea mays ssp. parviglumis)
subject to habitat degradation in southwest Mexico
(submitted by Aimee J. Schulz <aschulzj@iastate.edu>)
Full Author List: Schulz, Aimee J1; Gepts, Paul2; Hufford, Matthew B1
1
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA, USA
50011
2
Plant Sciences Department, University of California, Davis, One Shields Avenue, Davis, CA, USA 95616
Crops were domesticated from wild taxa, in many cases, thousands of years ago. These wild progenitors can
often still be found sympatric to their domesticated counterparts and can serve as a source of variation for the
genetic improvement of modern varieties. However, the realization of this genetic potential depends critically on
the conservation of wild populations. With little protection in place, concerns regarding habitat degradation and
the overall decline of wild maize populations have prompted this study. Five populations of Zea mays ssp.
parviglumis collected in Jalisco, M exico were planted in a common garden using a randomized compete block
design (RCBD) with five replicates. Eleven phenotypic traits correlated with plant fitness were measured. In
addition, previously generated microsatellite genotypes of the five populations were evaluated to determine
levels of neutral genetic diversity. Plants whose seed were sourced from larger populations had greater genetic
diversity and possessed phenotypic traits associated with higher fitness, while plants sourced from smaller
populations had traits characteristic of lower fitness. Plants from larger populations germinated more quickly,
reached anthesis sooner, demonstrated a higher level of photosynthetic activity, and produced more biomass,
suggesting a direct correlation between fitness of a population and genetic diversity. These results emphasize the
importance of preserving large populations of Zea mays ssp. parviglumis to limit inbreeding depression and
maintain the genetic diversity and adaptive potential of this germplasm.
Funding acknowledgement: National Science Foundation (NSF)
172
P207
Incorporation of functional information into genomic prediction models in maize
(submitted by Guillaume Ramstein <gr226@cornell.edu>)
Full Author List: Ramstein, Guillaume P 1; Buckler, Edward S2
Cornell University, 175 Biotechnology Building, Ithaca, NY 14853
2
USDA-ARS, 159 Biotechnology Building, Ithaca, NY 14853
1
Genomic prediction applied to plant breeding has achieved satisfactory accuracy for estimating the breeding
value of individual plants. However, underlying models have typically utilized genomic marker data for
capturing relatedness to individuals in a target breeding population, rather than depicting functional relationships
between marked loci and phenotypic traits of interest. As a result, genomic prediction models have often lacked
persistency in accuracy across population backgrounds.
This study aims to assess the benefit of annotation and expression information about marked loci to capture
robust functional relationships between such loci and traits of interest. Here we develop and calibrate genomic
prediction models on a diverse panel of 282 maize lines and test such models on breeding populations
represented by 25 families in the Nested Association M apping panel, each comprising up to 200 inbred lines.
Genomic prediction models use as input genomic marker data, but also leverage predictions about selection
intensity and/or gene expression levels of genes around marked loci. Selection intensity is based on conservation
features such as GERP scores and gene expression levels are predicted based on motif detection by convolutional
neural networks.
Our analyses assay the usefulness of diverse panels as reference for estimating breeding values in populations
that are genetically distinct, but relevant to breeding applications. In such context, functional information may
result in estimated effects of genomic loci that are more consistent across population backgrounds, hence
reducing the importance of calibrating genomic prediction models on specific panels constrained to be
genetically related to the target breeding population.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
173
P208
Influence of arbuscular mycorrhiza on stress resilience in a European maize
diversity panel
(submitted by Peter Muth <p.muth@lmu.de>)
Full Author List: Muth, Peter 1; Bauer, Eva2 ; Schön, Chris-Carolin2 ; Gutjahr, Caroline1 3
Faculty of Biology, Genetics, Ludwig-Maximilians University of Munich, 82152 Martinsried, Germany
2
Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
3
Plant Genetics, T UM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
1
Climate change is predicted to increase extended drought periods in many regions and even in temperate climates.
T hese pose threats to agricultural production and solutions to increase the stress resilience of crops are needed.
Arbuscular mycorrhiza (AM) is a symbiosis of plant roots with AM fungi, which extend the reach of root systems
through their extraradical hyphal network. AM improves uptake of mineral nutrients - especially phosphate (P) - and
has also been described to increase drought stress resistance. Increased plant performance due to AM was reported to
be subject to natural variation.
Here we examined the response to artificial AM-inoculation of the Dent parental founder lines of the maize EU NAM
population (Bauer et al. 2013) under varying field conditions, including drought. T he DH lines were grown for two
seasons, with or without inoculation with the AM-fungus Rhizophagus irregularis. T he three test sites were (1) a
conventionally-cropped rain-fed field, (2) a field with drought stress induced by a mobile rainout shelter, and (3) a lowP field.
Roots of all lines showed high AM colonization, both in the Rhizophagus-treated plots and in control plots due to
autochthonous AM fungi. Average root colonization across lines depended on the environment but did not change due
to Rhizophagus inoculation. Year, environment and inoculation influenced root colonization of individual lines. Under
drought stress, the average grain yield was higher in AM-inoculated lines than in control plots in year one, whereas no
significant difference was observed in year two. In the rain -fed field no average yield improvements occurred in either
year, whereas inoculation markedly improved average grain yield under low-P conditions. Individual lines profited
differently from AM-inoculation in the different environments.
T hese results lay a basis for a further elucidation of the factors underlying host -symbiont functional compatibility and
indicate that benefits from AM-inoculation depend on the environmental conditions.
Funding acknowledgement: BayKimaFit project association by the Bavarian State Ministry of Env ironment and
Consumer Protection
P209
Inheritance of short-season maize (Zea mays L.) senescence patterns
(submitted by Valerie Craig <craigv@uoguelph.ca>)
Full Author List: Craig, Valerie 1; Lee, Elizabeth A. 1 ; Earl, Hugh 1; Bowley, Steve1; Berg, Aaron2
Department of Plant Agriculture; University of Guelph; Guelph, Ontario, Canada, N1E0G6
2
Department of Geography; University of Guelph; Guelph, Ontario, Canada, N1E0G6
1
Maize (Zea mays L.) exhibits two patterns of senescence in the late grain filling period, either rapid senescence of the
photosynthetic tissues (die and dry) or delayed senescence (stay green). In short season environments such as Canada,
these patterns of senescence are significant since green leaf tissue present at maturity can affect the moisture content of
the grain and delay harvest. Although data on maize senescence patterns can be co llected, late season confounding
factors such as leaf diseases and environmental conditions can make accurate phenotyping difficult. T he goal of this
research is to develop a method for assigning senescence patterns early in the grain filling period to eliminate
confounding factors, as well as to understand the inheritance of senescence patterns across many genotypes.
Preliminary observations from 4 genotypes over 2 years showed that response to sink removal in the early grain filling
period correlated wit h senescence pattern. In the present study, 130 genotypes developed by a North Carolina Design II
mating scheme were used to assess senescence pattern heritability. A fixed wing unmanned aerial vehicle (UAV)
(Lancaster Rev5, PrecisionHawk) with multispectral RG-NIR and BG-NIR sensors were used to capture physiological
changes caused by prematurely removing the primary sink. Sinks were terminated 3 -weeks after silking in a single row
of a 2-row plot. In addition, a chlorophyll meter (SPAD 502 Plus, Spectrum T echnologies) was used to record
chlorophyll concentrations at sink termination and plant maturity. This research is designed to test if senescence pattern
is a heritable trait to aid breeders when making decisions on what germplasm to keep in breeding pro grams.
Funding acknowledgement: Natural Sciences and Engineering Research Council of Canada (NSERC), Canadian
Foundation for Innovation (CFI), Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA)
174
P210
Insights into heterotic patterns and allelic diversity of U.S. dent maize from
expired plant variety protection inbreds
(submitted by Mike White <mrwhite4@wisc.edu>)
Full Author List: White, Mike 1; Gage, Joseph 1; Vaillancourt, Brianna 2; Buell, C. Robin 2; Mikel, Mark 3; de Leon,
Natalia1; Kaeppler, Shawn 1
1
Department of Agronomy, University of Wisconsin, 1575 Linden Dr., Madison, WI 53706
2
Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824
3
Department of Crop Sciences and Roy J. Carver Biotechnology Center, Univ. of Illinois, 2608 Institute for Genomic
Biology, 1206 W. Gregory Dr., Urbana, IL 61801
The privatization and consolidation of commercial maize breeding in the United States has resulted in a highly
competitive industry. As a result, developers of elite maize inbreds pursue forms of intellectual property
protection to secure their proprietary germplasm. One form of intellectual property protection is the Plant Variety
Protection (PVP) system where novel inbred lines are protected for a period of 18-20 years. Upon expiration of
the PVP certificate, the previously protected PVP inbred is publically released via the North Central Plant
Introduction Station. Expired-PVP inbred lines can be an excellent source of elite germplasm to enhance or
initiate a breeding program. However, this can be challenging due to the cryptic information on background and
use of these lines, and frequent representation of novel nuances of heterotic families that have been optimized by
multiple breeding cycles to novel germplasm pools within proprietary breeding programs. A panel of 328
expired-PVP inbred lines was genotyped over 899K SNPs derived from RNA-sequencing. A hierarchical cluster
analysis grouped these expired-PVP lines based on genetic similarity into heterotic sub-groups. An
ADM IXTURE analysis was performed to approximate the genomic presence of eight heterotic sub-groups.
These analyses define the heterotic composition of the inbreds in the current set of publicly available expiredPVP germplasm. In conjunction with information provided in PVP certificates; the utilization of heterotic subgroups was estimated for Pioneer Hi-Bred, Dekalb-Pfizer, and Holden’s Foundation seed companies’ elite
germplasm from 1978-1998. To explore the effect of crossing between and among canonical heterotic patterns,
500 unique hybrids derived from expired-PVP inbreds were evaluated in a multi-environment yield trial
experiment. This information can greatly expedite the process of utilizing this set of elite germplasm for the
improvement of maize.
Funding acknowledgement: United States Department of Agriculture (USDA)
175
P211
Reconstruction of Ancestral Genotypes in a Multiparental Parallel Selection
Population
(submitted by Heather Manching <hcorn@udel.edu>)
Full Author List: Manching, Heather K 1; Dumas, Michael1; Weldekidan, T eclemariam 1; Shao, Eric2; Wills, David3 4; de
Leon, Natalia5; Flint-Garcia, Sherry 3 4; Holland, Jim 6 7; Lauter, Nick 8 9; Murray, Seth 10; Xu, Wenwei11; Wisser,
Randall1
1
Department of Plant and Soil Sciences; University of Delaware; Newark, DE, USA 19716
2
Robert R. McCormick School of Engineering and Applied Science, No rthwestern University; Evanston, IL, USA
3
USDA-ARS; Columbia, MO, USA 65211
4
Division of Plant Sciences; University of Missouri; Columbia, Missouri, USA 65211
5
Department of Agronomy; University of Wisconsin; Madison, Wisconsin, USA 53706
6
USDA-ARS; Raleigh, NC, USA 27695
7
Department of Crop Science; North Carolina State University; Raleigh, NC, USA 27695
8
USDA-ARS; Ames, IA, USA 50011
9
Interdepartmental Genetics Graduate Program; Iowa State University; Ames, IA, USA 50011
10
Department of Soil and Crop Sciences; T exas A&M University; College Station, T X, USA 77845
11
Lubbock Research and Extension Center, T exas A&M AgriLife Research, Lubbock, T X, USA
Genetic diversity is fundamental to environmental adaptation and breeding. However, capitalizing on exotic
germplasm, which harbors unique genetic variation, is challenging, because maladaptive phenotypes for some
traits can skew the phenotypic effects for other traits being evaluated in their non-adapted, but targeted
environment. Therefore, understanding the genetic response to selection for traits underlying adaptation is crucial
for overcoming genetic barriers to crop improvement. We created a TROPICal Synthetic (TROPICS) population
of maize from seven tropical inbred lines and performed parallel selection for early flowering time across a
latitudinal transect (eight locations spanning from Puerto Rico to Wisconsin) for two generations. During each
generation of selection and at each location, 384 individuals were genotyped from the extreme tails in flowering
time and from the base population (~12,000 total samples) which have been genotyped using genotyping-bysequencing (GBS). The optimum number of imputable markers was determined by assessing the accuracy of
imputation as a function of different thresholds for genotype call rates. Using this maximized marker density,
reconstruction of founder haplotype blocks for each of the 12,000 samples is being used to explore patterns of
recombination and determine founder contributions in selected populations. Allele frequency differences
between phenotypic extremes of the population were evaluated (extreme mapping), and several highly significant
associations were detected across generations in the same location, but were not present across all environments.
Populations from locations that exhibited the greatest phenotypic response to selection showed the greatest
differences in allele frequency at markers with significant differentiation. Ultimately, integrating genome-wide
imputation, reconstruction of ancestry blocks and tests for selection will provide new insight into the response to
selection and the identification of potential barriers to environmental adaptation. These analyses are ongoing and
the latest results from this study will be presented.
Funding acknowledgement: United States Department of Agriculture (USDA)
176
P212
Maize resistance to parasitism : life-cycles synchronisation matters
(submitted by Inoussa Sanane <inoussa.sanane@u-psud.fr>)
Full Author List: Sanane, Inoussa 1 2 ; Dillmann, Christine2; Marchadier, Elodie2; Kaiser-Arnaud, Laure1; Jeannette, Remi1;
Legrand, Judith 2
1
Génétique Quantitative et Evolution– Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay ;
Gif-sur-Yvette, France, 91190
2
Evolution, Génomes, Comportements et Ecologie, CNRS, IRD, Université Paris-Sud Université Paris-Saclay ; Gif sur
Yvette, France, 91190
Plants can escape herbivores either by building up defenses such as plant secondary compounds, or by shortening their
life-cycle so that they become mature before herbivore attacks. In France, Lepidoptera stem borers (pyralids) have a
two-generations/year life-cycle. In spring, adult females lay eggs on young leaves. During summer, second generation
caterpillars enter plant stems and dig galleries until ears. Completion of life-cycle occurs in non-harvested cobs during
winter. Among tools for biological pest controls, sowing early maize varieties is recommended because maize stems
are stronger when the second-generation larvae arise and better resist invasion.
T o analyse how plant phenology shifts interfered with Lepidoptera stem borers life-cycle, we used the plant material
coming from two independent Divergent Selection Experiments (DSEs) for flowering time in maize, that have been
conducted in Plateau de Saclay for more than twenty generations. T he two initial populations consisted in two seed lots,
each from a single inbred line, F252 or MBS. At each generation, we selected and selfed early and late flowering
plants. T he resulting Early and Late evolved populat ions exhibited pronounced phenotypic divergence for flowering,
while preserving original characteristics of the initial inbreds.
DSEs experimental designs from generation G20 and G21 were used to measure pyralids prevalence in Early and Late
populations from either F252 or MBS genetic backgrounds. Altogether range of variation for flowering time was
comprised between 1300 (mid-july, Early F252) and 1900 (mid-august, Late MBS) degree-days. Pyralids prevalence
was more important in Early than in Late MBS populations. For F252, there was no differences between Early and Late
populations, but average prevalence depended on the date of arrival of adults from the second generation (year effect).
Hence, in our plant material, sensitivity to parasitism is more relat ed to synchronization between insect and plant life
cycles than to maturity of leaves.
Funding acknowledgement: labex BASC
P213
Mapping loci that modify the efficacy of Teosinte crossing barrier 1
(submitted by Merritt Burch <merritt.b.burch@sdstate.edu>)
Full Author List: Burch, Merritt B1 ; Auger, Donald L 1
South Dakota State University; Departmet of Biology and Microbiology; Brookings; South Dakota; USA; 57006
1
Teosinte crossing barrier 1 (Tcb1) is a genetic cross-incompatibility factor that is responsible for blocking non-selftype pollen in silks. Originally found in teosintes, Tcb1-s (strong allele) has been introduced into modern maize
varieties conferring resistance to tcb1 pollen. Previous studies using a similar cross incompatibility system,
Gametophye factor 1 (Ga1-s) suggest that the cell wall modification enzyme ZmPme3, a pectin methylesterase, along
with multiple modifying QT L loci contribute to the effectiveness of silks at resisting foreign pollen types. In Tcb1, little
is known about the genetic modifiers and, more importantly, what the underlying biological mechanism is for this cross
incompatibility. Cross-incompatibility systems like Tcb1 and Ga1 can be beneficial to breeders and farmers when only
certain pollen types are desired on specialty maize crops. It was observed that nearly all the F1's of various inbreds,
including B73, crossed by W22 Tcb1-s demonstrate strong incompatibility with tcb1 pollen. One exception was Mo17,
whose F1s had weaker resistance. In this study we used recombinant inbred lines (RILS) from the intermated B73 Mo17 (IBM) population crossed with homozygous W22 Tcb1-s plants to test the efficacy of the various F1s at blocking
tcb1 pollen. T he F1s were tested by first challenging the Tcb1-s silks with R1 C1 tcb1 pollen and the next day
pollinated the same silks with r1 c1 Tcb1-s pollen. T he resulting ears were scored for the percentage of colored kernels.
Six quantitative trait loci (QT L) were detected on chromosomes 1, 3, 5, and 7 that explained 28.9% of the phenotypic
variability. Most modifying QT L loci showed simple additivity effects and epistatic interactions between loci. Further
exploration into these genomic regions and the underlying candidate genes is underway, these results could shed light
on the genetic and physiological mechanisms controlling Tcb1.
Funding acknowledgement: National Science Foundation (NSF), SDSU Experimental Station
177
P214
Mapping QTLs for Kernel Row Number and Fasciated Ear by SNP-Based Bulk
Segregant Analysis in Maize
(submitted by Silvio Salvi <silvio.salvi@unibo.it>)
Full Author List: Giuliani, Silvia1; T uberosa, Roberto 1; Salvi, Silvio 1
1
Department of Agricultural and Food Sciences, University of Bologna, viale Fanin 44, Bologna, Italy, 40127.
In maize, the number of kernel rows (KRN) of the ear is one of the most important grain yield components. Both
QTLs and M endelian mutations (such as abnormally shaped - Fasciated - ear mutants) have been discovered for
this trait and utilized to gain information on the molecular genetic control of ear development. In this study, two
Italian maize inbred lines were identified to show extreme phenotypes in terms of ear fasciation and low KRN,
respectively and utilized to develop three recombinant inbred line (RIL) populations. Two of the populations (A
and B) had the fasciated ear type inbred line as parent, while the third population (C) was generated by crossing
the elite line B73 with the low KRN line. The three populations were thoroughly phenotyped for ear morphology
and KRN in F5 and F6 generations and showed an overall continuous type of variation for ear traits. We next
attempted to map QTLs for fasciated ear and KRN using bulk segregant analysis (BSA) based on a high-density
maize SNP array (15k Illumina Infinium) in two successive years. Bulks included 15 plants (extremely fasciated
ear plants or wild-type ear plants for populations A and B, and plants with highest or lowest KRN for population
C). Preliminary results showed the presence of major QTLs segregating and affecting both ear fasciation and
KRN.
P215
MAZE - Accessing arbuscular mycorrhiza-mediated drought stress resistance in
a maize diversity panel
(submitted by Florian Berger <flo.berger@lmu.de>)
Full Author List: Berger, Florian 1; Gutjahr, Caroline 2
Faculty of Biology Genetics, University of Munich (LMU), Martinsried, Germany
2
Plant Genetics, T echnical University of Munich, Freising-Weihenstephan, Germany
1
Drought is one of the major constraints limiting productivity of crops, such as maize, worldwide. M ethods and
tools to limit negative effects of drought on yield are highly desired. Arbuscular mycorrhiza (AM ) is a
mutualistic symbiosis between more than 80% of land plants and fungi of the phylum Glomeromycota. The fungi
provide plants with mineral nutrients in exchange for carbohydrates and lipids. AM associations with plants have
been shown to enhance maize performance under drought stress conditions. Previous studies showed that the
positive effect of AM symbiosis on plant performance depends on the maize genotype, suggesting that AM
responsiveness is subject to genetic variation. To identify genotype specific AM -responsiveness we aim at
investigating drought stress resistance of 24 European maize Dent inbred lines in association with the AM fungus
Rhizophagus irregularis. In pilot experiments, we show increased root and shoot fresh weight of maize plants
associated with R. irregularis. Currently, we are establishing conditions to perform a phenotypic screen to
characterize genotype-dependent performance differences in response to AM fungi under well-watered and
drought stress conditions.
Funding acknowledgement: German federal ministry of Education and Research (BM BF)
178
P216
Natural variation for starch composition and processing characteristics of maize
(submitted by Mark Holmes <holme616@umn.edu>)
Full Author List: Holmes, Mark W 1; Weimer, Monika2; Bernardo, Rex 1; Annor, George2; Hirsch, Candice N1
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
2
Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108
1
Nixtamalization is an alkaline cooking process used in the production of corn chips and tortilla products. The
cooked kernels, referred to as nixtamal, need to have uniform moisture profiles within batches to ensure proper
processing and quality control of the final product. However, the compositional factors affecting water uptake
during nixtamalization are not well understood. Amylose and amylopectin content are hypothesized to
significantly affect nixtamal moisture, as the two starches have well characterized differences in moisture uptake
and retention. To test this hypothesis, we selected 100 spectrally and genetically diverse lines for compositional
analysis. Amylose and amylopectin ratios were analyzed with high performance liquid chromatography (HPLC).
Amylose chain lengths were also measured using an iodine affinity assay. Nixtamal moisture content was
measured using a small scale nixtamalization assay. Significant variation in nixtamal moisture (35-55%) was
observed, with amylose in the starch ranging from 69 to 86%, and the remainder of the starch being amylopectin.
These traits are being incorporated with other compositional traits including total starch, protein, fiber, oil, and
sugar in a machine learning framework to build a model to predict nixtamal moisture content.
Funding acknowledgement: PepsiCo
P217
Navigating the maize of short-season ancestry
(submitted by Laura Manerus <lmanerus@uoguelph.ca>)
Full Author List: Manerus, Laura 1; Lee, Elizabeth A. 1; Robinson, J.A.B2
1
Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2W1, Canada
2
Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
Preliminary statistical analysis on early, intermediate, and late maize germplasm lines suggest that the early
germplasm pool have a broader group of ancestral lines than what was originally proposed. A series of NC
Design II yield trials were conducted in 2016 as part of the Genomes to Fields (G2F ) project. Lines from
recently expired PVP certificates (off-PVP lines) or second generation lines of the off-PVP lines were chosen
based on diversity of originator (company and geographic) and on usage in commercial hybrids. The lines were
also stratified to generate a set of hybrids for testing in the Early G2F environments, the Intermediate and the
Late G2F testing environments. The early group is believed to have less genetic diversity due to a genetic
bottleneck from selection for earliness. However, the DII Early set exhibited the greatest genetic variation as a
percentage of the total variation for grain yield (23% vs. 15% vs. 5%), plant height (12%, vs. 6% vs. 5%), and
days to silking (9%, vs. 3%, vs. 1%). The DII Early set exhibited significant additive genetic variation in both the
males and females for grain yield, however, the DII Intermediate and DII Late sets did not exhibit any significant
genetic variation on the female side for grain yield. This has led to the hypothesis, the modern early season
germplasm base has founder lines that are not part of the founders of the corn belt dent germplasm base, which
will be examined in this study. A sample of short season germplasm represented by inbred lines from AAFC,
NDSU, early flowering off-PVP lines, and CG lines derived from short season commercial hybrids will be used
to determine the relationship of the proposed 7 founder lines with this germplasm pool and what this germplasm
pools most likely founders lines are.
Funding acknowledgement: NSERC, OM AFRA
179
P218
Omics-based prediction of hybrid grain yield in maize
(submitted by Felix Seifert <felix.seifert@cropseq.com>)
Full Author List: Seifert, Felix1 2 ; Thiemann, Alexander 2; Schrag, Tobias A. 3; Rybka, Dominika2 ; Melchinger, Albrecht E. 3;
Frisch, Matthias4; Scholten, Stefan 2 3
1
cropSeq bioinformatics, Ahornstr. 14, 22043 Hamburg, Germany
2
Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
3
Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599 Stuttgart, Germany
4
Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392 Giessen, Germany
Modern plant breeding uses hybrid breeding to achieve higher yields by exploiting heterosis, the increased vigor of
hybrids over their parental inbred lines, as well as taking advantage of uniform F1 populations.
Large numbers of parental inbred lines can be generated through doubled-haploid technology, but it is not feasible to
evaluate all their combinations in field trials. Genomic prediction supports the selection of inbred lines and their
combinations which are most promising to result in high hybrid grain yield and thereby increases the efficiency of the
selection process.
In this study we analyzed the relation of parental differences in SNP, messenger RNA expression and small RNA
expression profiles with hybrid grain yield. While larger differences in SNP and messenger RNA expression of parental
inbred lines are related to higher hybrid grain yield, the opposing trend was observed for small RNA expression.
We developed a prediction approach relying on positively and/or negatively associated differences of the analyzed
omics datasets with hybrid grain yield. T he prediction accuracies were compared for different prediction approaches as
well as test-cross scenarios for all three omics types. T he comparison resulted in the conclusion that different omics
types and prediction approach variants should be favored depending on the test -cross scenario to provide the optimal
prediction accuracy.
Funding acknowledgement: DFG
P219
Phenotypic and genetic dissection of cold tolerance in maize using controlled
environments and in-field evaluations
(submitted by Calli Anibas <canibas@wisc.edu>)
Full Author List: Anibas, Calli M. 1 ; Miller, Nathan D. 2 ; Hirsch, Cory D. 3; Enders, Tara A. 4 ; Springer, Nathan M. 4; Kaepler,
Shawn M. 1 ; Spalding, Edgar P. 2 ; De Leon, Natalia1
1
Department of Agronomy, University of Wisconsin, Madison, WI 53706
2
Department of Botany, University of Wisconsin, Madison, WI 53706
3
Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108
4
Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
Earlier planting is an important factor that positively contributes to increased maize yields. Identifying varieties that
combine improved germination, emergence, and vigor at early growth under suboptimal temperatures is an important
breeding objective. Our goal is to determine the genetic architecture of maize cold sensitivity in controlled
environments as it relates to in-field performance. A set of 33 inbred lines were selected for their cold tolerance
variability and were evaluated in replicated field trials in 2016 and 2017. Replications were planted on March 22,
March 29, and April 5 both years,46 - 26 days before optimal planting, May 1, which generated cold temperature
treatments. Seedlings were screened for emergence, the percentage of plants whose coleoptiles penetrated the soil
surface from the total planted, and seedling vigor, a rank scale which combined emergence, emergence rate determined
by growing degree units (GDUs) to 50% emergence and growth rate determined as GDUs from leaf stages V1 to V5.
Germination ranged from 0 to 93%, while 5 genotypes ranked highly cold vigorous (1- 2) and 8 highly cold susceptible
(9-10). Inbred lines B97 and P39 were among the most resistant genotypes, whereas B73 showed relative susceptibility
to suboptimal temperatures. Given the diverse performance of these three lines, we evaluated the recombinant inbred
line (RIL) of the Nested Association Mapping populations B73 X B97 and B73 X P39 in two controlled environments
with contrasting temperature treatments, 14 o/12 oC (cold) or 26 o/24 oC (control) 12 hour day and night cycle. We
deployed a high-throughput imaging platform, the Maize Architecture Analysis Station (M.A.P.S), to screen emergence
and seedling growth for 200 RILs from each population replicated twice per controlled treatment. T he information
collected will further our understanding about the genetic architecture of this economically important trait and facilitate
the comparison of phenotypic response of controlled environment evaluations with field conditions.
Funding acknowledgement: National Science Foundation (NSF), Forage Genetics International
180
P220
Phenotypic and genomic indicators of breeding program sustainability:
application to a north European grain maize program
(submitted by Antoine Allier <antoine.allier@inra.fr>)
Full Author List: Allier, Antoine 1; T eyssèdre, Simon 2; Lehermeier, Christina 2; Moreau, Laurence 1; Charcosset, Alain 1
UMR de Génétique Végétale, INRA – Université Paris-Sud – CNRS, 91190 Gif-sur-Yvette, France
2
RAGT 2n, BP 3336, 12033 Rodez, France
1
Successful plant breeding programs rely on balanced efforts between the development of competitive cultivars in
the short term and the maintenance/improvement of genetic diversity to guarantee longer term progress in the
genetic pool. Response to selection per breeding cycle is determined by selection intensity, selection accuracy as
well as the additive genetic variance of the trait. Hence, characterization of additive genetic variance and its
determinants in breeding populations is important for evaluating the progress expected from selection.
We propose indicators based on temporal phenotypic and genotypic data to analyze realized genetic gain and
evaluate its sustainability. Indicators were applied to a private (RAGT2n) early maize grain program implying a
Dent-Flint heterotic pattern.
The joint analysis of genetic gain and additive genetic variance over one decade of selection revealed a
significant positive genetic gain for grain yield in both Dent and Flint populations, along with a tendency towards
a decrease of the additive genetic variation. Recent genetic diversity introduction in the Flint population
contained this reduction and resulted in a higher additive genetic variance compared to the Dent population.
High-throughput SNP genotyping highlighted a slight trend towards a decrease in diversity in Dents and a more
stable diversity in Flints. It permitted to identify regions of the genome with a particularly low diversity, mainly
localized in pericentromeric regions, which might gain to be enriched by new introductions of external genetic
resources.
Since temporal series of phenotypic and genotypic data are available in most public or private breeding
programs, the presented approach can easily be implemented in the context of Genomic Selection.
Funding acknowledgement: RAGT2n, CIFRE-ANRT, INRA
P221
Plant phenotyping reveals genetic and physiological factors of plant performance
(submitted by Thomas Altmann <altmann@ipk-gatersleben.de>)
Full Author List: Muraya, Moses M. 1 2; Junker, Astrid1; Chu, Jianting1; Zhao, Yusheng1; Klukas, Christian 1; Reif,
Jochen C. 1; T schiersch, Henning1; Riewe, David1; Meyer, Rhonda C. 1; Knoch, Dominic 1; Heuermann, Marc 1; Altmann,
T homas1
1
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben; Germany; Seeland, 06466
2
Chuka University; Kenya; Chuka
Whole plant phenotyping integrated with genotyping and molecular profiling is used to uncover determining
factors and mechanisms of plant (growth) performance. It relies on IPK facilities for automated cultivation,
transport, and imaging of plants in climate controlled phytotron/glasshouse cabins equipped with diverse camera
and illumination systems and a broad range of environmental sensors. Beyond GWAS-based detection of QTL
for final biomass, water consumption, and water use efficiency, repeated non-invasive size monitoring of 261
maize dent lines revealed the complex genetics of growth dynamics: 12 main effect QTL and 6 pairs of epistatic
interactions displayed markedly different temporal patterns of activity. Some also affected relative growth rates
and 4 additional growth dynamics QTL were detected using nonparametric functional mapping and multivariate
mapping approaches. Thus, integrated time-resolved analyses are required addressing further physiological (e.g.
PS II efficiency) and architectural features found to vary strongly among IPK Genbank accessions.
181
P222
Plant Transformation Services
(submitted by Hyeyoung Lee <leehye@missouri.edu>)
Full Author List: Lee, Hyeyoung1; Zou, Yanjiao 1; Bui, Hien 1; Zhang, Zhanyuan 1
Plant T ransformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
65211
1
University of M issouri (M U) Plant Transformation Core Facility was established in 2000. The key mission of the
Facility is to enhance both basic and applied plant biology research by providing plant transformation services
and advancing transgenic technologies. Since 2000, the Facility has been providing state-of-the-art plant
transformation services. The services are on fees for cost recovery only, not for profit. The facility staff is
dedicated to providing various types of transformation services with a focus on maize (Zea mays), soybean
(Glycine max), switchgrass (Panicum virgatum), and sorghum (Sorghum bicolor). The service categories include
both standard and customized transformation. Transformation systems for all crops utilize Agrobacteriummediated approaches and somatic embryogenesis processes except for soybean. The Agrobacterium-mediated
cot-node transformation system coupled with organogenesis regime is employed for soybean transformation.
Research activities are geared towards developing high-throughput transformation systems, effective small RNAmediated gene silencing, gene stacking through coordinated transgene expression, and precise genome
modifications to meet the needs of crop improvement and genome discoveries. M ore details on the facility
operations and experiences as well as its impact on research collaborations and funding opportunities will be
discussed wherever appropriate during the presentation. Readers should find out more about M U Plant
Transformation Core Facility at http://plantsci.missouri.edu/muptcf/, email to Zhanyuan J Zhang at
zhangzh@missouri.edu, or call facility office at 573-882-6922 for specific service questions.
P223
Population structure and genetic diversity of different maize genotypes
(submitted by Snezana Mladenovic Drinic <msnezana@mrizp.rs>)
Full Author List: Mladenovic Drinic, Snezana D. 1; Nikolic, Ana S. 1; Kovacevic, Dragan R. 1; Markovic, Ksenija 1;
Andjelkovic, Violeta B. 1; Kravic, Natalija B. 1; Srdic, Jelena Z. 1
1
Maize Research Institute Zemun Polje, Belgrade, Serbia
Knowledge of genetic diversity and population structure among inbred lines provides a better understanding of
the genetic relationship between genotypes. A set of 40 maize inbreds belonging to five different kernal types
(white, yelow and orange kernel, sweetcorn and popcorn) from Gene Bank of M aize Research Institute „Zemun
Polje“ was subjected to molecular marker analysis with the aim of revealing genetic diversity and population
structure. Preliminary research was done using 20 informative SSR markers. Total number of detected alleles
was 104 with an average of 4.3. PIC value for all tested markers was greater than 0.6. The greatest Ho was
detected for sweetcorn while the lowest for white kernel maize group. Number of private alleles was the highest
for orange kernel maize group and the greatest number per genotype (4) was found for yelow kernel maize
genotypes. Better congruence with pedigree information was revealed using PCA than cluster analysis.
Variability among individuals was greater than inter-population variability which is not unexpected conidering
the fact that lot of inbreds inside one group are of very different origin. Selected genotypes will be further
investigated with a greater number of markers in order to better describe Gene Bank genotypes which will be
used in future breeding programs to better explore the genetic variability within and between groups to generate
new lines and hybrids.
Funding acknowledgement: M inistry of Education, Science and Technological Development of the Republic of
Serbia (TR-31068).
182
P224
Post breeding
(submitted by Anna Giulini <annapiamaria.giulini@crea.gov.it>)
Full Author List: Giulini, Anna P. M. 1; Bianchi, Pier Giacomo 1
CREA-DC Research Centre for Plant Protection and Certification, Via Venezian, 22, Milan, IT ALY 20133
1
The EU regulates the marketing of plant rep roductive material of plant species, ensuring that EU criteria for
health and quality are met. EU legislation is based on: registration of varieties or material and certification or
inspection of lots of seed and plant propagating material before marketing. The common catalogues of varieties
of agricultural plant and vegetable species list the varieties which can be marketed in the EU.
In Italy the procedure to list a new maize variety contemplates two years of field trial, coordinated by CREA -DC.
The variety will be list if it meets standards on: Distinctness, Uniformity, Stability (DUS test) and Value for
cultivation and use.
A key point in this work is to establish the distinctness of new plant material from all varieties of common
knowledge. Candidate varieties will be compared first on the paper (official description) and second side-by-side
in the field with similar other varieties already knowledge present in our reference collection (RC). In the RC,
indeed, should be present all varieties listed or protected (CPVO-UPOV); any other variety in common
knowledge. The establishment and the maintenance of the RC for comparative testing and evaluation in growing
trials lead to considerable time and cost expenditures, and large reference collections may be a major challenge
for Examination offices (EOs).
Besides some characteristics, observed for the description of the new variety during the DUS test, have strong
environmental influences as a result the valuation of the appropriate state of expression is not as much reliable
within the years and between the EOs.
In this time the network of entrusted Examination Offices is working to develop innovative solutions to face
difficulties of ever increasing trial size and related costs, as centralization of DUS of cert ain species, R&D
projects to build harmonize databases including e.g. phenotypical data (ring tests amongst entrusted EOs as
prerequisite) and molecular profiles and pictures.
P225
QTL for photosynthetic and yield performance in IBM population under two
different heat scenarios during flowering time
(submitted by Domagoj Simic <domagoj,simic@poljinos.hr>)
Full Author List: Galic, Vlatko 1; Franic, Mario 1; Jambrovic, Antun 1; Ledencan, T atjana 1; Simic, Domagoj1
1
Agricultural Institute Osijek, Juzno predgradje 17; Osijek, Croatia, 31000
It was demonstrated that extreme heat as a stressor could have more critical role for maize production than
drought in temperate areas. Accumulation of extreme temperatures (>30°C) is associated with increased vapor
pressure deficit (VPD) as a function of temperature and relative humidity used recently in maize genetic studies.
The objectives of this three-year study were 1) to compare photosynthetic performance during flowering with
grain yield, and 2) to analyze quantitative trait loci (QTL) for the performance in testcrosses of IBM population
under two different heat scenarios. PIABS - performance index for energy conservation from photons absorbed
by PSII to the reduction of intersystem electron acceptors was used as a parameter for the photosynthetic
performance. Two distinct geographic regions of Croatia (Osijek) and Turkey (Ayvalik) differed considerably in
VPD during flowering time (in average 2.5±0.3 and 3.4±0.3 kPa, respectively). The correlations between PIABS
and yield were notably stronger in environments with higher VPD (Turkey) reaching r=0.59. Inclusive composite
interval mapping (ICIM ) revealed a larger number of significant, but mostly environmentally dependent QTLs
for PIABS and grain yield. Some of them were associated to tolerance to heat stress because they were specific
to heat scenarios. Our complete quantitative genetic analysis for series of photosynthetic and agronomic traits
will be used for assessing the photosynthetic performance of maize genotypes as a function of grain yield in heat
stress environments.
Funding acknowledgement: Croatian Science Foundation (HRZZ), Project 5707
183
P226
QTL mapping and genomic predictions for silage quality traits in a multiparental
hybrid design
(submitted by Adama Seye <adama.seye@inra.fr>)
Full Author List: Seye, Adama I 1 ; Bauland, Cyril1 ; Giraud, Héloïse2 ; Charcosset, Alain1; Moreau, Laurence1
1
Génétique Quantitative et Evolution—Le Moulon, Institut National de la Recherche Agronomique, Université Paris–Sud,
Centre National de la Recherche Scientifique, AgroParisTech, Université Paris–Saclay; Gif-sur-Yvette, F-91190, France
2
Bayer CropScience; T echnologiepark-Zwijnaarde 38; Gent, 9052, Belgium
Maize (Zea mays L.) is commonly used as silage for cattle feeding or for biogas production in Northern Europe.
Improving whole plant biomass degradation is therefore a major breeding objective. Hybrid varieties selected for silage
generally result from crosses between Dent and Flint heterotic groups. It is therefore of key interest to identify loci
(QT L) involved in the General (GCA, parental values) and Specific Combining Ability (SCA, cross specific value)
components of hybrid value and find out in each group favorable alleles that can be combined in hybrids. We
implemented an original factorial design of 951 Flint x Dent hybrids obtained by crossing inbred lines issued from two
multiparental connected designs, one specific of each group. Inbred lines were genotyped for 20K SNPs and hybrids
were phenotyped in eight environments for silage production and quality traits (measured by near infrared
spectroscopy). For each quality trait, we (i) estimated GCA and SCA variance components, (ii) performed QT L
detection using new approaches adapted to our hybrid design and (iii) genomic predictions of GCA and SCA
components. We found a predominance of GCA over SCA in hybrid genetic variance. In total 230 QT Ls were detected
with only two showing significant SCA effects at the whole genome level and more than 80% of GCA QT L were
specific of one heterotic group. Each QT L explained less than 10% of the within-population phenotypic variance and
96% of them co-localized with at least one QT L of another trait suggesting pleiotropic effects. Good GCA predictive
abilities were obtained with both QT L and genomic models but genomic models outperformed QT L ones. T hese results
illustrate the complex genetic architecture of silage quality traits and are consistent with the divergence between
heterotic groups. T his work opens new prospects for improving maize hybrid performances for both biomass
productivity and degradability.
Funding acknowledgement: French National Research Agency, ProMaïs SAM-MCR program, West Africa
Agricultural Productivity Program.
P227
QTL mapping for fusarium seedling rot resistance in the recombinant inbred
crosses derived from MAGIC maize population
(submitted by Popi Septiani <popi.septiani@santannapisa.it>)
Full Author List: Septiani, Popi1 ; Lanubile, Alessandra2; Stagnati, Lorenzo2 ; Busconi, Matteo2 ; Nelissen, Hilde3; Pè, Mario
Enrico 1 ; Dell'Acqua, Matteo 1; Marocco, Adriano 2
1
Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy, 56127
2
Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy, 29100
3
VIB Centre for Plant Systems Biology, Ghent, Belgium, B-9052
Fungal infection by Fusarium verticillioides is cause of substantial reductions in maize yield and grain quality
worldwide. Developing natural resistance in maize genotypes is an effective way to achieve sustainable control of F.
verticillioides in the field, and breeding for resistance may be accelerated by identifying the quantitative trait loci
(QT L) responsible for disease resistance. T he multi-parent advance generation intercross (MAGIC) maize population,
built by the intercross of eight diverse inbred lines, was used to identify resistance QT L on a set of highly diverse
recombinant inbred lines (RILs). Phenotyping for F. verticillioides seedling rot (FSR) resistance was conducted with a
rolled towel assay (RT A) allowing a fast screening to identify resistant RILs. We identified three major FSR QT L that
were further dissected using transcriptomic and sequencing data to reveal candidate genes. As maize is cultivated
mostly as hybrids, the study of F. verticillioides resistance in hybrid background may significantly contribute to the
production of maize hybrids having higher field resistance. We developed a novel maize population crossing the
MAGIC RILs to produce recombinant inbred crosses (RIXs). RIXs were produced by crossing RILs in a chain design
over two seasons in Italy. T heir genomic diversity was derived from the haplotype composition of RILs in each
crossing pair, thus not requiring further genotyping. T he RT A screening for FSR was performed so far on 250 RI Xs,
reporting broad variation for the trait. These results will be used to study the heterotic contribution to FSR resistance in
maize.
Funding acknowledgement: European Union’s Horizon 2020 Grant Agreement No 678781 (MycoKey), International
doctoral programme in Agrobiodiversity Scuola Superiore Sant’Anna Pisa Italy
184
P228
QTLs affecting sweet corn carbohydrate content and eating quality in sugary1
(submitted by Kathleen Miller <kmiller46@wisc.edu>)
Full Author List: Miller, Kathleen M. 1; T racy, William F. 1
University of Wisconsin-Madison, Department of Agronomy, Madison, WI, USA 53706
1
There are three main endosperm genotypes for commercial sweet corn varieties: sugary (su1), sugary enhancer
(su1se1) , and supersweet (sh2) . The “sugary enhancer” genotype is a double mutant su1/su1, se1/se1 and
widely grown in fresh market production. Sugary enhancer quality has been attributed to an excellent texture,
good flavor, elevated sweetness, and a thin pericarp. However, sugary enhancer genotype trials show
inconsistencies in sugar and starch accumulation indicating other loci also contribute to sugary enhancer quality.
The objective of this research is to identify quantitative trait loci (QTLs) of modifier loci of sugary enhancer
quality in a su1 background in sweet corn, using F 5 recombinant inbred lines (RILs) derived by single seed
descent (SSD). Two populations were developed from biparental crosses of divergent sweetness, one
heterozygous for se1 and one homozygous. A linkage map of 20,000 SNPs was developed using a genotyping by
sequencing (GBS) method. With this, novel QTL on chromosome 5 and 6 were found to influence sucrose, total
sugar and starch content in Population 1. A QTL matching the se1 region was found to be most significant in
Population 2. A new predictive platform using Near Infrared Spectroscopy (NIRS) was developed to measure
starch, phytoglycogen, total sugar, sucrose, fructose, and glucose at the fresh eating stage and at the dry harvest
stage. This was validated with 10% random subsample using enzymatic lab assays and has a high throughput
predictive ability with a high R2.
Funding acknowledgement: United States Department of Agriculture (USDA)
P229
Relationships between resistances to Fusarium and Aspergillus ear rots and
mycotoxins contamination in maize kernels
(submitted by Slavica Stankovic <sstojkov@mrizp.rs>)
Full Author List: Stankovic, Slavica Z 1; Obradovic, Ana M 1; Nikolic, Milica V1; Savic, Iva J1; Krnjaja, Vesna S2;
Delic, Nenad S1; Stankovic, Goran J1
1
Maize Research Institute Zemun Polje, 11185 Belgrade, Serbia
2
Institute for animal husbandry, 11185 Belgrade, Serbia
Ear rots caused by different Fusarium and Aspergillus species are one of the most dangerous food and feed safety
challenges in maize production. The majority of the inbreds and hybrids are susceptible. The aim of this research
was to identify inbred corn lines resistant to pathogenic and toxigenic species - Fusarium graminearum Schwabe,
Fusarium verticillioides (Sacc.) Nirenberg and Aspergillus flavus Link and fumonisin and aflatoxin
accumulation. In field trials, a select group of 40 inbred lines was inoculated into the silk channel with fungal
spore suspension. After harvest, ears were rated for rot and evaluated for levels of aflatoxin or fumonisin
contamination. Only four inbred lines showed high level of resistance to all three investigated species, and had
low levels of both mycotoxins contamination. The highest number (65%) of investigated genotypes showed
moderate resistance to all three tested pathogenic species. A highly significant correlation between the resistance
to F. verticillioides and Aspergillus flavus was established. However, the correlation between the resistance to
Fusarium graminearum and the other two species was positive, but not statistically significant. Area of the ear
rotted by F. verticillioides and A. flavus was significantly correlated to toxin production for both fumonisin (r =
0.69) and aflatoxin (r = 0.51), indicating that inbreds aflatoxin resistance may also be good sources of fumonisin
resistance.
Funding acknowledgement: M inistry of Education, Science and Technological Development of the Republic of
Serbia (TR-31023)
185
P230
Romania’s 3,000 inbred lines collection as a reservoir of genetic diversity and the
use of its cytolines in linking phenotype to genotype
(submitted by Mihai Miclaus <mihai.miclaus@icbcluj.ro>)
Full Author List: Miclaus, Mihai1; Calugar, Roxana1 2; Vana, Carmen 1 2; Suteu, Dana1; Bacila, Ioan 1; Has, Voichita2;
Bruggmann, Remy 3
1
National Institute for Biological Sciences, Cluj-Napoca, Romania
2
Agricultural Research and Development Station, T urda, Romania
3
Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
A collection of more than 3,000 maize inbred lines is being preserved in Romania’s six stock centers, the
Agricultural R&D Station, Turda, being the most important one. These lines are a “hidden treasure” worth
investigating. We previously genotyped a subset of 90 inbred lines from this collection (Suteu et al., 2013, PLoS
One) uncovering its allelic richness and therefore its potential in breeding programs worldwide. We are currently
analyzing 250 more inbred lines and we are planning to genotype-by-sequence 1,200 more this year, in an effort
to unlock the full potential of the Romanian germplasm in terms of predictive breeding. Concurrently with
harnessing the power of heterosis to create superior hybrids, (based on the heterotic pools defined by genotyping)
local breeders have also created cytolines by transferring the nucleus of valuable inbred lines to other cytoplasms
through repeated backcrosses. Such cytolines show improved phenotypical traits. Using RNA-seq, we have
defined a core set of genes that are differentially regulated in the cytoplasm-donor lines compared to their
nucleus donor line in relation to three traits of interest (yield, taller plants and increased resistance to Fusarium).
We argue that the genes we identified are responsible for the cytolines’ improved phenotypes.
Funding acknowledgement: Romanian National Authority for Scientific Research, CNDI-UEFISCDI
P231
Root phenotypic and transcriptomic variation in the European maize landrace
Petkuser in response to cold
(submitted by Felix Frey <ffrey@uni-bonn.de>)
Full Author List: Frey, Felix P 1; Baldauf, Jutta A1; Presterl, T homas3; Ouzunova, Milena3; Schön, Chris-Carolin 2;
Hochholdinger, Frank 1
1
Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Universität Bonn, Friedrich -EbertAllee 144, 53113 Bonn, Germany
2
Department of Plant Breeding, T echnische Universität München, Liesel-Beckmann-Str. 2, 85354 Freising, Germany
3
KWS SAAT AG, 37555 Einbeck, Germany
M ost commercial maize cultivars in temperate Europe are not sown before M ay due to their cold susceptibility.
Increasing their cold tolerance can prevent yield losses, which occur due to late cold stress events during spring.
Furthermore, cold tolerant cultivars have greater yield potential due to an earlier sowing date. European
landraces have a great yet untapped potential in improving cold tolerance, as they harbor high genetic diversity
for cold tolerance, which can be made available to breeders. The response of plant roots to environmental
stresses like cold is not well understood up to present. However, roots have essential functions for plant growth
such as anchorage and the uptake of water and nutrients. We aim to assess the phenotypic diversity present in
European landraces with respect to cold tolerance.
Therefore we screened a doubled-haploid population generated from the landrace Petkuser for cold tolerance
during early root development using high-throughput controlled platforms and automated analyses of root traits.
Significant genotypic variation for cold tolerance was found within the population with growth rates ranging
from 16% to 72% at cold conditions compared to control conditions. To assess the influence of gene expression
differences on cold tolerance we selected a set of 20 extreme genotypes for transcriptome sequencing, which is
currently in progress.
Identification of candidate genes for cold tolerance and the association of gene expression with phenotypic traits
related to cold tolerance in roots is a major focus of our experiments and will help to further understand the
genetic mechanisms controlling cold tolerance in maize. These results will also help to improve breeding of cold
tolerant cultivars.
Funding acknowledgement: German Federal M inistry of Education and Research (BM BF)
186
P232
ThaliaDB, a tool for data management and genetic diversity data exploration
(submitted by Delphine Steinbach <delphine.steinbach@inra.fr>)
Full Author List: Beaugrand, Alice B1; De Oliveira, Yannick D 1; Madur, Delphine M 1; Bauland, Cyril B1; Nicolas,
Stéphane N1; Moreau, Laurence M 1; Charcosset, Alain C1; Steinbach, Delphine S1
1
Genetique Quantitative et Evolution - Le Moulon; Gif sur Yvette; France 91190
Diversity and association genetics studies lead to manipulate a large number of individual, lines, clones and/or
populations. M oreover, emergence of high-throughput technologies for both genotyping and phenotyping
generates a large amount of data. These data need to be stored and managed in order to make requests and to
organize datasets to be able to perform genetic diversity data exploration and association genetics analysis. The
new version of ThaliaDB, V3.2, is developed for scientists to facilitate their data management and analysis. The
database holds genetic resources data (germplasm/accessions), seed lots, samples, markers and genotyping and
phenotyping datasets (fields environments, multiple traits and conditions). It is well adapted for data, useful to
apply GWAS or genomic selection methods. It can manage high-throughput results coming from different
projects and experiments and propose several views and options to explore these data and to give access to them
for reuse. This Web tool offers to users a Select (Data view) mode and an Admin (Data administration and
loading) mode. Data confidentiality is maintained using user accounts and specific levels of rights can be set on
data. It enables data extraction in CSV format. A version exists today in our lab with maize data produced from
projects of A. Charcosset’s GQM S team and theirs partners. Perspectives are to use it for tomato, wheat and
poplar data. The software is currently in improvement with funding of Amaizing, Investment for the future,
project. It is developed in Python under Framework Django, running under PostGreSQL and M ongoDb
databases management systems. Contact: delphine.steinbach@inra.fr for more information and collaboration.
Funding acknowledgement: French National Agency (ANR) and French National Institute for Agnonomical
Research (INRA)
P233
The dynamics of adaptive response under strong selection regime in small
populations
(submitted by Arnaud Desbiez-Piat <arnaud.desbiez-piat@u-psud.fr>)
Full Author List: Desbiez-Piat, Arnaud1; T enaillon, Maud I. 1; Huet, Sylvie2; David, Olivier 2; Dillmann, Christine 1
1
Génétique Quantitative et Evolution – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisT ech, Université ParisSaclay ; Gif-sur-Yvette, France, 91190
2
MaIAGE, INRA, Université Paris-Saclay ; Jouy en Josas, France, 78350
Two independent Divergent Selection Experiments (DSEs) for flowering time in maize have been conducted
under agronomical conditions in Plateau de Saclay for more than twenty generations. The two initial populations
consisted in two seed lots, each from a single inbred line. At each generation, we selected and selfed early and
late flowering genotypes. By selecting from such a narrow genetic basis, we expect to have enriched populations
for (epi)genetic differences controlling flowering time, while preserving the original characteristics of the initial
inbreds. Using genetic markers and transcriptomic data, we identified a number of (epi)genetic differences. In
order to address questions related to the role of new mutations versus standing variation in the response to
selection, and to the rate and limits of adaptation, we have implemented a revised version of the animal model
that explicitly accounts for new mutations. In this model, the observed response to selection is treated as a
quantitative trait, driven either by shifts in average phenotype or plastic changes. From the dynamics of the
selection response, we quantified the input of new mutations over generations. In addition, we implemented a
population genetic model that describes the fate of a new mutation, in this high selection-high drift design. We
discuss how, in these conditions, drift can accelerate fixation of adaptive mutations.
Funding acknowledgement: INRA, Labex Basc
187
P234
The effects of artificial selection on stability and GxE in the Iowa stiff stalk synthetic
maize population
(submitted by Bridget McFarland <bamcfarland@wisc.edu>)
Full Author List: McFarland, Bridget A. 1 ; Falcon, Celeste M. 1; Gage, Joseph L. 1 ; Jarquin, Diego 2; Romay, Cinta3; Consortium,
G2F4 ; Kaeppler, Shawn M. 1; de Leon, Natalia1
1
University of Wisconsin- Madison; Madison, WI, USA
2
University of Nebraska-Lincoln; Lincoln, NE, USA
3
Cornell University; Ithaca, NY, USA
4
genomes2fields.org
A plant’s expressed phenotype is a function of the genotype, the environment and the differential response of genotypes
to variable environments, known as the genotype-by-environment (GxE) interaction. While GxE affects plant
performance, little is known about how artificial selection for high productivity has altered this adaptation response of
genotypes to environmental variations. T he focus of this project is to assess how selectio n has affected various
agronomic traits, how GxE responses have been altered through selection and to determine biological controls of GxE
due to this selection process. In 2016 and 2017, inbreds ranging from highly selected (recently expired plant variety
protection) to founder lines from the Iowa Stiff Stalk Synthetic (BSSS) maize population were crossed to the tester
3IIH6 and evaluated in replicated trials across 32 locations as part of Genomes to Fields GxE Project. Agronomic and
productivity traits were measured for the set of hybrids. GxE explained 13.8% of the phenotypic variability of grain
yield. T o evaluate the performance of unselected and selected lines relative to each other across environments, a
Finlay-Wilkinson regression and stability analysis were used. Yield slope and mean square error (MSE) from the
regressions demonstrate that selection for yield in maize lines resulted in a decrease in slope range from 0.6 -1.3
(environmental mean/hybrid) in the selected set to 0.2-1.5 in the unselected group. T here was also a significant
reduction in the range of MSE from 1.6-4.0 in the selected set compared to 1.1-9.9 for the founder set. Genotype
responses of slope near 1 and reduction in MSE suggest that the highly selected lines are more stable in pe rformance
across environments compared to lines that have undergone less selection. T his work will enable future phenotype genotype associations of phenotypes and genotypes to enhance our understanding of GxE and breeding approaches.
Funding acknowledgement: United States Department of Agriculture (USDA)
P235
The effects of host and environment on the maize microbiome
(submitted by Jason Wallace <jason.wallace@uga.edu>)
Full Author List: Wallace, Jason G. 1 ; Kremling, Karl A. 2 ; Walters, William A. 3; Lepak, Nicholas K. 5 ; Ley, Ruth E. 3; Buckler,
Edward S. 2 4 5
1
Department of Crop and Soil Sciences, T he University of Georgia, Athens, Georgia, USA
2
Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, USA
3
Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tuebingen, Germany
4
Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA
5
United States Department of Agriculture – Agricultural Research Service, Ithaca, New York, USA
Every maize plant has billions of microscopic organisms living in, on, and around it. T hese microbial communities—
collectively called a “microbiome”—have great potential to influence plant growth, but the extent of t heir influence and
the degree to which the host plant shapes them is unknown. We address the question of how much influence the host
and the environment have on microbiomes by looking at bacteria in the maize rhizosphere (roots) and phyllosphere
(leaves). T hese two communities show very different makeups: the rhizosphere is highly complex, while the
phyllsophere is dominated by <20 bacterial taxa. Environment is the largest driver of the rhizosphere community; host
genetics has little direct effect but does show strong gene-by-environment interaction. Broad- and narrow-sense
heritability analyses in both communities show that a subset of microbes are moderately affected by host genetics
(heritability of 0.3-0.6), while the majority show little effect of the maize genotype. We also identify several metabolic
pathways in the phyllosphere that may be shaped by host genetics. T aken together, these results indicate that the maize
host exerts only partial control over the makeup of its rhizosphere and phyllosphere communities, and in many cases
the environment and/or stochastic chance play a larger role. In addition, the metabolic capacity of these communities
may be more important than their taxonomic identity. More work needs to be done to determine to what extent these
communities affect their host plant, and to determine if and how manipulating them can benefit agriculture.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture (USDA),
University of Georgia; Cornell University; Max Planck Institute for Developmental Biology
188
P236
The phenotypic characterization of the BALANCE maize panel reveals high
potential to discover genetic determinants involved in drought response
(submitted by Clemetn Buet <clement.buet@biogemma.com>)
Full Author List: Lopez, Jeremy 1; Blancon, Justin 1; Lassagne, Herve 1; Desmaizieres, Gregory 1; Dubreuil, Pierre1;
T ixier, Marie-Helene1; Praud, Sebastien 1
1
BIOGEMMA, Centre de Recherche, Route d'Ennezat, Chappes 63720, France
Relevant phenotyping plays a major role to understand the genetics of quantitative traits involved in the adaptive
response to drought. The high phenotypic diversity of the BALANCE maize panel (derived from a M AGIC
population) makes it a suitable material for the analysis of such a trait and for high throughput phenotyping
efforts. To target the morpho-physiological traits that affect yield in drought condition, the BALANCE panel has
been phenotyped in a network of field experiments in contrasting environments. Twenty -seven field experiments
(combinations location x year x water regime) were performed across France, Hungary, Romania and Chile.
Classical agronomical traits such as yield and its components, flowering time, plant height were collected in the
field trials. Innovative phenotyping, such as spectral reflectance measurements using multispectral sensors
mounted on a UAV, were also measured in a few trials: this gives access to vegetation indices, growth rate and
staygreen through the plant cycle. Root architecture in relationship with drought condition is investigated in a
greenhouse platform through the current M IRGA project (ANR Funding). Environmental conditions are taken
into account in all experiments in order to classify trials into well-defined stress scenarios. Soil water status is
characterized to model water balances in the field. Adapted experimental designs and statistical approaches are
used to improve the accuracy of phenotypic values. The heritability for each trait is calculated. This accurate and
relevant phenotyping of the BALANCE panel developed by BIOGEM M A coupled with its deep molecular
characterization makes it an attractive resource to better understand mechanisms underlying adaptive response to
drought stress and ease the identification of relevant candidate genes.
P237
The ProSpect of traditional and molecular breeding.
(submitted by Nicola Bacciu <nicola.bacciu@keygene.com>)
Full Author List: Bacciu, Nicola 1; Bouman, Niek 1; Huvenaars, Koen 1; Doeswijk, T imo 1; van Ham, Roeland1
1
KeyGene, Agro Business Park 90, 6708 PW Wageningen, T he Netherlands
In modern breeding, many different selection strategies are at the disposal of the breeder. Which one to use
depends on three key factors: i) genetic complexity of the trait(s) that need to be improved, ii) number of traits to
be improved simultaneously, and, iii) available resources (financial, logistics, etc.). Currently, the decision often
relies on experience, tradition and intuition, and draft cost calculations for candidate scenarios. However, when
multiple and more complex traits are being set as targets for a new breeding program, choosing the optimal
selection strategy may become extremely challenging. In such circumstances, it is valuable to be able to integrate
knowledge and experience with tools to simulate and evaluate breeding scenarios in silico. This allows a breeder
to systematically consider many of the variables that impact a breeding program. The breeding platform ProSpect
developed by KeyGene provides exactly such a system. The platform provides an open strategic decision support
system to explore costs and benefits of a wide range of breeding scenarios. M ost notably, the system enables
testing the most advantageous applications of three major selection strategies, i.e. phenotype selection (PS),
M arker Assisted Selection (M AS) and Genomic Selection (GS), and combinations of those in the context of
complex breeding programs. ProSpect enables users to find answers to their breeding questions not only by
running predefined simulations, but also by further developing the platform according t o their own specific
needs. Results from different selection strategy scenarios will be shown and compared.
189
P238
The Zea French Biological Resource Centre: conservation and utilization of
maize genetic resources in France
(submitted by Anne Zanetto <anne.zanetto@inra.fr>)
Full Author List: Zanetto, Anne 1; Palaffre, Carine2; Bauland, Cyril2 7; Beigbeder, Jean 4; Castel, Stéphanie2; Gouesnard,
Brigitte3; Lambert, Antoine 4; Raynaud, Christophe 5; Welcker, Claude6; Charcosset, Alain 7
1
INRA, UMR AGAP, Site de Lavalette ; Cirad - Avenue Agropolis ; 34398 Montpellier Cedex 5 France
2
INRA, UE SMH : Unité Expérimentale SMH Maïs, Inra Nouvelle-Aquitaine-Bordeaux, 2297, route INRA 40390
Saint-Martin-de-Hinx, France
3
INRA, UMR AGAP, Campus de la Gaillarde, Inra - Place P. Viala, 34060 Montpellier Cedex 1, France
4
ProMaïs, 17 rue du Louvre – 75001 Paris, France
5
INRA, UE Diascope, Domaine de Melgueil, 34130 Mauguio, France
6
INRA, UMR LEPSE, Univ. Montpellier, 34060, Montpellier, France
7
UMR Génétique quantitative et évolution, Ferme du Moulon, 91190 Gif/Yvette, France
M aize genetic resources are organized in France through the French maize genetic resources network. It includes
public (INRA) and private actors (ProM aïs association). M aize Genetic resources include 1600 open pollinated
populations and 4600 inbred lines. Their management is run by the Zea BRC (Biological Resource Center)
shared between the UM R AGAP (populations) and the maize Experimental Unit of Saint M artin de Hinx (inbred
lines). At national level, the Zea BRC is included in the French network RARe (Infrastructure Ressources
Agronomiques pour la Recherche) and in the Plant network ARCAD. The basic activities of the Zea BRC are
conservation, distribution and multiplication of populations and inbred lines. Genetic resources are distributed
following international rules either with the International Treaty on Plant Genetic Resources for Food and
Agriculture, the Nagoya Protocol or private rules (depending on the accession status). Information on genetic
resources is available in the national database (Siregal) and a national portal (Florilège). Information on the
traditional cultivation and use practices of populations can also be found on the Promaïs website.
A large fraction of these genetic resources have been characterized for their genotypic diversity and phenotypic
variation by the CRB and partner research labs. Genotyping of populations and first cycle inbred lines revealed
new features regarding the introduction and spread of maize in Europe, as well as local geographical trends
(Brandenbourg et al., 2017, Nicolas et al., Diaw et al., this meeting). Broad or heterotic group specific panels of
inbred lines have been defined within CornFed, DROPS and Amaizing projects to conduct Genome Wide
association mapping revealing key loci for flowering time, heat and drought tolerance (M illet et al., 2016,
Bouchet et al., 2017, Gouesnard et al., Blein-Nicolas et al., this meeting). These valuable resources allowed the
development of multi-parental populations and introgression libraries to further dissect the genetic mechanisms
of adaptation traits.
Discussions have been started at European level, to build a European Zea network to reinforce the means in
conservation ant utilization of European maize genetic resources. The network would also permit a better sharing
of taskforces and means in Europe and avoid gaps and losses in temperate genetic resources in Europe.
190
P239
Three chromosomal segments have a strong effect on photosynthesis and ability
of maize plants to transition to autotrophy under chilling conditions
(submitted by Catherine Giauffret <catherine.giauffret@inra.fr>)
Full Author List: Lourgant, Kristelle 1; Clipet, Camille1 3; Chemin, Claire1; Negro, Sandra3; Sellier-Richard, Hélène2;
Rabier, Dominique2; Decaux, Benoît 2; Hû, Jean-François2; Madur, Delphine3; Combes, Valérie3; Bauland, Cyril3;
Palaffre, Carine4; Castel, Stéphanie4; Altmann, T homas5; Brunel, Dominique6; Le Paslier, Marie-Christine6; Nicolas,
Stéphane3; Moreau, Laurence3; Charcosset, Alain 3; Giauffret, Catherine 1
1
UR AgroImpact, INRA, France
2
UE GCIE, INRA, France
3
UMR GQE–Le Moulon, INRA, Université Paris-Sud, CNRS, France
4
Unité expérimentale maïs, INRA, France
5
Max-Planck Institute for Molecular Plant Physiology, IPK, Germany
6
UR EPGV, INRA, Centre National de Génotypage, France
In maize, transition to autotrophic growth is hampered by cold temperatures. Plants from susceptible lines can
die after seed reserves have been exhausted if temperatures remain below 13°C. We used genome-wide
association mapping or linkage analysis to identify quantitative trait loci related to the ability of plants to
transition to autotrophy under chilling conditions.
We analysed a highly diverse panel of 293 dent lines. This panel was genotyped with a 50k SNP array and by
sequencing, providing approximately 500,000 useful markers for genome-wide approaches. The lines were
crossed to a flint tester and phenotyped as hybrids in cold greenhouses. We also analysed two doubled-haploid
populations derived from crosses between European dent inbred lines. The t wo populations of about 100
individuals each were genotyped with a 50k SNP array and approximately 700 markers from framework maps
were retained for QTL mapping. The inbred lines were phenotyped in cold greenhouses. Each panel or
population was evaluated for several traits including vigour rating after 4 weeks of cold treatment. For each panel
or population, a major QTL for vigour rating was highlighted.
Near-isogenic lines for each of these 3 QTL were constructed by marker-assisted backcrossing in cold-tolerant or
cold-sensitive recipient line followed by selfing. Pairs of QTL-NILs were phenotyped in a cold growth chamber.
All lines carrying the sensitive allele showed a strong reduction in vigour rating. A significant depression of
chlorophyll content and quantum yield efficiency of photosystem II was observed for the lines with a coldtolerant background and plant mortality occurred for the lines with a cold-sensitive background.
Further studies in field conditions will help breeders to decide how much att ention they should pay to such
alleles in their breeding programs.
Funding acknowledgement: ANR and France Agrimer (AM AIZING project), ANR, BMBF and M ICINN
(CORNFED project)
191
P240
Towards cloning of a major chilling tolerance QTL in maize
(submitted by Karin Ernst <karin.ernst@hhu.de>)
Full Author List: Ernst, Karin 1; Kirschner, Sandra1; Presterl, T homas2; Scheuermann, Daniela 2; Pestsova, Elena1;
Geiger, Hartwig3; Ouzunova, Milena 2; Westhoff, Peter 1
1
Heinrich-Heine-University Düsseldorf; Düsseldorf, Germany, 40225
2
KWS SAAT SE, Einbeck; Germany, 37555
3
University of Hohenheim, Stuttgart, Germany, 70599
Chilling tolerance is an important prerequisite for cultivation of high-yielding energy maize in central and
northern Europe. QTLs for chilling tolerance were identified in a double-haploid population constructed by a
cross of a chilling-sensitive and a chilling-tolerant line. One of the major QTLs explaining 34 % of the
phenotypic variation was mapped on chromosome 4. The QTL was validated by field tests of Near Isogenic
Lines (NILs) carrying small introgressions of the tolerant line in the genetic background of the sensitive line.
Different types of markers were developed to narrow down the QTL to an interval accessable for building a
BAC-contig. BAC libraries of both parental lines were constructed and BACs covering the QTL were isolated
and sequenced by Illumina, 454- and PacBio-technology. The reads were de novo assembled and contigs up to
120 kb were obtained. The contigs derived from the tolerant line were compared with those derived from the
sensitive line. Surprisingly most of the sequences seemed to be identical between the tolerant and sensitive line.
Hence the QTL could be diminished to an intervall of only 500 kb. Additional experiments were necessary to
narrow down unequivocally the chilling tolerance QTL to a certain gene within the 500 kb. Hence, to
complement this map-based cloning approach, the expression of the genes identified within this 500 kb region
was analysed by REAL-time PCR. While most of these genes showed no expression differences between tolerant
and sensitive lines, three of these genes showed chilling dependent expression differences in those lines. These
results were confirmed by Illumina sequencing of RNA.
Funding acknowledgement: Federal M inistry of Education and Research, Germany
P241
Transcriptomic analysis of senescence in maize inbred lines with different rate of
senescence
(submitted by Bernardo Ordas <bordas@mbg.csic.es>)
Full Author List: Caicedo, Marlon 1; Padilla, Guillermo 2; de la Fuente, María1; Ordas, Bernardo 1
Mision Biologica de Galicia (CSIC), Carballeira 8 Salcedo, Pontevedra, 36143
2
Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, Madrid 28040
1
Behind the physiological and metabolic changes occurring at maize senescence there are changes in the
expression of thousands of genes. We carried out a genomewide analysis of the changes in gene expression
during leaf senescence in seven inbred lines of maize which differed in the rate of senescence. The lines were
planted in a randomized completely block design with 2 replications in a single environment. Chlorophyll
content and CO2 exchange were measured from flowering to complete senescence each 15 days in the middle
part of the ear leaf of three plants per plot. Samples of the middle part of the ear leaf of three plants per plot were
taken and mixed each 15 days from flowering to complete senescence. RNA library construction and sequencing
were performed with TruSeq Stranded mRNA Library Prep Kit and HiSeq 4000 PE100 platform (Illumina Inc).
Following reads alignment, annotation, and a differential expression analysis we detected 1083 and 588 genes
that were up and down regulated, respectively, during the senescence in all seven lines. Because the genes were
consistently detected in different lines we are confident in their involvement in senescence. However, some
genes were detected in some lines, but not in others. For example, 1747 genes were detected only in 3 of the
lines, indicating that the genes expressed at senescence partially depend on the specific lines. The genes that were
down regulated were mainly involved in photosynthesis, while the genes up regulated were related to catabolic
processes. 196 of the differentially expressed genes codified for transcription factors; some of them are
homologous to transcription factors found in Arabidopsis in different signaling pathways, for example, ATAF1,
GLK1, PIF5, JUB1, or AtNAP.
Funding acknowledgement: Spanish National Plan of R+D, FEDER
192
P242
Turbocharging germplasm banks: genomic prediction goes into micro-world
(submitted by Xianran Li <lixr@iastate.edu>)
Full Author List: Li, Xianran 1; Leiboff, Samuel2; Yu, Xiaoqing1; Guo, T ingting1; T odt, Natalie2; Zhang, Xiaoyu3;
Muehlbauer, Gary 4; T immermans, Marja 5; Schnable, Patrick 1; Scanlon, Michael2; Yu, Jianming1
1
Iowa State University; Ames, IA, USA 50011
2
Cornell University; Ithaca, NY, USA 14853
3
University of Georgia; Athens, GA, USA 30602
4
University of Minnesota; St. Paul, MN, USA 55108
5
Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA 11724
Effective evaluation of millions of genetic stocks is challenging, but it represents a great opportunity towards
achieving global food security. Genomic prediction is a promising strategy to explore the potential of germplasm
banks. Accurate predictions have been obtained for height, yield, and other macro-phenotypes. However, no
studies have been reported on whether genome prediction is applicable for the micro-phenotype at the cellular
level. Here, we tested the power of genomic prediction for nine maize traits measured from shoot apical
meristem (SAM ), which generates all above-ground organs. With 435,713 SNPs, we predicted the SAM cellular
phenotypes for 2,687 maize diverse inbreds with models trained from 369 maize inbreds. The mean prediction
accuracy from empirical validation with 500 inbreds reached 0.54, suggesting that genomic prediction can be
applied for cellular phenotypes. Significantly higher prediction accuracies were further achieved by leveraging U
statistics (upper bound of reliability) developed from genomic information alone. Our study expanded territories
of genomic prediction for turbocharging germplasm banks from macro-phenotype space into micro-phenotype
space.
Funding acknowledgement: National Science Foundation (NSF)
P243
Unleashing genetic diversity by increasing meiotic recombination : an in silico
benchmark
(submitted by Elise Tourrette <elise.tourrette@inra.fr>)
Full Author List: T ourrette, Elise1; Falque, Matthieu1; Martin, Olivier C. 1
Génétique Quantitative et Evolution – Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisT ech, Université ParisSaclay; Ferme du Moulon; 91190 Gif-sur-Yvette; France
1
Genetic diversity is the fodder of genetic progress during selection processes, whether natural or artificial.
Recombination during meiosis generates genetic diversity via the formation of crossovers which thus shuffle
allelic combinations. Crossovers are heterogeneously distributed along chromosomes (hot and cold regions). This
is important because for example in maize, 30% of the genes are in very cold regions and they arise with
significant polymorphism. Selection can be impeded if advantageous alleles arise in such cold regions as they are
thus difficult to extract or separate from nearby disadvantageous alleles.
We have been studying the influence of recombination rate, recombination landscape and other parameters
(selection intensity, population size, genetic architecture such as the distribution and effects of QTLs) on the
behavior of genetic gains and diversity when populations are subject to recurrent selection in breeding programs.
Our approach is based on simulations using a quantitative genetics framework. We focus on plant breeding in
maize, barley, cacao and Arabidopsis, investigating different ways of modifying recombination according to
what is known to be possible experimentally today: modification of the genome-wide recombination rate
(HyperRec technology), enhancement of recombination in cold pericentromeric regions (e.g., in the context of
triploids), and targetting hot spots to specific parts of the genome.
To extract information about the behavior of the population througout in silico breeding programs, we measure
different observables, including genetic gain, genetic diversity, linkage disequilibrium and also the
coupling/repulsion status between loci. With our simulations, we identify how the different breeding choices and
scenarios for modifying recombination influence the genetic gains achieved across successive generations.
Funding acknowledgement: labex SPS (M ERCI project), CAREB consortium
193
P244
Utilizing GWAS Results to Preferentially Treat Genomic Markers in Prediction
Model
(submitted by Brian Rice <brice6@illinois.edu>)
Full Author List: Rice, Brian R1; Lipka, Alexander E 1
1
Department of Crop Sciences, University of Illinois, T urner Hall, MC-046 1102 South Goodwin Avenue Urbana, IL
61801
Some of the most important agronomic crop traits are complex and thus governed by many genetic components
of various effect sizes. In order to translate this complex genomic variability into genetic gain and crop
improvement as effectively as possible, there is a critical need to explore the p erformance of variations on the
basic genomic selection (GS) approach across a wide variety of genetic architectures. Using simulated data, we
evaluated the performance of an approach that augments the Ridge Regression Best Linear Unbiased Prediction
(RR-BLUP) GS model with fixed effect markers from a genome-wide association study (GWAS) conducted on a
training set. Previous work in maize and rice suggest that this model should be ideal for predicting traits that
have several large-effect genetic components, as well as many more components of smaller effect. We expand
upon this work by evaluating traits simulated under a diverse set of genetic architectures from the "GoodmanBuckler" maize diversity panel. For each simulated trait, we evaluated the prediction accuracy of RR-BLUP
models that included various numbers of peak-associated GWAS SNPs as fixed effect covariates. The results
indicate that for certain genetic architectures, setting a preferential subset of markers from GWAS as fixed
effects improved prediction accuracy. Expansion of this work will have implications in maize breeding as
researchers continue to explore the utilization of the various types and amounts of data becoming readily
available.
P245
ZmAuxRP1, encoding an auxin-regulated protein, coordinates the balance
between growth and defense in maize
(submitted by Tao Zhong <zhongtaomvp@163.com>)
Full Author List: Ye, Jianrong1; Zhong, T ao 1; Zhang, Dongfeng1; Wang, Lina1; Ma, Chuanyu1; Yao, Lishan 1; Zhang,
Qianqian 1; Zhu, Mang1; Xu, Mingliang1
1
National Maize Improvement Center of China, China Agricultural University; 2 West Yuanmingyuan Ro ad; Beijing,
P. R. China 100193
To optimize fitness, plants must efficiently allocate their resources between growth and defense. Although
phytohormone crosstalk has emerged as a major player in balancing growth and defense, the molecular basis by
which plants manage this balance remains largely elusive. Previously, we identified a quantitative diseaseresistance locus, qRfg2, in maize against Gibberella stalk rot. Through map-based cloning, we here demonstrate
that ZmAuxRP1 is the causal gene at qRfg2. ZmAuxRP1 encodes a plastid stroma-localized auxin-regulated
protein, which negatively regulates maize resistance to Gibberella stalk rot and Fusarium ear rot, but positively
root growth. ZmAuxRP1 is primed for instant response to pathogen challenge by implementing a rapid yet
transient reduction of its expression to facilitate defense-oriented reprogramming of the transcriptome.
ZmAuxRP1 promotes the biosynthesis of indole-3-acetic acid (IAA) and synchronically suppresses the formation
of benzoxazinoids, which are potent defensive compounds in maize innate immunity. ZmAuxRP1 presumably
acts as an integral regulator to modulate indole-3-glycerol phosphate (IGP) and/or indole flux at the branch point
between IAA and benzoxazinoid biosynthetic pathways. The concerted interplay between IAA and
benzoxazinoids can timely and efficiently regulate the growth–defense balance to optimize plant fitness.
Gene / Gene M odels described: ZmAuxRP1; GRM ZM2G063298
Funding acknowledgement: M inistry of Science and Technology of China, National Natural Science Foundation
of China
194
P246
ZmCCT9 enhances maize adaptation to higher latitudes
(submitted by Jinge Tian <tianjingelove@126.com>)
Full Author List: Huang, Cheng1; Sun, Huayue1; Xu, Dingyi1; Chen, Qiuyue1; Liang, Yameng1; Wang, Xufeng1; Xu,
Guanghui1; T ian, Jinge1; Wang, Chenglong1; Li, Dan 1; Wu, Lishuan 1; Yang, Xiaohong1; Jin, Weiwei1; Doebley, John 2;
T ian, Feng1
1
National Maize Improvement Center, China Agricultural University, Beijing, China 100193
2
Department of Genetics, University of Wisconsin, Madison, WI, USA, 53706
From its tropical origin in southwestern M exico, maize spread widely over a wide latitudinal cline in the
Americas. This feat defies the rule that crops are inhibited from spreading easily across latitudes. How the
widespread latitudinal adaptation of maize was accomplished is largely unknown. Through positional cloning
and association mapping, we resolved a flowering time quantitative trait locus (QTL) to a Harbinger-like
transposable element positioned 57 kb upstream of a CCT transcription factor (ZmCCT9). The Harbinger-like
element acts in cis to repress ZmCCT9 expression to promote flowering under long days. Knockout of ZmCCT9
by CRISPR/Cas9 causes early flowering under long days. ZmCCT9 is diurnally regulated and negatively
regulates the expression of the florigen ZCN8, thereby resulting in late flowering under long days. Population
genetics analyses revealed that the Harbinger-like transposon insertion at ZmCCT9 and the CACTA-like
transposon insertion at another CCT paralog ZmCCT10 arose sequentially following domestication and were
targeted by selection for maize adaptation to higher latitudes. Our findings help explain how the dynamic maize
genome with abundant transposon activity enabled maize to adapt over 90 degrees of latitude during the preColumbian era.
Gene / Gene M odels described: ZmCCT9; GRM ZM2G004483
Funding acknowledgement: the National Key Research and Development Program of China, the National
Natural Science Foundation of China, the Recruitment Program of Global Experts and the Fundamental Research
Funds for the Central Universities
P247
ZmCOPⅡ controls oil content in maize kernel
(submitted by Yingjia Han <hanyingjia325@163.com>)
Full Author List: Han, Yingjia 1 3; Zhao, Binghao 1 3; Fu, Xiuyi1; Xu, Jing1; Fang, Hui1; Li, Hui2; Chen, Wenkang1; Li,
Weiya1; Zhang, Lei1; Song, Xinran 1; Li, Jiangsheng1; Yang, Xiaohong1
1
National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural
University, Beijing, China, 100193
2
School of Biological Science and T echnology, University of Jinan, Jinan, Shandong, China, 250022
3
T hese authors contribute equally
M aize oil is highly valued as a resource of animal feed as well as vegetable oil for human consumption.
Increasing the kernel oil content not only improves its nutritional value, but also leads to the increase in
metabolizable energy. We previously identified ZmCOPⅡ, encoding coat protein complex II (COPII),
significantly associated with oil content in maize kernel by genome-wide association analysis. Whereas, it
remains unknown how ZmCOPⅡ regulates oil content. In this study, we validated the function of ZmCOPⅡ by
generating overexpression transgenic maize plants and CRISPR-Cas9 mediated null mutants. As expected,
overexpressing ZmCOPⅡ decreased oil content while knocking out of ZmCOPⅡ increased oil content. This
result indicate ZmCOPⅡ negatively regulate oil accumulation in maize kernel. To further elucidate the
molecular mechanism of ZmCOPⅡ regulating oil accumulation, multiple experiments, such as expression
analysis, yeast-two hybrids, and etc., were going on.
Funding acknowledgement: Chinese Postdoctoral Science Foundation
195
P248
A single gene knock-out resource for maize: filling gaps in the genome with targeted
Ds-GFP insertions
(submitted by Chunguang Du <duc@montclair.edu>)
Full Author List: Du, Chunguang1; Xiong, Wenwei1 ; Chatterjee, Mithu2 ; Li, Yubin 2 ; Wang, Qinghua2; Wang, Harrison2; He,
Limei2 ; Huang, Jun 2 ; Segal, Gregorio 2 ; Dooner, Hugo 2
1
Department of Biology, Montclair State University, Montclair, NJ USA 07043
2
Waksman Institute, Rutgers University, Piscataway, NJ USA 08854
T he availability of a mutant line in which a single gene has been disrupted gives biologists a powerful tool in
understanding that gene’s action. T hus, sequence-indexed collections of single insertions are critical resources for
elucidating gene function in organisms with a sequenced genome. Our NSF-PGRP-funded project is generating and
sequence-indexing a collection of Ds transposon insertions in transgenic maize by taking advantage of next -generation
sequencing (NGS) technologies. Specifically, our goals are to: (1) Assemble a set of 120 roughly equidistant Ds*
launching platforms carrying a GFP marker that allows simple visual selection of element transposition from any
region of the genome; (2) Sequence-index several thousand Ds* insertion sites from dozens of model platforms by
NGS of 3-dimensional DNA pools on an Illumina MiSeq platform and data deconvolution with our InsertionMapper
pipeline tool; and (3) Place all relevant information in our web-searchable database of insertion site sequences
(http://acdsinsertions.org) cross-referenced to stocks available from the Maize Genetics Stock Center. At present, 86
launching platforms have been mapped to all 20 chromosome arms of the maize genome. Along, we have mapped
14,184 transposed Ds* target sites to the reference B73 genome with the help of InsertionMapper. All the lines are
listed in our database http://acdsinsertions.org, and 10.155 have been already sent to the Maize Genetics Stock Center
for distribution. Future plan: to sequence-index Ds transpositions from chromosome arms that are currently not well
covered. Our objectives are: (1) T o generate a collection of 700 Ds* transpositions from each of 8 Ds* launching
platforms located in poorly covered chromosome arms. (2) T o sequence-index the additional collection of 5,600 new
Ds* insertions by NGS of 3-D DNA pools. T ogether with the >14,000 transposant stocks currently at hand, this new
collection will complete the Ds*-based single-gene knockout resource for maize.
Funding acknowledgement: National Science Foundation (NSF)
P249
Accuracy of the UniformMu resource is improved 15% by mapping Mu insertions
in its native W22 genome
(submitted by Donald McCarty <drm@ufl.edu>)
Full Author List: McCarty, Donald1; Koch, Karen1
1
University of Florida, Gainesville, FL USA 32611
T he UniformMu National Public Resource for transposon -induced mutants includes 72,000 germinal insertions mapped
in 14,024 seed stocks that are distributed to maize researchers world-wide by the Maize Coop Genetics Stock Cent er.
UniformMu was constructed in a W22 (ACR) inbred background also used for Ac/Ds transposon resources. Mu
insertions in UniformMu were initially mapped using the reference B73 genome. T he high -quality W22 genome
assembly created by the W22 Sequencing Consortium (www.maizegdb.org/genome) enabled re-mapping of insertions
in the UniformMu genome. Of 68,866 Mu insertions assigned unique locations in the W22 genome, locations of 10,041
insertions (14.6%) differed in W22 and B73. T hese included 4,660 insertions found only in W22 showing that use of
the W22 reference genome increased the total number of mapped insertions by nearly 7%. A similar number of
insertions (4,865, 7.1%) were detected in both genomes, but assigned to different chromosomes. By contrast, le ss than
1% of insertions that mapped to the same chromosome in both genomes were displaced by greater than 10 Mb. T he
prevalence of differences in chromosome assignment suggested that sub-fractionation of duplicate genes contributes to
divergent map locations in W22 and B73. Consistent with this hypothesis, misassigned insertions were enriched in
three well-characterized, syntenous regions associated with whole-genome duplication in maize evolution: Chr 9L Chr 1S; Chr 10L - Chr 2S; Chr 5S - Chr 1L. In each case, misassigned insertions showed a clear bias for one
chromosome segment of each pair. While this pattern indicated biased fractionation, the expected bias favoring
conservation of sub-genome A sites in the B73 genome occurred in only two of three dup lications. T his pattern
suggests that biased fractionation operates at a regional level rather than on a sub-genome-wide basis. By eliminating
mapping errors due to inbred differences, the new W22 genome sequence improves reliability of the UniformMu
resource.
Funding acknowledgement: National Science Foundation (NSF)
196
P250
Atypical transposable element copies predict functional consequence
(submitted by Michelle Stitzer <mcstitzer@ucdavis.edu>)
Full Author List: Stitzer, Michelle C. 1 ; Anderson, Sarah N. 2; Springer, Nathan M. 2 ; Ross-Ibarra, Jeffrey 1 3
Department of Plant Sciences and Center for Population Biology; University of California, Davis; Davis, CA 95616
2
Department of Plant and Microbial Biology; University of Minnesota; St. Paul, MN 55108
3
Genome Center; University of California, Davis; Davis, CA 95616
1
Despite being genomic parasites, transposable elements (T Es) dominate the genomic landscape of maize, contributing
the vast majority of DNA sequence. Although T Es disrupt the genomic environment they land in, generating mutations
and altering epigenetic signatures of adjacent sequences, they have overtaken the genomes of all Zea. T he negative
effect of T Es on host fitness is mitigated by the separation of islands of genes in seas of transposons throughout the
maize genome, such that genic euchromatin is limited in its interaction with T Es. But clear cases exist where these
boundaries break down. For example, the maize allele of teosinte branched 1 (tb1) selected during domestication
harbors a Hopscotch LT R retrotransposon insertion 65 kb upstream of the gene’s coding sequence, and was selected for
during domestication due to its impact on phenotype. T his T E copy is distinguished from related copies throughout the
genome from the same family by high levels of CHH methylation, and presence in a high recombination region, despite
being far from genes.
T o identify such aberrant T Es, without any prior knowledge of selection, we used features of the T E itself and the
genomic environment it inserted into to develop expectations of how long natural selection would maintain each T E
allele in maize populations. We identified thousands of T Es that have avoided removal by selection despite containing
features differentiating them from related copies. By imputing inheritance of regions of the genome encompassed by
these T Es to NAM RIL progeny, we find these regions disproportionately contribute to phenotypic variation, and are
found near genes with tissue specific expression. We prioritize these outlier T Es for their contribution to molecular and
phenotypic differentiation between maize lines. T hese analyses and future work to distinguish whether these T Es are
polymorphic between maize lines will facilitate prediction of their consequences.
Funding acknowledgement: National Science Foundation (NSF)
P251
Buried treasures: the maize transposable elements Dotted and Mrh
(submitted by Yubin Li <liyubin@caas.cn>)
Full Author List: Li, Yubin 1; Dooner, Hugo K. 2
1
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China, 100081
2
Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854
T ransposable elements (T Es) are the major components of most sequenced genomes. Over 90% of the maize genomic
DNA sequences are T Es and T E-derivatives. Among them, various families of class II transposons (DNA transposons)
play a major role in shaping the genome. Most of them are nonautonomous driven by autonomous transposons whose
presence and interactions are usually revealed genetically.
Dotted (Dt) was the first maize element characterized genetically as causing mutations at another locus, prior to its
recognition as a T E. We are attempting to isolate it because of its enormous historic importance in the development of
the concept of controlling elements. From a segregating population of the Dt/a1-rDt two-element system, we have
cloned sequences amplified with primers based on the sub-terminal regions of its receptor element rDt. Sequence
analysis revealed the presence of candidate Dt elements encoding a conserved hAT family dimerization domaincontaining protein. We are in the process of identifying which of these corresponds to Rhoades’ classic Dt element.
T he autonomous transposon Mrh is known genetically to regulate its receptor element rMrh at the A1 locus. T he 80-bp
terminal inverted repeats of rMrh are 70% identical with Jittery’s over the first 50 bp, so, like Jit, Mrh most likely
belongs to the Mutator superfamily. We have amplified Mrh-related sequences using primers based on the rMrh
terminal inverted repeats. Sequence analysis indicates a high conservation (more than 85% identity) of the encoded
Mrh transposase to the known JIT A transposase of Jittery, the second cloned autonomous element of Mutator
superfamily. We have examined the possible genetic int eraction between Jittery and Mrh and have shown that Jittery is
able to trans-activate the rMrh element at the A1 locus, as Mrh does. Our on-going efforts are to investigate how
transposon specificities originate within a superfamily, an important issue in transposon evolution.
Funding acknowledgement: National Science Foundation (NSF), CAAS Elite Youth Program Grant
197
P252
Characterization and mapping of the required to maintain repression10 locus
affecting paramutation
(submitted by Emily McCormic <mccormic.11@osu.edu>)
Full Author List: McCormic, Emily J1; Hollick, Jay B1 2
1
Department of Molecular Genetics, T he Ohio State University, Columbus, OH 43210
2
Centers for RNA Biology and Applied Plant Sciences, T he Ohio State University, Columbus, OH 43210
Paramutation at the Pl1-Rhoades (Pl1-Rh) allele of the purple plant1 (pl1) locus results in meiotically heritable
1
changes in gene regulation that are influenced by trans-homolog interactions . Plants with a fully-expressed Pl1Rh allele exhibit dark anther coloration, while plants with a repressed paramutant derivative (denoted Pl’ ) lack
anther coloration. The transcriptional and post-transcriptional repression of Pl1-Rh is facilitated by required to
maintain repression (rmr) factors 2. We previously reported on eight different rmr factors identified by mutations
induced with ethyl methanesulfonate (EM S) pollen treatment. At least six of these factors are required for the
3,4,5,6,7,8
biogenesis of 24-nucleotide sRNAs
that may direct de novo cytosine methylation.
Genetic complementation tests and molecular mapping were used to determine that two recessive mutations,
ems062986 and ems073240, define a novel locus provisionally designated rmr10. Results of genetic tests with
the ems062986 mutation indicate that normal rmr10 function is required for the meiotic maintenance of Pl’ states
9
but not for facilitating paramutations at the booster1 locus. RNA-seq data and a bioinformatics pipeline are
currently being used to identify likely candidate genes, and the effects of rmr10 function on pl1 RNA levels is
being determined using qRT-PCR. Bulk low molecular weight RNA profiles will also be evaluated to
characterize possible effects on small RNA accumulations. Results of these efforts expand our understanding of
basic mechanisms controlling meiotically -heritable changes in gene regulation.
1. Hollick et al. 1995 Genetics | 2. Hollick and Chandler 2001 Genetics | 3. Nobuta et al. 2008 PNAS | 4. Hale et al. 2007 PLoS Biol. | 5. Erhad
et al. 2009 Science | 6. Stonaker et al. 2009 PLoS Genet. | 7. Barbour et al. 2012 Plant Cell | 8. A. Narain and J. Hollick, unpublished | 9. Miller
et al. 2013 Genome Res.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
P253
Characterization of polymorphic transposable element content between maize
inbred lines
(submitted by Alex Brohammer <broha006@umn.edu>)
Full Author List: Brohammer, Alex B. 1; Anderson, Sarah N. 2; Noshay, Jaclyn 2; Zhou, Peng2; Stitzer, Michelle C. 3;
Ross-Ibarra, Jeffrey 3; Springer, Nathan M. 2; Hirsch, Candice N. 1
1
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA 55108
2
Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA 55108
3
Department of Plant Sciences, University of California Davis, Davis CA, USA 95616
Extensive transposable element (TE) variation has been shown between maize inbred lines on a loci-by-loci
basis. However, genome-wide documentation of TE variation between inbred lines and consequences on
transcriptional, epigenetic, and phenotypic variation has not previously been possible. With de novo assemblies
of multiple maize inbred lines and de novo annotation of TEs within those assemblies now available, we are now
poised to address this question on a genome-wide scale. Utilizing independent annotations of TEs in the B73,
PH207, and W22 de novo genome assemblies, a detailed analysis of polymorphic TEs was conducted. A
computational approach that utilizes sequences flanking TE insertions as well as anchor points between the three
genomes has been developed to identify both non-nested and nested TE insertions unique to each genome.
Preliminary analyses demonstrated high rates of TE polymorphism and showed the rate of polymorphism varies
with respect to TE class. Future efforts will focus on identifying the phenotypic consequences of variable TE
insertions and their potential influence on transcriptional and epigenetic variation within maize.
Funding acknowledgement: National Science Foundation (NSF), M NDrive Global Food Ventures
198
P254
Cold induces transcriptional and methylation changes in the sensitive line B73
(submitted by Clémentine Vitte <clementine.vitte@inra.fr>)
Full Author List: Achour, Zeineb1; Sellier, Hélène2; Pichon, Jean-Philippe3; Duborjal, Hervé3; Leveugle, Magalie3; Le
Guilloux, Martine1; Caius, José4 5; T aconnat-Soubigou, Ludivine4 5; Brunaud, Véronique4 5; Paysant-Le Roux,
Christine4 5; Joets, Johann 1; Giauffret, Catherine 6; Vitte, Clémentine1
1
INRA, CNRS, Université Paris–Sud, AgroParisT ech / UMR Génétique Quantitative et Evolution (GQE) - Le Moulon,
Gif-sur-Yvette, France
2
INRA UE Grandes Cultures Innovation Environnement (GCIE), Estrées-Mons, France
3
Biogemma, Chappes, France
4
CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Saclay / Institute of Plant Science (IPS2)
Orsay, France
5
CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité / Institute of Plant Science (IPS2), Orsay, France
6
INRA UR Recherche Agroressources et Impacts environnementaux (AgroImpact), Estrées-Mons, Péronne, France
In Northern Europe, maize development leads to high financial and environmental drying costs at harvest. Early
sowing has been proposed as a strategy to overcome this problem, but this cycle shift subjects plants to cold in
the first phase of their development. Such an early and prolonged cold affects maize metabolism, leading to yield
reduction. Origin of this physiological modification is not well understood, and detection of candidate genes
using genetic-based studies is challenging. Whether DNA methylation changes are involved in this phenotype
remains to be elucidated.
Here, we analyze the impact of cold on methylome and transcriptome of the sensitive line B73. After 21 days of
cold treatment, this genotype shows a chlorotic phenotype, as well as a delay in development. A total of 6937
genes were differentially expressed genes between “Cold” and “Standard” plants, with a slight majority of
downregulated genes. Gene ontology analyses highlight an increase in DNA replication, DNA repair, and RNA
processing functions and a decrease in photosystem activity. This is in accordance with the phenotype observed,
and pinpoints that cold is indeed sensed as a physiological stress.
Cold induces genome-wide methylation changes, with an overall increase of methylation in “Cold” plants. Local
modifications are also observed, with a total of 699 Differentially M ethylated Regions (DM Rs) between the two
plant sets. The majority of these DM Rs vary in both CG and CHG levels, and are located upstream and
downstream of Transposable Elements (TEs). Another 30% varies only in CHG and is located in genes carrying
TEs. A smallest fraction varies only in CG and is located in genes and away from TEs. These results suggest that
cold induces both changes in TE spreading, regulation of TEs in genes, and gene body methylation.
Funding acknowledgement: French National Research Agency (ANR)
199
P255
Discovering the epigenetic memory of stress response in maize
(submitted by Cristian Forestan <cristian.forestan@unipd.it>)
Full Author List: Forestan, Cristian 1; Farinati, Silvia1; Pavesi, Giulio 2; Rossi, Vincenzo 3; Varotto, Serena1
Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE), University of Padova,
Viale dell’Università 16, 35020 Legnaro (Italy)
2
Department of Biosciences, Universit y of Milan, Via Celoria 26, 20133 Milano (Italy)
3
CREA - Unità di Ricerca per la Maiscoltura, Via Stezzano 24, 24126 Bergamo (Italy)
1
Stress perception and adaptation in plants require a variety of physiological, biochemical, transcriptional, and
epigenetic responses. Dynamic changes in chromatin structure and concomitant transcriptional variations play an
important role not only in stress response, but are also involved in epigenetic memory mechanisms. Histone
marks and gene expression patterns could be indeed stably maintained during cell division and sexual
reproduction, once the triggering stimulus has been removed. There is good evidence that chromatin may play a
pivotal role in somatic memory phenomena and although many progresses have been made in understanding
chromatin modifications implicated in plant response to environmental triggering conditions, we are still far from
connecting molecular genetics and developmental data around environment and chromatin.
In order to understand whether environmental memories are created and eventually propagated, we integrated
transcriptional and epigenetic data from maize plants subjected to a mild and prolonged drought stress and after
the complete recovery from the stress. We observed that extensive transcriptional changes present soon after the
stress application were only partially reset after the recovery stage. Concomitantly, ChIP-Seq analyses revealed a
direct correlation between transcriptional variation and H3K4me3 or H3K9ac histone modification enrichment at
the majority of stress-regulated gene loci. The facultative heterochromatin mark H3K27me3 was instead
associated to a few developmentally regulated genes misregulated by the applied stress. In addition, several
stress-responsive genes in which histone marks variations persist after the recovery stage were identified,
indicating a form of stress memory.
Based on the emerged fundamental role of epigenetic mechanisms in regulating stress response and adaptation
we are further evaluating the identified targets in the progeny of the stressed plants and in plants subject to
repeated stress pressure
P256
Distinct pattern of DNA methylation in different subnucleosomal domains
(submitted by Jian Chen <jianchen@cau.edu.cn>)
Full Author List: Chen, Jian 1; Li, En 1; Zhang, Xiangbo 1; Dong, Xiaomei1; Yi, Fei1; Song, Weibin 1; Zhao, Haiming1;
Lai, Jinsheng1
1
State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics
and Breeding, China Agricultural University, Beijing, 100193, P. R. China
DNA methylation and nucleosome positioning are two essential epigenetic modification of most eukaryotic
genome. However, the specific relationship between DNA methylation and nucleosome positioning has remained
elusive, particularly, methylation pattern inside of octamer nucleosomes is not been investigated. Here we report
a comprehensive survey of methylation variation in subnucleosomal level, and found the variation was mainly
reflected by the difference between the central and peripheral domains of nucleosomes, which are corresponded
to DNA bound to (H3-H4)2 tetramer and H2A-H2B dimers, respectively. Overall, CG methylation is enriched at
central domain for nucleosomes in transposable elements and exons, but is enriched at peripheral domain for
nucleosomes in intergenic regions. By contrast, CHG and CHH methylation tends to occurred at peripheral
domain in most cases. Subnucleosomal DNA methylation pattern is cooperatively modulated by the act ivities of
different methyltransferases, which DRM 1/2 and CM T2/3 preferentially mediate the methylation at central and
peripheral domain, respectively. Subnucleosomal DNA methylation pattern is also affected by demethylation
process, including DM E-mediated demethylation, which preferentially happened at central domain. In general,
our results demonstrated the variation and regulation of DNA methylation in different subnucleosomal domains
for the first time, which is helpful for further understanding of the function of DNA methylation.
Funding acknowledgement: National Natural Science Foundation of China (91435206; 31421005), 948 project
(2016-X33), National Postdoctoral Program for Innovative Talents (BX201600149)
200
P257
Documenting the role of transposable elements in DNA methylation variation in
maize
(submitted by Jaclyn Noshay <nosha003@umn.edu>)
Full Author List: Noshay, Jaclyn M 1; Anderson, Sarah N1; Zhou, Peng1; Stitzer, Michelle C2 ; Ji, Lexiang3 ; Schmitz, Robert J4 ;
Springer, Nathan M 1
1
Department of Plant and Microbial Biology, University of Minnesota, St. Paul MN
2
Department of Plant Sciences, University of California Davis, Davis CA
3
Institute of Bioinformatics, University of Georgia Athens, Athens GA
4
Department of Genetics, University of Georgia Athens, Athens GA
A majority of the maize genome is comprised of transposable elements (T Es). T hese T Es can influence chromatin state
and expression of nearby genes. Previous studies have documented numerous diff erences in DNA methylation among
maize inbred lines. However, it has been difficult to determine whether these differences in DNA methylation are
purely epigenetic or the result of nearby changes in DNA sequence. T he availability of de novo genome assembli es for
B73, PH207 and W22 provides an opportunity for a genome-wide analysis of the role of T Es in DNA methylation
variation. Deep whole genome bisulfite sequencing (WGBS) data was generated for these three genotypes and used to
identify thousands of differentially methylated regions (DMRs). T hese include DMRs that have alterations in CG, CHG
or CHH methylation as well as various combinations of these context-specific changes. Many of these DMRs are
located within or near T Es. Comparisons of the genome structure and T E annotation of B73, PH207 and W22 allowed
the identification of a set of conserved and polymorphic T E insertions. The DNA methylation patterns flanking
conserved T E insertions were assessed to determine whether the spreading of DNA methylation from T Es is consistent
among genotypes. T he regions flanking polymorphic T Es were analyzed to document the prevalence of DMRs
resulting from a T E insertion. T hese analyses reveal many examples in which T Es influence DNA methylation of
nearby sequences. Fut ure work will focus on understanding how these changes in DNA methylation triggered by T Es
could influence expression of nearby genes.
Funding acknowledgement: National Science Foundation (NSF)
P258
Identification and characterization of regulatory sequences in Zea mays
(submitted by Maike Stam <m.e.stam@uva.nl>)
Full Author List: Oka, Rurika 1; Weber, Blaise1; Zicola, Johan2 ; Anderson, Sarah N. 3; Hodgman, Charlie4; Gent, Jonathan I. 5 ;
Wesselink, Jan-Jaap6 ; Springer, Nathan M. 3; Hoefsloot, Huub C.J. 1 ; T urck, Franziska2; Stam, Maike1
1
University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
2
Max Planck Institute for Plant Breeding, Carl-von-Linné 10, 50829 Cologne, Germany
3
University of Minnesota, 1479 Gortner Avenue, St Paul, MN 55108, USA
4
University of Nottingham, Sutton Bonington, LE12 5RD, UK
5
Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
6
Diagenode, S.A, Rue du Bois Saint -Jean 3, 4102 Liège, Belgium
Correct temporal and spatial regulation of gene expression is crucial for the successful development of an organism.
Regulation of gene expression is in part accomplished through the coordinated action of cis-regulatory elements such as
transcriptional enhancers. Whereas regulatory sequences are still poorly characterized in plants, they have been
extensively characterized in mammals. Active enhancers are for example found to be associated with specific features
such as particular histones marks, chromatin accessibility, low DNA methylation, presence of enhancer-specific
transcripts and the ability to physically contact their target via the formation of chromatin loops.
Our study aims at a better identification and characterization of active enhancers in Zea mays. By making use of
published bisufite-seq data sets and newly generated DNAseI-seq, ChIP-seq and RNA-seq data sets, about 1,500
putative regulatory sequences have been identified in young seedling and husk tissue. T hese include known and
experimentally validated enhancers in maize. T he enhancer candidates are characterized by low DNA-methylation,
increased chromatin accessibility, and, unlike in animal systems, an asymmetric enrichment of H3K9ac. T issue specificity of enhancer candidates was defined based on the tissue(s) they were identified in. Currently, enhancer
candidates are characterized in more detail.
Weber et al. (2016) Trends in Plant Science 21, 974. doi: 10.1016/j.tplants.2016.07.013.
Oka et al. (2017) Genome Biology 18:137. doi: 10.1186/s13059-017-1273-4.
Funding acknowledgement: United States Department of Agriculture (USDA), European Commission (Seventh
Framework-People-2012-ITN Project EpiTRAITS)
201
P259
Identification of new maize (root) mutants by Mu-seq
(submitted by Caroline Marcon <marcon@uni-bonn.de>)
Full Author List: Marcon, Caroline 1; Win, Yan Naing1; Altrogge, Lena2; Schoof, Heiko 2; Hochholdinger, Frank 1
Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn,
Germany
2
Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn,
Germany
1
The well-described M utant-seq (M u-seq) approach enables the development of sequence-indexed reverse genetic
mutant databases in maize (M cCarty et al., 2013, Liu et al., 2016). M u-seq simultaneously enables genome-wide
identification and mapping of new Robertson´s Mutator insertion sites in individual F 2-families of large
mutagenized maize populations. We generated M u-seq libraries by crossing an active Mutator line into the
inbred lines B73 and Co125. The inbred line Co125 was selected because it is representing a genetic resource for
central European maize research due to its stable growth properties under temp erate climatic conditions. After
self pollinating the F 1-generation, segregating F 2-families were introduced in the M u-seq pipeline. In our initial
M u-seq library, consisting of 576 F 2-families in B73 genetic background, 20,081 germinal insertions representing
11,457 different gene models were detected. As a proof of concept, a new mutant allele of the roothair defective
3 (rth3) gene was identified in one of the mutagenized families. The mutant rth3 is affected in root hair
elongation (Wen and Schnable, 1994; Hochholdinger et al., 2008). Furthermore, forward genetic screens of the
mutagenized families, in germination paper rolls, enable the identification of seedling mutant phenotypes 10-12
days after germination. Among other phenotypes, screening of ~25% of the 576 lines identified a striking dwarf
mutant affected in root and shoot development. To identify genes identified in this forward genetic screen bulked
segregant RNA-seq (BSR-seq) analyses (Liu et al., 2012) will be performed.
P260
Maize centromeres expand in the large genome background of Oaxaca and Zea.
luxurians
(submitted by Na Wang <na.wang25@uga.edu>)
Full Author List: Wang, Na 1; Gent, Jonathan I 1; Dawe, R. Kelly 1 2
1
Plant Biology, 120 East Green Street , Athens, GA, 30602
2
Genetics, 120 East Green Street, Athens, GA, 30602
Little is known about how centromere size and location are determined. Previous work in maize has revealed that
centromere size among grass species is highly correlated with total genome size, and maize centromeres expand
when transferred into a larger genome background of oat. However, whether centromeres will expand if we
intentionally enlarge the genome size of a specific species is still unknown. M aize is a model organism for
investigating these topics because of its genetic resources, including extreme diversity of centromere types
between homologous chromosomes. In this study, we test the hypothesis that centromere size positively
correlates with genome size in maize species by introducing the chromosomes of B73 into Oaxaca and
Zea.luxurians background plant, both Oaxaca and Zea.luxurians have a larger genome than B73. To increase the
genome size while keeping centromere 2 and 5 homozygotes from B73, we have crossed B73 with Oaxaca and
Zea.luxurians for several times. The genome size of these different lines have been estimated by the amount of
DNA in cell nuclei from flow cytometry. The results showed that the genome size is bigger in the hybrids of B73
X Oaxaca and B73 X Zea.luxurians than in B73. The CENH3-ChIP experiment results suggested that four
centromeres (centromere 2, 3, 8, 9) are expanded in the BC1F2 hybrids of B73 and Oaxaca, F2 of B73 and
Zea.luxurians. These data provide new insights into the relationship between centromere size and genome size in
maize species.
Funding acknowledgement: National Science Foundation (NSF)
202
P261
Parent-of-origin dependent nucleosome organization and its role on the
regulation of genetic imprinting in maize endosperm
(submitted by Tong Li <litong@cau.edu.cn>)
Full Author List: Dong, Xiaomei1; Chen, Jian 1; Li, T ong1; Lai, Jinsheng1
State Key Lab For Agrobiot ech of National Maize Improvement Center, China Agricultural University, Beijing
100193, P. R. China
1
Genomic imprinting confers allele-specific expression of genes depending on their parental origin. Nucleosomes,
the fundamental units of chromatin, play a critical role in gene transcriptional regulation. However, it remains
unknown whether differential nucleosome organization is related to the allele-specific expression of imprinted
genes. Here we generated a genome-wide map of allele-specific nucleosome occupancy in maize endosperm and
presented an integrated analysis of its relationship with parent-of-origin dependent gene expression and DNA
methylation. We found that about 2.3% of nucleosomes showed significant parental bias in maize endosperm.
The parent-of-origin dependent nucleosomes preferentially exist as single isolated nucleosomes. Parent-of-origin
dependent nucleosomes were significantly associated with the allele-specific expression of imprinted genes, with
nucleosomes positioned specifically in the promoter of non-expressed alleles of imprinted genes. Furthermore,
we found that most of the paternal specifically positioned nucleosomes (pat -nucleosomes) were associated with
parent-of-origin dependent differential methylated regions, suggesting functional link between the maternal
demethylation and the occurrence of pat-nucleosome. M aternal specifically positioned nucleosomes (matnucleosomes) were independent of allele-specific DNA methylation, but seem to be associated with allelespecific histone modification. Our study provides not only the first genome-wide map of allele-specific
nucleosome occupancy in plants but also a mechanistic connection between chromatin organization and genetic
imprinting.
Funding acknowledgement: he National Natural Science Foundation of China
P262
Reduction of DNA methylation during early embryogenesis enhances growth
heterosis of maize plants
(submitted by Susanne Edelmann <susanne.edelmann@uni-hamburg.de>)
Full Author List: Edelmann, Susanne 1; Grant-Downton, Robert 2; Seifert, Felix 1; T hiemann, Alexander 1; Scholten,
Stefan 1 3
1
Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany, 22609
2
Department of Plant Sciences, University of Oxford, OX1 3RB, UK
3
Institute for Plant Breeding, Population Genetics and Seed Science, University of Hohenheim, Germany, 70599
Heterosis is the superior performance of heterozygous hybrid offspring compared to the parental homozygous
inbred lines. It has been widely hypothesized to be associated with epigenetic modifications such as DNA
methylation. The aim of this work was to test whether DNA methylation patterns established during early
embryogenesis impacts upon the heterotic response. We treated maize embryos of inbred lines and hybrids with
5-aza-2’-deoxycytidine (aza), a DNA methyltransferase inhibitor. The treatment was restricted to one application
of aza starting one day after pollination by using an in vitro embryo sac culture system. DNA methylation
analysis by Reduced Representation Bisulfite Sequencing (RRBS) showed natural and artificially induced
methylation dynamics between developmental stages of maize. The successful demethylation of symmetric CG
and CHG contexts by the early aza-treatment was confirmed in 7 day -old embryos and in seedlings of inbred
lines. Thus, hypomethylation of DNA was induced in the early embryo and maintained to the seedling stage.
Growth rates of inbred and hybrid seedlings were used to determine the effect of methylation inhibition on this
key heterotic trait. Comparing plants derived from aza-treated embryos and their untreated control group
demonstrated a significant increase of the growth heterosis upon demethylation. In contrast, a later aza
application to 14 day-old embryos affected growth in general, but not growth heterosis. Together our results
indicate that DNA methylation patterns that establish during early maize embryogenesis have a negative effect
on growth heterosis formation at developmental stages after germination.
203
P263
RNA polymerase IV contributes to hybrid vigor
(submitted by Jay Hollick <hollick.3@osu.edu>)
Full Author List: Hollick, Jay B1
T he Ohio State University, Department of Molecular Genetics, Centers for RNA Biology and Applied Plant Sciences,
Columbus, OH, USA 43210
1
M aize RNA polymerase IV (RNAP IV) affects genome-wide RNAP II-based transcription1 and is responsible for
defining tissue-specific expression patterns of specific alleles 2,3. RNAP IV also mediates and maintains
transcriptional repression of alleles undergoing paramutation4 – a meiotically-heritable change in gene regulation
facilitated by trans-homolog interactions 5. Paramutation behaviors of certain red1 and purple plant1 alleles
controlling anthocyanin pigment production provide clear examples of single locus heterosis 6,7, leading to
speculations that similar behaviors contribute to hybrid vigor 7,8. Here it is reported that absence of RNAP IV
function in B73 inbred parents impacts the heterotic traits of B73 / M o17 hybrids. Hybrid gains in both plant
height and grain yields are contributed by RNAP IV function in parental sporophytes. Understanding the
genomic features that recruit RNAP IV and the various roles both RNAP IV and RNAP IV-generated 24
nucleotide RNAs play in defining RNAP II transcription patterns promises novel opportunities for predicting and
controlling biomass production. Indeed, the differences between uniting gametes responsible for heterosis need
not be M endelian in nature7,9.
1. Erhard et al. 2015 Genetics | 2. P arkinson et al. 2007 Dev Biol | 3. Erhard et al. 2009 Science | 4. Erhard et al. 2013 Plant Cell | 5. Hollick
2017 Nat Rev Genet | 6. Styles and Brink 1969 Genetics | 7. Hollick and Chandler 1998 Genetics | 8. Kermicle and Alleman 1990 Development
| 9. Shull 1948 Genetics
Gene / Gene M odels described: rpd1; GRM ZM2G007681
Funding acknowledgement: National Science Foundation (NSF)
P264
Single-pollen sequencing for the study of novel meiotic phenotypes
(submitted by Benjamin Berube <bberube@cshl.edu>)
Full Author List: Berube, Benjamin 1; Regulski, Mike1; Grimanelli, Daniel2; Martienssen, Rob1
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
2
Institut de Recherche pour le Développement, UMR 5096, 34394 Montpellier, France
M eiotic recombination is a fundamental evolutionary driver and an indispensible tool for agricultural breeding.
Advances in next-generation sequencing, coupled with genoty ping by sequencing approaches, have allowed for
the development of large-scale, population level assessments of crossover frequency and localization, as well as
the construction of high-density linkage maps for quantitative trait mapping. Despite these advances, unbiased,
genome-wide study of recombination in meiotic mutants remains difficult. The computational complexity of
identifying crossovers in hybrid populations, constraints on the availability of plant material, and variable
contributions of both the maternal and paternal genomes all pose significant challenges. Here, we describe the
adaptation of single-cell DNA sequencing methodologies to individual maize pollen grains. Sequencing of pollen
grains from biparental hybrid populations, coupled with statistical modeling of recombination breakpoints,
allows for genome-wide, high-resolution mapping of crossover intervals. Using this approach, the distortion of
patterns of recombination in DNA methyltransferase mutants is being characterized.
Funding acknowledgement: National Science Foundation (NSF), Howard Hughes M edical Institute (HHM I)
204
P265
The maize Ufo1 mutant results from ectopic over expression of an endosperm
specific gene
(submitted by Surinder Chopra <sic3@psu.edu>)
Full Author List: Wittmeyer, Kameron 1; Cui, Jin 1; Chatterjee, Debamalya 1; T an, Qixian 1; Jio, Yinping2; Lee, T zuufen 4; Meyers, Blake3; Ware, Doreen 2; Chopra, Surinder 1
1
Department of Plant Science, Pennsylvania State University, University Park, PA 16802
2
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
3
T he Donald Danforth Plant Science Center, St. Louis, MO 63132
4
DuPont Pioneer, Johnston, Des Moines, IA 50131
The maize mutant Unstable factor for orange1 (Ufo1) is a dominant modifier of tissue specific expression of
pericarp color1 (p1). Thus p1 has been used here as a reporter for the presence/absence of Ufo1. The common
feature of Ufo1-p1 interactions is that several epigenetically silent p1 alleles are up regulated. Our global gene
expression studies show that Ufo1 up-regulates genes enriched for GO categories for resp onse to various stimuli
such as ROS and high light intensity. Genes involved in DNA replication and ribosome biogenesis are down
regulated. The overall picture is that Ufo1-1. plants show elevated levels of stress under normal growth
conditions. Using transcriptomic data we identified a candidate gene (named G7) in the mapping region. In wild
type, G7 is specific to endosperm but in Ufo1-1 mutant it is ectopically overexpressed 45 to 200 fold higher in
the three tissues used for RNAseq. Using PacBio long read assembly, we found that in Ufo1-1, G7 has a CACTA
insertion within the first intron. Regulation of expression of G7 by the DNA methylation status of the CACTA
transposon explains the incomplete penetrance and poor expressivity of Ufo1-1. Overexpression of G7 explains
pleiotropic defects as well as the dominance of Ufo1-1 as confirmed by analysis of its silent epialleles.
Funding acknowledgement: National Science Foundation (NSF)
P266
The transposon landscape of the inbred W22
(submitted by Thomas Brutnell <tbrutnell@danforthcenter.org>)
Full Author List: Brutnell, T homas1; T he, W22 Sequencing Consortium 1
Donald Danforth Plant Science Center, St. Louis, MO, 63132
1
The maize W22 genome has served as a foundation for maize genetics for nearly 60 years. Using short read
sequencing technology we have assembled the genome and annotated the transp oson content. We have also
mapped an extensive collection of active Dissociation and Mutator transposons to the genome. Our analysis
indicates over 177,000 that can be classified into nearly 27,000 families. Comparisons to the B73 genome
revealed extensive heterogeneity in LTR and TIR composition and distribution between the two genomes. Of the
approximately 250 Mutator insertions present in both genomes, only about half share a common insertion site.
The others occupy unique positions, usually within 500 bp of a gene, raising the possibility of extensive inbredspecific cis-regulatory variation on gene expression. By mapping Dissociation and Mutator insertions mobilized
in the W22 genome to this reference genome, we were able to accurately position approximately 10,000
previously unmapped Mu insertions and over two hundred Ds insertions. In summary, this high quality W22
assembly provides a foundation for comparative genomics in maize and an important resource for functional
genomics.
Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture
(USDA)
205
P267
Using chromatin features to identify and understand intergenic transcriptional
regulatory elements in maize
(submitted by William Ricci <william.ricci@uga.edu>)
Full Author List: Ricci, William A. 1; Lu, Zefu2; Ji, Lexiang2; Schmitz, Bob2; Zhang, Xiaoyu1
Department of Plant Biology; University of Georgia, Athens, GA, 30602
2
Department of Genetics; University of Georgia, Athens, GA, 30602
1
Transcriptional cis-regulatory elements (CREs) modulate the expression of genes via the action of sequencespecific DNA binding factors. CREs confer specificity for when and where genes are expressed during
development and in response to stimuli. The importance of characterizing and cataloging the regulatory elements
of a genome is akin to the importance of cataloging the protein-coding regions. However, identifying CREs
poses a challenge because (1) they may act on target genes in an orientation- and distance-independent manner,
and (2) sequence conservation may be limited to small transcription factor binding sites. The limitation of
sequence-based methods necessitates the incorporation of epigenomic features for identifying CREs.
Specifically, the structural and biochemical features of chromatin may be used as a proxy for the presence of
CREs. The chromatin signatures of human CREs have been characterized extensively and a minimum set of
structural and biochemical features are often used to locate CREs. However, a set of predictive chromatin
features has yet to be developed for CREs in plants. We have generated datasets on DNA accessibility (ATACseq), cytosine methylation (M ethylc-seq), transcriptional status (RNA-seq and RNA PolII ChIP-seq) and histone
N-terminal covalent modifications (ChIP-seq) in the model crop Zea mays. Preliminary analyses reveal an
abundance of putative CREs in the gene-distal intergenic space. A small set of chromatin attributes can parse the
gene-distal putative CREs into distinct groups that are enriched for either acetylated histone H3 or trimethylated
H3K27. These two groups of putative CREs appear to regulate genes with distinct functions—i.e., acetylated
CREs correlate with dynamically regulated, stimuli-responsive genes and H3K27me3 CREs correlate with
developmentally regulated genes.
Funding acknowledgement: National Science Foundation (NSF)
P268
Using GRO-Seq as a tool to understand transcriptional regulation in maize
(submitted by Allison McClish <mcclish.23@osu.edu>)
Full Author List: McClish, Allison 1; Hollick, Jay 1 2
Department of Molecular Genetics, T he Ohio State University
2
Centers for RNA Biology an Applied Plant Sciences, T he Ohio State University
1
Global Run-On Sequencing (GRO-Seq) reads identify nascent transcription occurring across the entire genome1.
In maize, GRO-Seq has been used to define regions where transcription rates are dependent on RNA polymerase
2
IV (Pol IV) function . In Arabidopsis, Pol IV RNAs are processed into 24 nucleotide (24nt) sizes that facilitate
RNA-directed DNA methylation (RdDM )3. It remains unclear in either maize or Arabidopsis whether Pol IV
itself or Pol IV-dependent cytosine methylation affects Pol II function 4. Comparisons of GRO-Seq profiles from
dicer-like3 mutants having virtually no 24nt RNAs and rpd1 mutants having neither Pol IVa nor Pol IVb
function should distinguish these two potential regulatory mechanisms. Current efforts to characterize and
optimize the nuclei isolations and in vitro transcription reactions needed to create GRO-Seq libraries will be
presented. Using hybridization of radiolabeled nascent RNAs with single-gene riboprobes, the effects of Sarkosyl
5
(reported transcription initiation inhibitor ) are being evaluated and optimal elongation times are being
determined. Nuclei isolated from various tissue types and developmental stages are also being evaluated for in
vitro transcriptional competency and thus suitability for GRO-Seq library production. GRO-Seq profiles
generated from nuclei treated with alpha-amanitin (Pol II-specific inhibitor) will potentially identify nascent Pol
IV and/or Pol V transcripts. GRO-Seq profiles of specific mutants will also be compared to distinguish Pol II
6, 7
transcription specifically affected by Pol IVa or Pol IVb . Ultra-deep coverage of GRO-Seq reads will assist
future genome annotations, including gene model validations, enhancer calls, defining 3’ pretermination
transcription and other intergenic regions of non-coding transcription.
1
Core et al. 2008 Science | 2 Erhard et al. 2015 Genetics | 3 Matzke and Mosher. 2014 Nature Reviews Genetics | 4 Hale et al. 2009 PLoS
Genetics | 5 Gariglio et al. 1974 FEBS Letters | 6 Stonaker et al. 2009 PLoS Genetics | 7 Sidorenko et al. 2009 PLoS Genetics
Funding acknowledgement: National Science Foundation (NSF)
206
Bacciu, Nicola P237
Bacila, Ioan P230
Baer, Marcel P75
Bagman, Anne-Maarit P28
Bai, Fang P61
Baier, John W. P31
Bakan, Bénédicte P90; P126
Baker, R. Frank T3; P44
Balboni, Martina P140
Baldauf, Jutta A. T24; P231
Baldy, Aurélie P181
Balint-Kurti, Peter J. P165
Balliau, Thierry P191
Barbazuk, W. Brad P5; P61
Barber, Wesley T29
Baret, Frédéric T18
Barret, Pierre T1; P106
Barrière, Yves P181
Barron, Brady P44
Barros, Beatriz A T16
Bartlett, Madelaine E. P112
Baruch, Kobi P8
Basler, Georg P24
Bass, Hank W. T25; P22; P33; P107
Basu Roy, Sayantani P147
Battilani, Paola P156
Bauer, Eva P8; P62; P189; P195; P208
Bauland, Cyril B. P159; P176; P181; P194;
P199; P226; P232; P238; P239
Baum, April P148
Baxter, Ivan P37
Bayle, Vincent T1; P106
Bear Don’t Walk IV, Oliver P123
Beaubiat, Sébastion P181
Beaugrand, Alice B P232
Beckett, Travis P200
Becraft, Philip W. P136
Beemster, Gerrit T32
Begcy, Kevin P97; P104
Beigbeder, Jean P238
Beissinger, Timothy P139; P157
Belcram, Harry P7
Bell, Bryan P12
Bellinger, Marschal Allen P88
Berg, Aaron P209
Berger, Florian P215
Bergès, Hélène T1; P106
Bernardes de Assis, Joana T2; P85
Bernardo, Rex P216
Bernau, Vivian P152
Bertolini, Edoardo T25
Berube, Benjamin P264
Besbrugge, Nienke P57
Best, Norman B. P41
Beydon, Genséric T1; P106
Bezrutczyk, Margaret P40
Author Index
Abbitt, Shane P28
AbdElgawad, Hamada T32
Abraham Juarez, Maria J P114
Abramov, Aleksej P76
Achour, Zeineb P254
Ackerman, Arlyn P168
Addo-Quaye, Charles A. P127
Aesaert, Stijn P89
Agha, Husain I P157
Aguilar Gutierrez, Estefania P178
Aguilar, Cristina P161
Aguirre-Liguori, Jonas P198
Albert, Patrice S. P45
Albertsen, Marc T2
Albinsky, Doris P69
Alexander, Martin A. P110
Allen, Douglas K P67
Allier, Antoine P220
Allsman, Lindy P88
Almekinders, Conny P151
Alonso, Raymundo P161
Altmann, Thomas P221; P239
Altrogge, Lena T24; P259
Alvarez Prado, Santiago PL2; T17; P100; P269
Alvarez-Iglesias, Lorena P174
Alves, Meire C T16
Amoiroglou, Anastasia P99
Anderson, Alyssa A P114
Anderson, Sarah N. T28; P250; P253; P257;
P258
Andjelkovic, Violeta B. P163; P188; P223
Andorf, Carson M. T12; P16; P17; P18; P19;
P20
Anibas, Calli M. P219
Annor, George P216
Aquino, Bruno P42
Aranda, Jocelyne P88
Arca, Mariangela P194
Arendsee, Zebulun P23
Arp, Jennifer J P67
Arruda, Paulo P42
Arshad, Waheed PL3
Arteaga-Vázquez, Mario P119
Asaro, Alexandra P37
Aspinwall, Brooke P30
Audigeos, Delphine P150
Auger, Donald L P213
Ávila, Alma X. P161
Avoles-Kianian, Penny T30
Avramova, Viktoriya P62
Aydinoglu, Fatma P117
Azevedo, Gabriel C T16
Babic, Vojka P163
207
Butrón, Ana P202
Byount, Tiffany P125
Bérard, Aurélie P29
Böhm, Juliane P195
Caballero-Pérez, Juan P119
Cabrera-Bosquet, Llorenç PL2; P7; P100; P269
Cahill, James F. T31
Cai, Lichun P186
Caicedo, Marlon P180; P241
Caius, José P254
Calugar, Roxana P230
Camacho Villa, Tania Carolina P151; P152
Čamdžija, Zoran P201
Campbell, Michael S. P11
Cang, Jing P43
Cannon, Ethalinda K. P16; P17; P19; P20
Caplan, Jeffrey P165
Carneiro, Andrea A. T16
Cassab, Gladys I. P161; P204
Casstevens, Terry P34
Castel, Stéphanie P7; P238; P239
Castelletti, Sara P164
Castorina, Giulia P68; P87
Castro Flores, Luis Armando P152
Cates, Robert P51
Cengiz, Rahime P171
Chaignon, Sandrine T1; P7; P106
Chang, Pearl P15
Char, Si Nian P40
Charcosset, Alain C. T7; T17; P7; P29; P160;
P176; P177; P185; P191; P194; P197; P199;
P220; P226; P232; P238; P239
Chatterjee, Debamalya P265
Chatterjee, Mithu P248
Chaumont, François T17; P118
Chaya, Timothy P165
Chemin, Claire P239
Chen, Baojian P105
Chen, Changbin T30
Chen, Chen P54; P205
Chen, Jian P14; P256; P261
Chen, Junyi P91
Chen, Keting T5
Chen, Lu T26
Chen, Pao-Yang P15
Chen, Qiuyue P175; P246
Chen, Shaojiang P105; P205
Chen, Wenkang P186; P247
Chen, Yihan P66
Chen, Zong-Liang T13; P51
Cheng, Jianlin P54
Cheng, Miles P94
Cheng, Zhukuan P80
Chettoor, Antony P52
Chevalier, Céline P29
Chiara, Matteo P68
Bian, Chao P98
Bianchi, Pier Giacomo P224
Biazotti, Bárbara Bort P42
Bihmidine, Saadia T3
Birchler, James A. P45; P54; P70; P120; P148
Blake, Michael T8
Blancon, Justin T18; P236
Blein-Nicolas, Mélisande P191
Bogard, Matthieu P159
Bolser, Dan P21
Bommert, Peter P96; P134; P142
Bontinck, Michiel P57
Borrega, Nero P74
Borrelli, Virginia P49
Bosio, Mickael P158
Bossuyt, Shari P89
Bouman, Niek P237
Bouwmeester, Harro J. P71
Bovina, Riccardo P132
Bowley, Steve P209
Bozinovic, Sofija P188
Bradat, Siobhan P28
Bradbury, Peter J. P34
Brambilla, Vittoria P49
Braud, Max P124
Braun, David M. T3; P44; P48
Braun, Ian R. P6
Brauner, Pedro C. P189; P195
Brenton, Zach P155
Brettschneider, Reinhold P108; P128
Bridges, William P139
Briggs, Steven P. P114
Brigolin, Christian J. P61
Broeckhove, Jan T32
Brohammer, Alex B. T28; P32; P253
Broman, Karl W. P187
Brown, Brian P111
Bruggmann, Remy P230
Brulé, Lenaïg P53
Brunaud, Véronique P7; P254
Brunel, Dominique P239
Brunkard, Jacob P114
Brunner, Arco T2
Brush, Parker L. P44
Brutnell, Thomas P. P67; P69; P266
Bubert, Jessica T29
Bucher, Marcel T20
Buckler, Edward S. T8; T19; T22; P34; P36;
P56; P207; P235
Buell, C. Robin P1; P187; P210
Bueno-Hernández, Brandon P204
Buet, Clement P162; P184
Bui, Hien P222
Burbano, Hernan T8
Burch, Merritt B. P213
Busconi, Matteo P156; P227
208
de Meaux, Juliette P198
de Neve, Amber E. P110
de Sousa, Sylvia M T16
de Vos, Dirk T32
DeBlasio, Stacy P86
Deans, Natalie P127
Decaux, Benoît P239
Decousset, Laurent P184
Degenhardt, Joerg T19
Del Valle-Echevarria, Angel R. T31
Delić, Nenad S. P188; P201; P229
Della Porta, Adriana P46
Delluc, Caroline P126
Dell’Acqua, Matteo P151; P179; P227
Demesa-Arevalo, Edgar P86
Demuynck, Kirin P57; P81
Dennis, Jonathan H. P33
Denton, Alisandra K. P26
Desbiez-Piat, Arnaud T7; P233
Desmaizieres, Gregory P236
Desplat, Nelly P184
Deutzmann, Rainer P91
Diaw, Yacine P177
Diepenbrock, Christine P193
Dietze, Miranda P19; P20
Dilkes, Brian P. P37; P127
Dillmann, Christine T7; P172; P173; P212;
P233
Ding, Charlene P99
Ding, Lei P118
Ding, Yezhang T21
Dittberner, Hannes P198
Doan, Tu P12
Doebley, John F. P2; P246
Doeswijk, Timo P237
Dombey, Rodolphe T27
Domergue, Frédéric P68
Dong, Jiaqiang P9
Dong, Juan P98
Dong, Lemeng P71
Dong, Xiaomei T14; P256; P261
Dong, Xin P105
Dong, Zhaobin P101
Dooner, Hugo K. P248; P251
Dorantes-Acosta, Ana P119
Doridant, Ingrid P158
Dorman, Karin T5
Doseff, Andrea P73
Douglas, Cook P168
Dresselhaus, Thomas P91; P95; P97; P104
Du, Chunguang P248
Du, Yan P80
Duarte, Jorge P29; P170
Duborjal, Herve P158; P184
Duborjal, Hervé P254
Dubreuil, Pierre P159; P162; P184; P236
Cho, Kyoung Tak P20
Chomet, Paul T3; P44
Chopra, Surinder P15; P265
Chris, Schmidt T8
Chu, Jianting P221
Chuck, George P94; P101
Chudalayandi, Siva T5
Chumak, Nina T2; P85
Claeys, Hannes T33; P86
Clark, Clayton J. P82
Clipet, Camille P239
Cloarec, Gladys P181
Cody, Jon P. P45; P70; P148
Cohen, Dan T18
Colasanti, Joseph P58
Cole, Rex A P141
Collier, Ray P60
Comadran, Jordi T1; P106
Comar, Alexis T18
Combes, Valérie P170; P176; P181; P194;
P199; P239
Combs, David K. P190
Conklin, Phillip T4
Consonni, Gabriella P68; P87
Consortium, G2F P234
Conti, Lucio P164
Corll, Jacob P61
Corti, Hélène P191; P198
Costich, Denise E. P151; P152; P153
Coupel-Ledru, Aude P100; P164
Coursol, Sylvie P7; P74; P181
Coussens, Griet P89
Craig, Valerie P209
Crow, Chayton P12
Cruz, Alberto P161
Cui, Jin P15; P265
D'Eustachio, Peter P21
da Silva, Viviane Cristina Heinzen P42
Dai, Mingqiu T26
Dalgalarrondo, Michèle P90; P126
Daly-Jensen, Kathleen P51
Daniel, Robertson P168
Darracq, Aude P29; P170
Davenport, Ruth P61
David, Jacques P177
David, Olivier P233
Dawe, R. Kelly P4; P30; P84; P145; P146;
P260
de Jaeger, Geert P57
de Jaeger-Braet, Joke P108
de la Fuente, María P241
de los Campos, Gustavo P167
de Leon, Natalia P1; P139; P187; P190; P192;
P210; P211; P219; P234
de Luis Balaguer, Maria Angels P99
de Oliveira, Yannick D. P232
209
Fu, Fangfang P30
Fu, Junjie P27
Fu, Miaomiao P72
Fu, Xiuyi P247
Fustier, Margaux-Alison P198
Gage, Joseph L. P1; P210; P234
Gaillard, Antoine P160
Galic, Vlatko P225
Gallavotti, Andrea T13; P51; P58; P83
Galli, Mary T13; P58; P83
Gao, Xiang P25
Gardiner, Jack M. P16; P17; P18; P19; P20
Gardner, Candice P183
Gaudinier, Allison P28
Gault, Christine M. P36
Gavazzi, Giuseppe P87
Gayral, Mathieu P90; P126
Ge, Fei P9
Geiger, Hartwig P240
Gendrot, Ghislaine T1; P7; P106
Gent, Jonathan I. P258; P260
Gepts, Paul P206
Gerlach, Nina T20
Giacopelli, Brian P127
Giauffret, Catherine P159; P160; P239; P254
Gibon, Yves P103
Gilles, Laurine M. T1; P106
Giraud, Héloïse P226
Girimurugan, S B P33
Giuliani, Silvia P132; P214
Giulini, Anna P. M. P224
Glaubitz, Jeffrey C. T8; P176; P199
Goldshmidt, Alexander T33
Gore, Michael A. P152; P193
Gouesnard, Brigitte P176; P177; P194; P199;
P238
Graeber, Kai PL3
Graham, Nathaniel D. P45; P70
Grant-Downton, Robert P262
Grau, Antonin P100
Graumann, Katja P107
Gray, John P73
Grcic, Nikola P188
Grimanelli, Daniel T27; P119; P264
Griveau, Yves P74; P181
Grosche, Christopher PL3
Grossniklaus, Ueli T2; P85
Grote, Karen T3; P44
Grotewold, Erich P73
Grčić, Nikola P201
Guill, Katherine E. P157
Guimarães, Claudia T T16
Gumber, Hardeep K P107
Gundlach, Heidrun P8
Guo, Ce P186
Guo, Tingting P169; P183; P242
Dukowic-Schulze, Stefanie T30
Dumas, Fabrice P7; P198
Dumas, Michael P211
Durbak, Amanda P133
Durham Brooks, Tessa P12
Eapen, Delfeena P204
Earl, Hugh P209
Edelmann, Susanne P262
Eeckhout, Dominique P57
Eggels, Stella P62
Eguiarte, Luis P198
El Hage, Fadi P74; P181
El-Walid, Mohamed P148
Eldridge, Brian Z. P48
Elmorjani, Khalil P90; P126
Elsik, Christine G. P18
Enders, Tara A. P219
Ernst, Karin P240
Esmeray, Mesut P171
Estrada, Amado L. P107
Eva, Bauer T8
Evans, Matthew MS P52; P141
Eveland, Andrea L. T25; T33; P124
Fabianska, Izabela T20
Fabien, Laporte P185
Fabio, Gomez Cano P73
Falcon, Celeste M. P234
Falque, Matthieu P147; P181; P198; P243
Fan, Yuan T26
Fang, Hui P247
Fanuel, Mathieu P90
Farinati, Silvia P255
Federici, Silvia P110; P115
Feil, Regina T33
Feng, Fan P66
Feng, Guanqiao P61
Feng, Yaping P9
Fernandes, John F. P13; P123
Ferrigno, Nick K P48
Fiedler, Isabell P123
Figueroa-Maya, Alejandra P161
Flament, Pascal P160
Flint-Garcia, Sherry A. P211
Forestan, Cristian P255
Fornara, Fabio P49
Fowler, John E. P122; P141
Fox, Tim T2
Franic, Mario P225
Frank, Mary P28
Frascaroli, Elisabetta P132
Freudenthal, Jan P10
Frey, Felix P P231
Frey, Monika P76
Friedberg, Iddo T12
Frisch, Matthias P218
Frommer, Wolf B. P40
210
Hufnagel, Barbara T16
Hughes, Thomas E. P136
Hunter, Charles T. T31
Hurtado, Juan M. P204
Huvenaars, Koen P237
Hölker, Armin P10
Hû, Jean-François P239
Ilut, Dan P34
Inzé, Dirk T32; P57; P81; P89; P118; P179
Jackson, David T33; P44; P86
Jackson, Kristina P51
Jackson, Scott A. T11
Jacquemot, Marie-Pierre P74; P181
Jaiswal, Pankaj P21
Jalovec, Alexis M. P107
Jambrovic, Antun P225
Jander, Georg T31
Jarquin, Diego P234
Javelle, Marie P102; P121
Jeanguenin, Linda T17
Jeannette, Remi P212
Ji, Chen P72
Ji, Lexiang P257; P267
Jia, Haitao P109
Jiao, Yinping P11; P21
Jimenez-Galindo, José Cruz P202
Jin, Weiwei P80; P246
Jio, Yinping P265
Joets, Johann P7; P29; P160; P170; P254
Johannes, Krause T8
Johnson, Lynn C. T8; P34
Johnston, Robyn P110; P115
Joshi, Trupti T13
Juarez, Jazmin Abraham P94
Julie B., Fievet P185
Julius, Ben T. P44
Junker, Astrid P221
Kaeppler, Heidi F. P60
Kaeppler, Shawn M. P1; P60; P139; P187;
P190; P192; P210; P219; P234
Kaiser-Arnaud, Laure P212
Kakrana, Atul P123
Kalinowska, Kamila P91
Kambhamettu, Chandra P165
Kantanka, Sarfo P65
Karimi, Mansour P89
Katam, Ramesh P125
Kao, Yu-Hsin P113
Kelly, Jacob A. P111
Kermarrec, Dominique P176; P199
Kermicle, Jerry P264
Kersey, Paul P21
Khakhar, Arjun T13
Khaled, Abdelsabour T1; P106
Khangura, Rajdeep P155
Kianian, Shahryar F. T30
Gupta, Parul P21
Gustafson, Timothy J. P1
Gustin, Jeffery L. P31; P65
Guthrie, Katherine P135
Gutierrez-Marcos, Jose F. P116; P120
Gutjahr, Caroline P138; P208; P215
Haase, Nicholas P190
Haberer, Georg P8
Hacisalihoglu, Gokhan P65
Hake, Sarah C. T15; P94; P110; P114; P115
Hamacher, Joachim P138
Hamilton, John P1
Hammes, Ulrich Z. P91
Han, Yingjia P247
Harness, Alex P13
Harper, Lisa C. P16; P17; P19; P20
Hartwig, Thomas P40
Has, Voichita P230
Hattery, Travis J. P92; P182
He, Limei P248
Heckmann, David P26
Heckwolf, Marlies P192
Heeney, Michelle P112
Hernandez, Maria Mateos P193
Hernández-Montes, Georgina P204
Heuermann, Marc P221
Hilgert, Uwe P155
Hillmann, Katie P149
Hirel, Bertrand P38; P53
Hirsch, Candice N. T28; P32; P92; P216; P253
Hirsch, Cory D. T28; P219
Hlavati, Daniel P127
Hochholdinger, Frank T24; P8; P75; P138;
P231; P259
Hockemeyer, Katelyn P182
Hodgman, Charlie P258
Hoefsloot, Huub C.J. P258
Hoelker, Armin C. P189
Hoffmann, Thomas P76
Hokin, Samuel P52; P141
Holland, James B. P165; P211
Hollick, Jay B. P127; P252; P263; P268
Holmes, Mark W. P216
Horner, David P68
Horschmann, Marc P40
Hou, Jie P54
Hsu, Fei-man P155
Huabang, Chen P50
Huang, Cheng P246
Huang, Jun P248
Huang, Liang liang T14
Huang, Wei P80
Huang, Xing P93
Huang, Yongcai P72; P93
Huet, Sylvie P233
Hufford, Matthew B. P4; P206
211
Lee, Young K. P21
Legay, Sylvain P181
Legland, David P74
Legrand, Judith P212
Lehermeier, Christina P220
Leiboff, Samuel T15; P94; P110; P115; P121;
P129; P130; P242
Leon, Sareen P88
Lepak, Nicholas K. P235
Leubner-Metzger, Gerhard PL3
Leveugle, Magalie P158; P184; P254
Lewis, Michael W. P110
Ley, Ruth E. P235
Li, Changsheng P71
Li, Chaobin P78
Li, Chengcheng P39
Li, Chunjian P138
Li, Dan P246
Li, En T14; P256
Li, Hui P247
Li, Jiangsheng P247
Li, Jiansheng P186
Li, Jing P23
Li, Jinlong P205
Li, Lin T26; P121
Li, Manfei P109
Li, Mengtao P43
Li, Qing T10; T26; T29
Li, Shengyan P43
Li, Tong P261
Li, Weiya P186; P247
Li, Xianran T11; P121; P169; P183; P242
Li, Xiaowei P186
Li, Xinchen P25
Li, Xingli P97; P105
Li, Xuexian P64
Li, Yu T8
Li, Yuan T14
Li, Yubin P248; P251
Li, Yunfei P80
Liang, Yameng P246
Lim, Sooyeon P59
Ling, Huiling P78
Ling, Qinyin P5
Linossier, Laurent P126
Lipka, Alexander E. T25; P244
Liseron-Monfils, Christophe P28
Lithio, Andrew T24
Liu, Bing P63
Liu, Chenxu P105; P205
Liu, Han T14; P25
Liu, Jianing P30
Liu, Jie T10
Liu, Peng P39; P44
Liu, Qiujie P83
Liu, Xiaolei T8
Kim, Kitae P94
Kim, Kyung Do T11
Kimberlin, Athen P130
Kimble, Ashten P133
King, Kyle P182
Kirschner, Sandra P240
Klaeser, Hannah P51
Klein, Harry P112
Klukas, Christian P221
Kluth, Jantjeline P134; P142
Knauer, Steffen P102; P121
Knoch, Dominic P221
Koch, Karen E. P39; P44; P46; P249
Kolagunda, Abhishek P165
Koo, Abraham P130
Korte, Arthur P10
Kortz, Annika P138
Kovacevic, Dragan R. P223
Kravic, Natalija B. P163; P223
Kremling, Karl A. T22; P36; P235
Krnjaja, Vesna S. P229
Kumar, Dibyendu P9
Kumar, Vivek P21; P28
Kumari, Sunita P21; P121
Kusmec, Aaron T9
Kyle, Kathleen E P33
Köhling, Vasco P134; P142
Laborde, Jacques P176; P199
Labrosse, Jérémy T18
Lacube, Sebastien PL2; P79; P269
Lafarge, Stephane P158
Laffaire, Jean-Baptiste T1; P106
Laffray, Amélie P176; P199
Lai, Jinsheng T14; P14; P25; P35; P64; P256;
P261
Lal, Shailesh K. P61
Lambert, Antoine P238
Lana, Ubiraci G P T16
Landi, Pierangelo P132
Lang, Zhihong P43
Langdale, Jane A. P136
Lanubile, Alessandra P49; P156; P227
Laplaige, Jérôme T1; P7; P106
Lassagne, Herve P236
Lauter, Nick T5; P92; P165; P182; P211
Lawrence-Dill, Carolyn J. T12; P6; P121
Le Guilloux, Martine P254
Le Paslier, Marie-Christine P29; P194; P239
Le Tourneau, Justin P18
Leach, Kristen A. P44
Ledencan, Tatjana P225
Lee, Ding Hua P143
Lee, Elizabeth A. P196; P209; P217
Lee, Hyeyoung P154; P222
Lee, Tzuu-fen P15; P265
Lee, Yang-Seok P116; P120
212
Martienssen, Rob T27; P264
Martin, Bruno P150
Martin, Federico P61
Martin, Olivier C. P147; P243
Martin-Magnette, Marie-Laure P7
Martinant, Jean-Pierre T1; P106
Martinell, Brian P60
Martinez-Ainsworth, Natalia P198
Martínez-Guadarrama, Jesús J P204
Martínez-Nava, Alejandro P161
Mary-Huard, Tristan P29; P194; P197
Maschmann, Sascha P96
Mateos, Maria P203
Mathew, Deepu P193; P203
Mathioni, Sandra P123
Matson, R.G. T8
Matthes, Michaela P133
Mayer, Klaus F.X. P8
Mayer, Manfred P10; P189
McCarty, Donald R. P39; P249
McCaw, Morgan E. P45
McClish, Allison P268
McCormic, Emily J. P127; P252
McCubbin, Tyler J. P44
McFarland, Bridget A. P234
McFarland, Frank P60
McGaugh, Suzanne E. P32
McKenna, Joseph P107
McLean Rodriguez, Francis Denisse P151
McNinch, Colton M. T5
McSteen, Paula P41; P133; P135; P137
Medina-Andrés, Rigoberto P204
Meier, Nate P12
Mejía-Guerra, M. Katherine T22
Melchinger, Albrecht E. P176; P189; P195;
P199; P218
Melissa, Kruse-Peeples T8
Mérai, Zsuzsanna PL3
Mergner, Julia P91
Mesarovic, Jelena P163
Messing, Joachim P9
Meyer, Rhonda C. P221
Meyers, Blake P15; P116; P120; P123; P265
Michaud, Caroline P119
Michel, Kathryn P187
Micklos, Dave P155
Miclaus, Mihai P230
Miculan, Mara P179
Mikel, Mark P210
Milhiet, Thomas P118
Miller, Kathleen M. P228
Miller, Nathan D. P31; P65; P219
Miller, Zachary T8; P34
Millet, Emilie J. PL2; P100; P269
Minow, Mark P58
Miyamoto, Amy J. P60
Liu, Yuhang P33
Liu, Zhipeng P35
Lledías, Fernando P204
Loneman, Derek M. T5; P182
Long, Connor P12
Longstaff, Muriel T. P111
Lopes, Simara M. T16
Lopez, Jérémy T18; P158; P236
Lopez, Miriam D. T5; P182
Lor, Vai S.N. P60
Lorant, Anne P2
Lorgeou, Josiane P150; P159; P160
Lourgant, Kristelle P239
Lu, Qiong T26
Lu, Zefu T13; P267
Lubkowitz, Mark A. P48
Lucas, Lance P12
Lunde, China P130
Lundgren, Jennifer M. P39
Lung, Pei-Yau P22; P33
Lunn, John T33
Luo, Anding P120
Lv, Yuanda P66
Lübberstedt, Thomas P183
Ma, Chuanyu P245
Ma, Fangfang P46
Ma, Xiaoli P102; P121
Ma, Xuxu P25; P35
Mabire, Clément P170
MacLean, Dustin P196
Madur, Delphine M. P170; P176; P181; P194;
P199; P232; P239
Mafu, Sibongile T21
Magalhães, Jurandir V T16
Maghoub, Umnia T5
Mahoy, Jill A. P60
Maillard, Morgan P158
Maina, Eric P73
Maistriaux, Laurie C. T17
Makarevitch, Irina P149
Malavieille, Serge P181
Malvar, Rosa Ana P174; P180; P202
Manching, Heather K. P211
Manerus, Laura P217
Mangel, Nathalie P150
Manicacci, Domenica P198
Manley, Bethan P69
Maple, Robert J. P116; P120
Marande, William P7
Marchadier, Elodie T7; P172; P173; P212
Marco, Cristina F. P155
Marcon, Caroline T24; P8; P259
Marion, Didier P90; P126
Markovic, Ksenija P223
Marocco, Adriano P49; P156; P227
Marroni, Fabio P179
213
Oka, Rurika P258
Okoro, Michael P155
Oldroyd, Giles P69
Olson, Andrew P11; P21; P28
Oltehua-López, Omar P119
Onokpise, Kome U. P33
Oppenheimer, Jara P96; P134; P142
Ordás, Bernardo P174; P180; P189; P202; P241
Ouma, Wilberforce Z. P73
Oury, Vincent P103
Ouzunova, Milena P189; P231; P240
Owens, Brenda F. P193; P203
Padilla, Guillermo P241
Palaffre, Carine P7; P238; P239
Panda, Kaushik P141
Pang, Junling P27
Papatheodorou, Irene P21
Parent, Boris PL2; P79; P269
Parvathaneni, Rajiv T25
Pasquer, Frédérique T2; P85
Paszkowski, Uta P69
Pateyron, Stéphanie P7
Pauwels, Laurens P42; P89
Pavesi, Giulio P58; P255
Pavlov, Jovan P188; P201
Pawlowski, Wojciech P. T30; P63
Paysant-Le Roux, Christine P254
Pè, Mario Enrico P151; P179; P227
Peddicord, Layton T5
Peevers, Jeanette T3; P44
Perez, David P82
Permentine, Chris P149
Persiau, Geert P57
Pesch, Lina T20
Pestsova, Elena P240
Peter, Bradbury T8
Peters, David W. P183
Petersen, Michael W. P60
Peñaloza, Maximiliano P204
Pichon, Jean-Philippe P29; P170; P184; P254
Piepho, Hans-Peter T24
Piranni, Ali P170
Piraux, François P150
Pook, Torsten P167
Portwood II, John L. P16; P17; P19; P20
Posekany, Tes P182
Praud, Sébastien T18; P158; P160; P162; P184;
P236
Preece, Justin P21
Presterl, Thomas P189; P231; P240
Prinsen, Els T32
Prodhomme, Duyen P103
Prusicki, Maria Ada P140
Punta, Ramu P34
Qi, Weiwei P66
Qiao, Pengfei P129; P155
Mladenovic-Drinic, Snezana D. P163; P188;
P201; P223
Mo, Weipeng P25
Mohammaddi, Mohsen P200
Monnahan, Patrick J. P32
Montes, Salvador P198
Monticolo, Francesco P58
Moore, Riley D. P92
Moose, Stephen P. T29; P67
Moreau, Laurence M. P160; P176; P181; P197;
P199; P220; P226; P232; P239
Moreno-Gonzalez, Jesus P176; P199
Morrow, Darren P123
Moss, Britney L. P51
Muehlbauer, Gary J. T26; P102; P121; P242
Multani, Dilbag P75
Muna, Demitri P21
Munoz-Torres, Monica P155
Muraya, Moses M. P221
Murphy, Katherine M T21
Murray, Seth C. P211
Muszynski, Michael G. T31
Muth, Peter P208
Myers, Bryn M. P92
Méchin, Valérie P74; P181
Müller, Benedikt P91
Müller, Dominik P195
Müller, Verena P75
Nadal, Marina P69
Naithani, Sushma P21
Nannas, Natalie J. P30; P145; P146
Negri, Barbara F. T16
Negro, Sandra P176; P191; P199; P239
Nelissen, Hilde T31; T32; P57; P81; P118;
P179; P227
Nelms, Bradlee D. T23
Nelson, Rebecca J. P165
Nemhauser, Jennifer L. T13
Nettleton, Dan T9; T24
Newton, Kathleen P148
Nguyen, Hung N. P18
Nicolas, Stéphane D. T17; P29; P170; P176;
P191; P194; P199; P232; P239
Niculaes, Claudiu P62
Nielsen, Torrey P111
Nieto-Sotelo, Jorge P161; P204
Nikolau, Basil J. T5; P182
Nikolic, Ana S. P223
Nikolic, Milica V. P229
Nikoloski, Zoran P24
Noble, JD P5
Nodet, Claire P160
Nordborg, Magnus PL1
Noshay, Jaclyn M. T28; P253; P257
Nukunya, Kate P99
Obradovic, Ana M. P229
214
Saski, Christopher P139
Satoh-Nagasawa, Namiko P86
Satterlee, Jack W. P129; P131
Savadel, Savannah D. P22; P33
Savic, Iva J. P229
Sawers, Ruairidh J. P69; P161
Scanlon, Michael J. T4; T11; P102; P110;
P115; P121; P129; P131; P242
Schaeffer, Mary L. P16; P17; P19; P20
Schaff, Claudia T19
Scheuermann, Daniela P240
Scheid, Ortun Mittelsten PL3;
Schlather, Martin P167
Schlüter, Urte P26
Schmelz, Eric A. T21
Schmitz, Robert J. T13; P257; P267
Schnable, Patrick S. T9; T26; P102; P121;
P129; P242
Schnittger, Arp T27; P108; P128; P140
Scholten, Stefan P218; P262
Schoof, Heiko T24; P259
Schopp, Pascal P195
Schott, David A. P20
Schrag, Tobias A. P218
Schroeder, Elly C. P92
Schulz, Aimee J. P206
Schulz, Burkhard P94
Schwab, Wilfried P76
Schwechheimer, Claus P91
Schön, Chris-Carolin T8; P8; P10; P62; P167;
P189; P195; P208; P231
Schünemann, Verena T8
Seetharam, Arun P23
Segal, Gregorio P248
Seidel, Michael A. P8
Seifert, Felix P218; P262
Sekhon, Rajandeep P139; P168
Sellier, Hélène P254
Sellier-Richard, Hélène P239
Sen, Sidharth T13
Sen, Taner P16
Senlin, Xiao P50
Septiani, Popi P227
Settles, A. Mark P31; P61; P65
Seye, Adama I. P226
Shamimuzzaman, Md T25
Shao, Eric P211
She, Wenjing T2; P85
Shen, Bo P28
Shen, Yi P80
Shen, Zhouxin P114
Shi, Jinghua P30
Shi, Junpeng P35
Shi, Xiaowen P54
Shi, Yun-Zhi P113
Shodja, Donya P61
Qin, Yuanxin P105
Qiu, Weihong P84
Quilleré, Isabelle P53
Rabier, Dominique P239
Rafal, Gutaker T8
Ramstein, Guillaume P P207
Rangel, Luz M. P161
Rasmussen, Carolyn P88
Raynaud, Christophe P238
Reboucas, Joao R. P190
Regulski, Michael T27; P264
Reif, Jochen C. P221
Renard, Agathe P160
Rensing, Stefan A. PL3
Ressayre, Adrienne T7; P172; P173
Revilla, Pedro P174; P176; P180; P199
Reymond, Matthieu P74; P181
Rhodes, Brian H. P67
Ricci, William A. P267
Rice, Brian R. P244
Richardson, Annis E. P110
Richter, Annett T19
Riewe, David P221
Rimbert, Hélène P170
Rio, Simon P197
Rita Lu, Jui-Hsien P15
Rivière, Nathalie P170
Robil, Janlo M. P133; P137
Robinson, J.A.B P217
Rocheford, Torbert R. P193; P200; P203
Rodriguez, Jonas P192
Rogniaux, Hélène P90
Rogowsky, Peter M. T1; P7; P29; P49; P106;
P160
Rojas, Claudia I. P161
Romay, M. Cinta T8; P34; P174; P234
Ronceret, Arnaud P143; P144
Ronfort, Joëlle P177
Ross-Ibarra, Jeffrey PL4; T6; T8; T28; P2;
P250; P253
Rossi, Vincenzo P58; P255
Rousselet, Agnès P7; P198
Rouster, Jacques P116
Rybka, Dominika P218
Salvi, Silvio P7; P132; P214
Sanane, Inoussa T7; P212
Sanchez, Jesus T8
Sanclemente, Maria-Angelica P46
Sangiorgio, Stefano P87
Santiago, Rogelio P202
Sanz Mora, Oscar P128
Sapkota, Sirjan P155
Saponaro, Philip P165
Sara, Larsson T8
Sarah, Hake P130
Sartre, Pascal P181
215
Tamim, Saleh P116; P120
Tan, Qixian P265
Tang, Vicki P52
Taramino, Graziana P75
Tardieu, François PL2; T17; P7; P79; P100;
P103; P160; P164; P191; P269
Tarkowská, Danuše PL3
Tayal, Aditi P18
Tello-Ruiz, Marcela K. P11; P21; P155
Tenaillon, Maud I. T7; P2; P172; P173; P198;
P233
Teyssèdre, Simon P220
The, W22 Sequencing Consortium P266
Thiemann, Alexander P218; P262
Thompson, Beth P99
Thornton, Kevin T6
Tian, Feng P175; P246
Tian, Jinge P246
Tian, Tian P138
Tian, Xiaolong P105; P205
Tidd, Jess F P48
Tiede, Tyler P193
Timmermans, Marja C. P102; P121; P129;
P242
Tixier, Marie-Hélène T18; P162; P184; P236
Todt, Natalie P242
Tolimir, Miodrag P201
Tollon-Cordet, Christine P176; P177; P199
Tonelli, Chiara P164
Tourrette, Elise P243
Tracy, William F. P1; P228
Tran, Thu M. T3; P133
Treible, Wayne P165
Triant, Deborah R P18
Tristan, Mary-Huard P185
Tschiersch, Henning P221
Tseng, Ching-Chih P113
Tseng, Kuo-Fu P84
Tseung, Chi-Wah P61
Tuberosa, Roberto P132; P214
Turc, Olivier P7; P103
Turck, Franziska P258
Turečková, Veronika PL3
Turner, Sarah D P157
Turpin, Zach M P33
Ullrich, Kristian K. PL3
Unger-Wallace, Erica P3
Unni, Deepak R. P18
Uyehara, Aimee N. T31
Vaillancourt, Brieanne P1; P187; P210
Vajk, Angus P94
Vallejo-Reyna, Miguel A. P161
van der Linde, Karina P123
van Ham, Roeland P237
van Hautegem, Tom P81
van Leene, Jelle P57
Si Nian, Char P86
Sidhu, Gaganpreet T30
Sidhu, Sukhmani P88
Simianer, Henner P167
Simic, Domagoj P225
Singh, Jugpreet P46
Singh, Urminder P23
Skirpan, Andrea P41
Skopelitis, Tara P86
Slotkin, R. Keith P141
Soenen, Baptiste P159
Soffritti, Giovanna P156
Song, Dandan P27
Song, Rentao P66; P78
Song, Weibin T14; P14; P25; P35; P64; P256
Song, Xinran P247
Sosso, Davide P40
Sounac, Nicolas P184
Sozzani, Rosangela P99
Spalding, Edgar P. P31; P60; P219
Spannagl, Manuel P8
Spielbauer, Gertraud P61
Springer, Nathan M. T11; T28; T30; P219;
P250; P253; P257; P258
Srdic, Jelena Z. P223
Srinivasan, Srikant T9
St. Aubin, Brian P114
Stagnati, Lorenzo P156; P227
Stam, Maike P258
Stankovic, Goran J. P229
Stankovic, Slavica Z. P229
Stark, Timo P76
Stateczny, Dave P96; P134; P142
Stein, Joshua C. P11; P21
Steinbach, Delphine S. P232
Steinhauer, Tyler P61
Stetter, Markus G. T6
Stevanović, Milan P188; P201
Stitzer, Michelle C. T28; P155; P250; P253;
P257
Strnad, Miroslav PL3
Storme, Veronique P81
Strable, Joshua P56; P110; P115
Su, Zhen P138
Sun, Huayue P246
Sun, Qi T30
Sun, Silong P35
Sun, Wei P109
Suteu, Dana P230
Swarts, Kelly T8
Swentowsky, Kyle W P84
Swyers, Nathan C. P45; P70
Sylvester, Anne W. P110; P115; P120
Sáenz-Rodríguez, Mery N P204
Taconnat-Soubigou, Ludivine P7; P254
Takasaki, Hironori P81
216
Weimer, Monika P216
Weiss, Jodi D. P145; P146
Welcker, Claude PL2; T17; P7; P100; P103;
P164; P191; P238; P269
Weldekidan, Teclemariam P211
Wesselink, Jan-Jaap P258
Westhoff, Peter P240
Whipple, Clinton J. P101; P111; P112
White, Michael R. P210
Widiez, Thomas T1; P106
Wiesner-Hanks, Tyr P165
Wilhelmsson, Per PL3
Williams, Edward J. P60
Williams, Jason J. P155
Williams, Mark E. T2
Wills, David M. P211
Wimalanathan, Kokulapalan T12; P3; P121;
P155
Win, Yan Naing P259
Wisser, Randall J. P165; P211
Wittmeyer, Kameron P15; P265
Wohlgemuth, Stephanie E. P39
Woodhouse, Margaret H. P16; P17; P19; P20
Wu, Hao P136; P155
Wu, Lishuan P246
Wu, Shan P39
Wu, Yaoyao P175
Wu, Yongrui P72; P93
Xiao, Yuguo P101; P111; P112
Xie, Shaojun P35
Xing, Lijuan P77
Xing, Yingying P78
Xiong, Wenwei P248
Xu, Dingyi P246
Xu, Guanghui P246
Xu, Jing P247
Xu, Liming P66
Xu, Miaoyun P47; P77; P166
Xu, Mingliang P245
Xu, Wenwei P211
Xu, Xiaosa P86
Yan, Jianbing T10; T26; P186
Yan, Shumei P66
Yandeau-Nelson, Marna D. T5; P92; P182
Yang, Bing P40; P86; P88
Yang, Bo P64
Yang, Hailong P99
Yang, Hua P54
Yang, Jiani P124
Yang, Jinliang P40
Yang, Jun P72
Yang, Ning P186
Yang, Qin P165
Yang, Wenyao P66
Yang, Xiaohong P186; P246; P247
Yao, Hong P41
van Lijsebettens, Mieke P89; P118
Vana, Carmen P230
Vanderhaeghen, Rudy P89
Vanous, Adam P183
Varela, Jose I. P190
Varotto, Serena P255
Vedder, Lucia T24
Vejlupkova, Zuzana P141
Venon, Anthony P7; P198
Vera, Daniel L. T25; P22; P33
Vi, Son L. T33
Vidal Martinez, Victor A. P152
Villa, Juan M. P161
Virlouvet, Laetitia P181
Vitte, Clémentine P7; P29; P160; P170; P254
Vollbrecht, Erik P3
Vázquez-Marcial, Leopoldo P161
Wagner, Ruth A. T3; P44
Walbot, Virginia T23; P13; P123
Wallace, Jason G. P235
Walsh, Jesse R. P16; P17; P19; P20
Walters, William A. P235
Wang, Baobao P35
Wang, Bo P11; P21
Wang, Chenglong P246
Wang, Chi-Ting P113
Wang, Chung-Ju Rachel P113; P143
Wang, Guiping P43
Wang, Guoying P27
Wang, Hai T22; P43
Wang, Haihai P93
Wang, Haiyang P55
Wang, Harrison P248
Wang, Jing P14; P27; P64
Wang, Jinyu T11
Wang, Lei P47; P77; P166
Wang, Lele P95; P105
Wang, Lina P245
Wang, Minghui T30
Wang, Na P260
Wang, Qinghua P248
Wang, Tianyu T8
Wang, Xin P35
Wang, Xufeng P175; P246
Ware, Doreen P4; P11; P21; P28; P121; P155;
P265
Warman, Matthew P122; P141
Waselkov, Katherine P178
Washburn, Jacob D. T22; P56
Wasikowski, Rachael P73; P155
Waybright, Aaron P152
Weber, Andreas PM P26
Weber, Blaise P258
Weeks, Rebecca P3
Wei, Sharon P11; P21
Weigel, Detlef T8
217
Zou, Yanjiao P222
Zwiener, Benjamin P12
Yao, Lishan P245
Ye, Jianrong P245
Yen, Ming-Ren P15
Yi, Fei P256
Yi, Gibum P59
Yi, Qiang P174
Youhui, Tian P50
Yu, Jianming T11; P102; P121; P169; P183;
P242
Yu, Peng P138
Yu, Xiaoqing P242
Yuan, Yue P66
Yue, Yihong P78
Yves Vigouroux, Yves P198
Zambelli, Federico P58
Zanetto, Anne P177; P238
Zavala, Cristian P152; P153
Zerbe, Philipp T21
Zhan, Jungpeng P155
Zhang, Bosen T29
Zhang, Dongfeng P245
Zhang, Jinfeng P22; P33
Zhang, Lei P247
Zhang, Lifang P28
Zhang, Min P47; P77
Zhang, Pei T26
Zhang, Qianqian P245
Zhang, Renyu P186
Zhang, Xiangbo T14; P64; P256
Zhang, Xiaoyu P242; P267
Zhang, Xuan P186
Zhang, Xuecai P161
Zhang, Zhanyuan P222
Zhang, Zhiwu T8; T19
Zhang, Zuxin P109
Zhao, Binghao P247
Zhao, Changzeng P45; P70
Zhao, Haiming T14; P14; P25; P35; P64; P256
Zhao, Hainan P35
Zhao, Han P66
Zhao, Jun P27
Zhao, Yusheng P221
Zhong, Tao P245
Zhong, Yu P205
Zhou, Adele T30
Zhou, Liangzi P95
Zhou, Peng T28; P253; P257
Zhou, Yingsi P35
Zhu, Mang P245
Zhu, Ming P77
Zhu, Tongdan P78
Zicola, Johan P258
Zilio, Massimo P87
Zivy, Michel P191
Zong, Na P27
Zou, Junjie P166
218
Participant List
Participant
Organization
Abramov, Aleksej
Technical University of Munich
Achour, Zeineb
Université Paris Sud - GQE Le Moulon
Ackerman, Arlyn
Clemson
Adkins, Lolita
University of California, Davis
Agha, Husain
University Of Missouri
Aguilar-Gutierrez,
Estefania
California State University, Fresno
Allard, Alix
RAGT2n
Allen, Ed
Monsanto
Allier, Antoine
INRA
Altmann, Thomas
IPK Gatersleben
Alvarez Prado, Santiago
INRA
Anderson, Alyssa
University of California, Berkeley
Anderson, Sarah N.
University of Minnesota
Andjelkovic, Violeta
Maize Research Institute Zemun Polje
Andorf, Carson
USDA-ARS (MaizeGDB)
Anibas, Calli
University of Wisconsin - Madison
Arp, Jennifer
Donald Danforth Plant Science Center
Arteaga-Vazquez, Mario
Universidad Veracruzana
Asaro, Alexandra
Washington University in Saint Louis / Donald Danforth Plant Science Center
Auger, Don
South Dakota State Unviersity
Avramova, Viktoriya
Technical University of Munich
Awale, Prameela
South Dakota State University
Aydinoglu, Fatma
Gebze Technical University (GTU)
219
Participant
O
Participant
Organization
Bacciu, Nicola
Keygene NV
Baer, Marcel
University of Bonn
Bakan, Bénédicte
INRA
Balboni, Martina
University of Hamburg
Baldauf, Jutta
University of Bonn
Barbazuk, Brad
University of Florida
Bartlett, Madelaine
University of Massachusetts Amherst
Bartos, Jan
Institute of Experimental Botany
Basler, Georg
Max Planck Institute of Molecular Plant Physiology
Bass, Hank
Florida State University
Bate, Nic
Syngenta
Bauer, Eva
Technical University of Munich
Bauland, Cyril
INRA
Baxter, Ivan
USDA-ARS/Donald Danforth Plant Science Center
Beaugrand, Alice
INRA GQE-LE MOULON
Beemster, Gerrit
University of Antwerp
Begcy, Kevin
University of Regensburg
Bellinger, Marschal
University of California, Riverside
Bensen, Robert
Syngenta
Berger, Florian
LMU Munich
Bertin, Isabelle
Euralis Services
Bertolini, Edoardo
Donald Danforth Plant Science Center
Berube, Benjamin
Cold Spring Harbor Laboratory
Best, Norman
University of Missouri
220
Participant
O
Participant
Organization
Bettinger, Laurent
Euralis Services
Bezrutczyk, Margaret
Heinrich Heine Univeristy
Bian, Chao
Rutgers University
Birchler, James
University of Missouri
Blancon, Justin
BIOGEMMA
Blankenagel, Sonja
Technische Universität München
Blavet, Nicolas
Institute of Experimental Botany
Blein-Nicolas, Mélisande
INRA
Bogard, Matthieu
Arvalis Institute de Vegetal
Bommert, Peter
University of Hamburg
Bontinck, Michiel
Ghent University
Borrelli, Virginia
Università Cattolica del Sacro Cuore
Boudet, Frantz
CAUSSADE SEMENCES
Boury, Stephane
Caussade Semences
Boynton, Tiffany
Florida Agricultural & Mechanical University
Bradbury, Peter
USDA-ARS
Braud, Max
Donald Danforth Plant Science Center
Braun, David
University of Missouri
Braun, Ian
Iowa State University
Brettschneider, Reinhold
University of Hamburg
Brohammer, Alex
University of Minnesota
Bruce, Wes
BASF
Brutnell, Tom
Danforth Plant Science Center
Bucher, Marcel
University of Cologne
221
Participant
Organization
Buckler, Ed
USDA-ARS
Buet, Clément
BIOGEMMA
Burch, Merritt
South Dakota State University
Burton, Lamar
Florida International University
Caicedo, Marlon
Mision Biologica Degwalicia (CSIC)
Campbell, Darwin
Iowa State University
Cannon, Ethy
USDA-ARS (MaizeGDB)
Cassab, Gladys
Institute of Biotechnology, UNAM
Castorina, Giulia
University of Milan
Chai, Yuchao
China Golden Marker (Beijing) Biotech Co.Ltd.
Charcosset, Alain
INRA
Chaumont, Francois
University of Louvain
Chen, Cuixia
Shandong Agricultural University
Chen, Lu
Huazhong Agricultural University
Chen, Keting
Iowa State University
Chen, Jian
China Agricultural University
Chomet, Paul
NRGene
Chopra, Surinder
Penn State Univ
Chumak, Nina
University of Zurich, Switzerland
Claeys, Hannes
Cold Spring Harbor Laboratory
Clipet, Camille
INRA
Cody, Jon
University of Missouri
Combes, Eliette
Limagrain Europe
Cone, Karen
National Science Foundation
222
Participant
Organization
Conklin, Phillip
Cornell University
Consonni, Gabriella
University of Milan, Italy
Conti, Lucio
Università degli studi di Milano
Contrain, Yvan
Limagrain Europe
Corll, Jacob
Oakland University
Costich, Denise
International Maize and Wheat Improvement Center (CIMMYT)
Coursol, Sylvie
INRA
Couton, Florence
Euralis Services
Craig, Valerie
University of Guelph
Cui, Jin
Pennsylvania State University
Daneva, Anna
VIB-PSB
Davenport, Ruth
University of Florida
Dawe, Kelly
University of Georgia
De Jaeger-Braet, Joke
University of Hamburg
De Leon, Natalia
University of Wisconsin, Madison
Deans, Natalie
The Ohio State University
Decousset, Laurent
BIOGEMMA
Degenhardt, Jorg
Halle University
Dell'Acqua, Matteo
Scuola Superiore Sant'Anna di Pisa
Demartino, Marjorie
University of California, Irvine
Demesa-Arevalo, Edgar
Cold Spring Harbor Laboratory
Derue, Carole
Euralis Services
Desbiez-Piat, Arnaud
University Paris-Saclay
Diaw, Yacine
Sup Agro
223
Participant
Organization
Dillmann, Christine
University Paris-Saclay
Ding, Lei
Université catholique de Louvain
Dong, Jiaqiang
Waksman Institute of Microbiology, Rutgers, the state university of New Jersey
Dooner, Hugo
Rutgers University
Doseff, Andrea
Michigan State University
Dr. Neß-Nietsch, Julia
CGS Crop Genetic Systems
Dresselhaus, Thomas
University of Regensburg, Germany
Du, Yanfang
Huazhong Agricultural University
Du, Chunguang
Montclair State University
Dubreuil, Pierre
BIOGEMMA
Dufour, Philippe
RAGT2n
Durham Brooks, Tessa
Doane University
Ebot-Ojong, Felicia
University of Georgia
Edelmann, Susanne
University of Hamburg
Eggels, Stella
Technische Universität München
Eldridge, Brian
Saint Michael's College
El'Hage, Fadi
University of Paris-Sud
Elsik, Chris
University of Missouri
El-Walid, Mohamed
University of Missouri
Ernst, Karin
University of Düsseldorf
Ersoz, Elhan
Benson Hill Biosystems
Eschholz, Tobias W.
Maisadour Semences
Evans, Matt
Carnegie Institution for Science, Dept of Plant Biology
Eveland, Andrea
Donald Danforth Plant Science Center
224
Participant
Organization
Fabre, Françoise
RAGT2n
Falque, Matthieu
INRA GQE - Le Moulon
Fatmi, Kader
Eurofins Analytics
Fernandes, John
Stanford University
Ferrigno, Nick
Saint Michael's College
Fievet, Julie
AgroParisTech
Forestan, Cristian
University of Padova
Fouquet, Romain
MONSANTO SAS
Fourneau, Michael
MAISADOUR Semences
Frascaroli, Elisabetta
University of Bologna
Freudenthal, Jan
University of Wuerzburg
Frey, Monika
Chair of Plant Breeding, Technical university of Munich
Frey, Felix
University of Bonn
Fritschi, Felix
University of Missouri
Gage, Joseph
University of Wisconsin - Madison
Gaillard, Antoine
MAISADOUR SEMENCES
Gallavotti, Andrea
Waksman Institute, Rutgers University
Galli, Mary
Waksman Institute, Rutgers University
Ganal, Martin
TraitGenetics GmbH
Gao, Xiang
China Agricultural University
Gardiner, Jack
University of Missouri
Gault, Christy
Cornell University
Gayral, Mathieu
Bordeaux University
Geiger, Hartwig H.
University of Hohenheim
225
Participant
Organization
Gerin, Gregoire
CAUSSADE SEMENCES
Giauffret, Catherine
INRA AgroImpact
Gossart, Gwenaelle
Euralis Services
Gouere, Laurent
Maïsadour Semences
Gouesnard, Brigitte
INRA
Gray, John
University of Toledo
Grcic, Nikola
Maize Research Institute Zemun Polje
Grimanelli, Daniel
Année
Grossniklaus, Ueli
University of Zurich
Grotewold, Erich
Michigan State University
Guillaume, Colin
Maïsadour Semences
Gumber, Hardeep
Florida State University
Guo, Mei
Beidahuang KenFeng Seed Co., Ltd
Guthrie, Katherine
University of Missouri Columbia
Gutierrez-Marcos, Jose
University of Warwick
Hacisalihoglu, Gokhan
FLORIDA A&M UNIVERSITY
Han, Yingjia
China Agriculture University
Hancer, Onur
QualySense AG
Harper, Lisa
USDA-ARS (MaizeGDB)
Hartwig, Thomas
Max Planck Institut
Hattery, Travis
Iowa State University
He, Yan
China Agricultural University
Hearne, Sarah
CIMMYT
Hermann, Katrin
Syngenta
226
Participant
Organization
Hirel, Bertrand
INRA - IJPB
Hirsch, Candy
University of Minnesota
Hochholdinger, Frank
University of Bonn
Hokin, Sam
Carnegie Institution for Science
Hollick, Jay
The Ohio State University
Hollis, Brieana
Florida A&M University
Holmes, Mark
University of Minnesota
Huang, Wei
China Agricultural University
Hufford, Matthew
Iowa State University
Hughes, Thomas
University of Oxford
Inze, Dirk
VIB-UGent Center for Plant Systems Biology
Jackson, Dave
Cold Spring Harbor Laboratory
Javelle, Marie
BIOGEMMA
Joets, Johann
GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. ParisSaclay, Gif-sur-Yvette, France
Jones, Todd
DuPont Pioneer
Kaeppler, Heidi
University of Wisconsin - Madison
Kaeppler, Shawn
University of Wisconsin – Madison
Kalinowska-Brandt,
Kamila
University of Regensburg, Germany
Katam, Ramesh
Florida A&M University
Kiani, Kian
BASF
Kloiber-Maitz, Monika
KWS SAAT SE
Knauer, Steffen
Center for Plant Molecular Biology, University of Tübingen
Koch, Karen
University of Florida
Köhling, Vasco
Universität Hamburg
227
Participant
Organization
Kol, Guy
NRGenen
Kortz, Annika
University of Bonn
Kusmec, Aaron
Iowa State University
La Rota, Mauricio
DowDupont Pioneer
Laclide, Franck
Euralis Services
Lai, Jinsheng
China Agricultural University
Lal, Shailesh
Oakland University
Lang, Zhihong
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences
Larue, Huachun
Monsanto
Laurine, Gilles
CNRS - INRA at LYON UNIVERSITY
Lauter, Nick
USDA-ARS, Ames, IA, USA
Lawrence-Dill, Carolyn
Iowa State University
Lee, Ding Hua
Academia Sinica
Lee, Elizabeth
University of Guelph
Lee, Yang-Seok
University of Warwick
Lee, Hyeyoung
University of Missouri
Leforestier, Diane
Maïsadour Semences
Leiboff, Samuel
UC Berkeley / Plant Gene Expression Center
Li, Chaobin
China Agrucultural University
Li, Tong
China Agricultural University
Li, Xugang
Shandong Agricultural University
Li, Pinghua
Shandong Agricultural University, China
Li, Changsheng
University of Amsterdam
Li, Kai
Institute of Genetics and Developmental Biology
228
Participant
Organization
Li, Xianran
Iowa State University
Li, Hui
University of Jinan
Li, Yubin
Biotechnology Research Institute, CAAS
Li, Xingli
Regensburg University
Li, En
China Agricultural university
Lipka, Alex
University of Illinois
Liu, Jianing
University of Georgia
Liu, Peng
University of Florida
Liu, Bing
Cornell University
Liu, Jie
Huazhong Agricultural University
Liu, Qiujie
Waksman Institute, Rutgers University
Lorant, Anne
UC Davis
Lourgant, Kristelle
INRA AgroImpact
Lu, Hong
China Golden Marker Biotech
Lubkowitz, Mark
Saint Michael's College
Lunde, China
Univ of California Berkeley/Plant Gene Expression Ctr
Ma, Xiaoli
University of Tuebingen
Mabire, Clément
INRA
Maclean, Dustin
University of Guelph
Maistriaux, Laurie
Université Catholique de Louvain
Makarevitch, Irina
Hamline University
Malvar, Rosa Ana
Mision Biologica Degwalicia (CSIC)
Manerus, Laura
University of Guelph
Mangel, Nathalie
ARVALIS INSTITUT DU VEGETAL
229
Participant
Organization
Maple, Rob
Warwick University
Marco, Cristina
Cold Spring Harbor Laboratory
Marcon, Caroline
CFG University of Bonn
Marion, Didier
INRA
Marocco, Adriano
Università Cattolica del Sacro Cuore
Martienssen, Rob
Cold Spring Harbor Laboratory
Martin, Olivier
INRA
Martinez, Natalia
GQE-Le Moulon
Martini, Johannes
KWS SAAT SE
Matthes, Michaela
University of Missouri - Columbia
Mayer, Michael
Euralis Services
Mccarty, Don
University of Florida
Mccaw, Morgan
Iowa State University
Mcclish, Allison
The Ohio State University
Mccormic, Emily
The Ohio State University
Mcfarland, Bridget
University of Wisconsin- Madison
Mclean Rodriguez, Francis
Denisse
Scuola Superiore Sant'Anna di Pisa
Mcsteen, Paula
University of Missouri
Melchinger, Albrecht E.
University of Hohenheim
Melkior, Stéphane
RAGT2n
Menz, Monica
Syngenta
Messing, Joachim
Rutgers University
Meyers, Blake
Donald Danforth Plant Science Center
Mezmouk, Sofiane
KWS SAAT SE
230
Participant
Organization
Michel, Kathryn
University of Wisconsin
Miclaus, Mihai
National Institute for Biological Sciences
Miller, Kathleen
University of Wisconsin-Madison
Millet, Jean-Marc
Euralis Services
Mittelsten Scheid, Ortrun
Gregor Mendel Institute
Mladenovic Drinic,
Snezana
Maize Research Institute
Monnahan, Patrick
University of Minnesota
Moose, Steve
University of Illinois
Morais De Sousa Tinoco,
Sylvia
Embrapa Maize and Sorghum
Moreau, Laurence
INRA
Moss, Brit
Whitman College
Müller, Verena
University of Bonn
Murigneux, Alain
Limagrain
Murphy, Katherine
UC Davis
Murray, Andrew
University of Georgia
Muszynski, Michael
University of Hawaii - Manoa
Nannas, Natalie
Hamilton College
Nelissen, Hilde
VIB-PSB
Nelms, Brad
Stanford University
Newton, Kathy
University of Missouri
Nichols, Jason
Syngenta Crop Protection, LLC
Nicolas, Stéphane
INRA
Niculaes, Claudiu
Technical University of Munich
Nieto-Sotelo, Jorge
Institute of Biology - UNAM
231
Participant
Organization
Noble, Jd
University of Florida
Nordborg, Magnus
Gregor Mendel Institute
Noreau, Philippe
Euralis Services
Noshay, Jaclyn
University of Minnesota
Nowack, Moritz
VIB-UGent Center for Plant Systems Biology
Oppenheimer, Jara
University of Hamburg
Ordas, Bernardo
Mision Biologica Degwalicia (CSIC)
Ouzunova, Milena
KWS SAAT
Owen, Julia
University of California Davis
Palaffre, Carine
INRA
Paszkowski, Uta
University Cambridge
Pauwels, Laurens
VIB/Ghent University
Pawlowski, Wojtek
Cornell University
Pecchioni, Nicola
CREA - Research Centre for Cereal and Industrial Crops
Peter, Rogowsky
CNRS - INRA at LYON UNIVERSITY
Pierre, Carolo
Euralis Services
Pook, Torsten
University of Goettingen
Portwood, John
USDA-ARS
Posekany, Tes
Iowa State University
Praud, Sébastien
BIOGEMMA
Quilleré, Isabelle
INRA - IJPB
Ramstein, Guillaume
Cornell University
Ranc, Nicolas
Syngenta
Resende, Marcio
University of Florida
232
Participant
Organization
Ressayre, Adrienne
INRA
Revilla, Pedro
Mision Biologica Degwalicia (CSIC)
Reymond, Matthieu
INRA
Ricci, Bill
University of Georgia
Rice, Brian
University of Illinois
Richardson, Annis
Univ of California Berkeley/Plant Gene Expression Ctr
Rio, Simon
INRA
Robil, Janlo
University of Missouri - Columbia
Rocheford, Torbert
Purdue University
Rodriguez, Jonas
University of Wisconsin Madison
Roldan, Dana
Euralis Services
Romestant, Michel
RAGT2n
Ronceret, Arnaud
Instituto de Biotecnologia- UNAM
Rossi, Vincenzo
Research Centre for Cereal and Industrial Crops - CREA
Ross-Ibarra, Jeffrey
University of California Davis
Rozenn, Le Guyader
INRA GQE-Le Moulon lab
Ruggiero, Barbara
Hybrigenics Services
Sachs, Marty
Maize Genetics COOP Stock Center
Salvi, Silvio
University of Bologna
Sanane, Inoussa
University Paris-Saclay
Sanclemente, MariaAngelica
University of Florida
Sanz Mora, Oscar
Hamburg University
Satterlee, Jack
Cornell University
Savadel, Savannah
Florida State University
233
Participant
Organization
Scanlon, Michael
Cornell University
Scheuermann, Daniela
KWS SAAT SE
Schlueter, Urte
Heinrich Heine University
Schnable, Pat
Iowa State University
Schoen, Chris
Technical University of Munich
Scholten, Stefan
University of Hohenheim
Schulz, Aimee
Iowa State University
Sehabiague, Pierre
MONSANTO
Seifert, Felix
cropSeq bioinformatics
Sekhon, Rajan
Clemson University
Septiani, Popi
Scuola Superiore Sant'Anna, Pisa, Italy
Settles, Mark
University of Florida
Seye, Adama
INRA
She, Wenjing
Department of Plant and Microbial Biology, University of Zürich,
Shi, Junpeng
China Agricultural University
Shi, Xiaowen
University of Missouri
Silva, Viviane
Unicamp
Simaskova, Maria
VIB-UGent Center for Plant Systems Biology
Simic, Domagoj
Agricultural Institute Osijek
Slewinski, Thomas
Monsanto
Song, Rentao
China Agricultural University
Sosso, Davide
Carnegie Science
Springer, Nathan
University of Minnesota
Stagnati, Lorenzo
Università Cattolica del Sacro Cuore
234
Participant
Organization
Stam, Maike
University of Amsterdam
Stankovic, Slavica
Maize Research Institute Zemun Polje
Stateczny, Dave
University of Hamburg
Steinbach, Delphine
INRA GQE-Le Moulon
Stetter, Markus
UC Davis
Stevanovic, Milan
Maize Research Institute Zemun Polje
Stirnweis, Daniel
KWS SAAT SE
Stitzer, Michelle
University of California, Davis
Strable, Josh
Cornell University
Studer, Anthony
University of Illinois Urbana-Champaign
Su, Yinghua
Shandong Agricultural University
Surault, Anne
Euralis Services
Surridge, Chris
Nature Plants
Swarts, Kelly
Ancient Genomics Group, Max Planck for Developmental Biology
Swentowsky, Kyle
University of Georgia
Swyers, Nathan
University of Missouri
Tallé, Vincent
AgroCampusOuest Rennes
Tardieu, Francois
INRA LEPSE
Taylor, Phil
Monsanto
Tello-Ruiz, Marcela Karey
Cold Spring Harbor Laboratory
Tenaillon, Maud
Génétique Quantitative et Evolution - Le Moulon
Thomasset, Muriel
GEVES
Thompson, Beth
East Carolina University
Tian, Feng
China Agricultural University
235
Participant
Organization
Tian, Xiaolong
China Agricultural University
Tian, Jinge
China Agricultural University
Tidd, Jess
Saint Michael's College
Timmermans, Marja
University of Tuebingen
Tixier, Marie-Hélène
BIOGEMMA
Tourrette, Elise
Université Paris Diderot
Tracy, Bill
University of Wisconsin-Madison
Tran, Thu
University of Missouri
Tseng, Ching-Chih
Academia Sinica, Taiwan
Vaghchhipawala, Zarir
KWS-GRC
Vajk, Angus
UC Berkeley
Van Der Linde, Karina
University of Regensburg
Van Hautegem, Tom
VIB
Vanous, Adam
Iowa State University
Varela, Jose
University of Wisconsin Madison
Varotto, Serena
University of Padova
Virlouvet, Laetitia
INRA
Vitte, Clémentine
CNRS - GQE Le Moulon
Vollbrecht, Erik
Iowa State University
Wagner, Ruth
Monsanto
Walbot, Virginia
Stanford University
Wallace, Jason
University of Georgia
Walsh, Jesse
MaizeGDB
Wang, Na
University of Georgia
236
Participant
Organization
Wang, Jing
China Agricultural University
Wang, Jinyu
Iowa State University
Wang, Kan
Iowa State University
Wang, Lei
Biotechnology research institute, Chinese Academy of Agricultural Sciences
Wang, Hong
KWS SAAT SE
Wang, Haiyang
South China Agriculture University
Wang, Lele
University of Regensburg
Warman, Matthew
Oregon State University
Washburn, Jacob
Cornell University
Weil, Cliff
National Science Foundation
Weiss, Jodi
Hamilton College
Welcker, Claude
INRA
Wen, Daxing
Shandong Agricultural University
Whipple, Clinton
Brigham Young University
White, Mike
University of Wisconsin-Madison
Widiez, Thomas
CNRS - INRA at LYON UNIVERSITY
Wimalanathan, Gokul
Iowa State University
Win, Yan Naing
University of Bonn, Germany
Wisser, Randy
University of Delaware
Woodhouse, Margaret
MaizeGDB
Wu, Yaoyao
China Agricultural University
Wu, Yongrui
Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of
Sciences
Wu, Wenwen
Euralis Services
Wurtele, Eve
Iowa State University
237
Participant
Organization
Xiao, Senlin
Institute of Genetics and Developmental Biology
Xie, Liuyong
Shandong Agricultural University
Xu, Miaoyun
Biotechnology research institute, Chinese Academy Agricultural Sciences
Yan, Jianbing
Huazhong Agricultural University
Yandeau-Nelson, Marna
Iowa State University
Yang, Xiaohong
China Agricultural University
Yang, Jun
National Key Laboratory of Plant Molecular Genetics, SIPPE, Shanghai, China
Yi, Gibum
Seoul National University
Yu, Zhong
China Agricultural University
Yu, Peng
Crop Functional Genomics, University of Bonn
Yu, Jianming
Iowa State University
Yufeng, Gao
China Golden Marker (Beijing) Biotech Co.,ltd
Zanetto, Anne
INRA, UMR AGAP
Zhang, Renyu
China Agricultural University
Zhang, Lifang
Cold Spring Harbor Laboratory
Zhao, Changzeng
University of Missouri
Zhao, Xiang Yu
Shandong Agricultural University
Zhao, Linmao
Shandong Agricultural University
Zhao, Jun
Biotech Res Institute, Chinese Academy of Agri Sci
Zhong, Tao
China Agricultural University
Zhou, Adele
Cornell University
Zilong Yang, Fay
NRGenen
Zivy, Michel
GQE-Le Moulon, CNRS
Zou, Junjie
Biotechnology Research Institute, Chinese Academy Agricultural Sciences
238
History of the Maize Genetics Conference
Year
2018
2017
2016
2015
2014
2013
2012
2011
2010
2009
2008
2007
2006
2005
2004
2003
2002
2001
2000
1999
1998
1997
1996
1995
1994
1993
1992
1991
1990
1989
1988
1987
1986
1985
1984
1983
1982
1981
1980
1979
1978
1977
1976
1975
Annual
60
59
58
57
56
55
54
53
52
51
50
49
48
47
46
45
44
43
42
41
40
39
38
37
36
35
34
33
32
31
30
29
28
27
26
25
24
23
22
21
20
19
18
17
Location
Saint-Malo, France
St. Louis, Missouri
Jacksonville, Florida
St. Charles, Illinois
Beijing, China
St. Charles, IL
Portland, OR
St. Charles, IL
Riva del Garda, Italy
St. Charles, IL
Washington, DC
St. Charles, IL
Asilomar, Pacific Grove, CA
Lake Geneva, WI
Mexico City, Mexico
Lake Geneva, WI
Kissimmee, FL
Lake Geneva, WI
Coeur d'Alene, ID
Lake Geneva, WI
Lake Geneva, WI
Clearwater Beach, FL
St. Charles, IL
Asilomar, Pacific Grove, CA
St. Charles, IL
St. Charles, IL
Asilomar, Pacific Grove, CA
Lake Delavan, WI
Lake Delavan, WI
Lake Delavan, WI
Madison, WI
Lake Delavan, WI
Lake Delavan, WI
Lake Delavan, WI
Champaign, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Dates
March 22-25
March 9-12
March 17-20
March 12-15
March 13-16
March 14-17
March 15-18
March 17-20
March 18-21
March 12-15
February 27 - March 2
March 22-25
March 9-12
March 10-13
March 11-14
March 13-16
March 14-17
March 15-18
March 16-19
March 16-19
March 19-22
March 13-16
March 14-17
March 16-19
March 24-27
March 18-21
March 19-22
March 21-24
March 8-11
March 2-5
March 25-27
March 20-22
March 21-23
March 29-31
March 10-11
March 12-13
March 13-14
March 14-15
March 8-9
March 10-11
March 11-12
March 12-13
March 13-14
March 8-9
239
Chair
Alain Charcosset
Erich Grotewold
David Braun
Mark Settles
Ann Stapleton
Phil Becraft
John Fowler
Erik Vollbrecht
Jane Dorweiler
Steve Moose
Thomas Brutnell
Anne Sylvester
Jay Hollick
Martha James
Mike Scanlon
David Jackson
Sarah Hake and Sue Wessler
Torbert Rocheford and Sue Wessler
Rebecca Boston and Sue Wessler
Julie Vogel and Cliff Weil
Mike McMullen
Paul Sisco
Paul Chomet
Karen Cone
Kathy Newton
Tim Nelson
Sarah Hake
Jim Birchler
Curt Hannah
Hugo Dooner
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Year
1974
1973
1972
1971
1970
1969
1968
1967
1966
1965
1964
1963
1962
1961
1960
Annual
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
Location
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Allerton Park, IL
Dates
March 9-10
March 10-11
March 11-12
March 13-14
March 14-15
March 15-16
March 16-17
March 11-12
March 12-13
March 13-14
March 14-15
March 9-10
March 17-18
March 18-19
March 12-13
1959
1
Allerton Park, IL
January 8-9
240
Chair
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
Earl Patterson
John Laughnan, Ed Coe, Gerry
Neuffer, and Earl Patterson
Notes
Notes
Notes
Notes
This conference received financial support from:
National Science Foundation
ANR/Amaizing
DuPont Pioneer
Syngenta
Monsanto
National Corn Growers Association
KWS SAAT AG
Bayer Crop Science
AGPM Maiz’Europ BASF Plant Science
Agro Paris Tech Caussade semences
INRA, BAP department Kenfeng Seed Co
Biogemma Euralis
Limagrain Maïsadour
Promaïs Benson Hill
We thank these contributors for their generosity!
Pedro Revilla