Abstract
Research on the evolutionary fate of duplicated genes in recurrent polyploids is scarce due to the difficulties in disentangling the different homeologs and alleles of duplicated genes. This chapter describes the detailed procedures to identify different homeologs and alleles of duplicated genes, to analyze their molecular characteristics, and to reveal their functional divergence by gene editing with CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9). Using the gene editing approach, we efficiently constructed multiple knockout mutant lines with single or simultaneously disrupted different homeologs or alleles in a recurrent polyploid fish, demonstrating its usability for targeting and mutating multiple divergent homeologs and alleles in recurrent duplicated genomes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Sessa EB (2019) Polyploidy as a mechanism for surviving global change. New Phytol 221:5–6
Cheng F, Wu J, Cai X et al (2018) Gene retention, fractionation and subgenome differences in polyploid plants. Nat Plants 4:258–268
Van de Peer Y, Mizrachi E, Marchal K (2017) The evolutionary significance of polyploidy. Nat Rev Genet 18:411–424
Meyer A, Van de Peer Y (2005) From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays 27:937–945
Amores A, Force A, Yan YL et al (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711–1714
Taylor JS, Braasch I, Frickey T et al (2003) Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res 13:382–390
Leggatt RA, Iwama GK (2003) Occurrence of polyploidy in the fishes. Rev Fish Biol Fisher 13:237–246
Van de Peer Y, Taylor JS, Meyer A (2003) Are all fishes ancient polyploids? J Struct Funct Genom 3:65–73
Zhou L, Gui JF (2017) Natural and artificial polyploids in aquaculture. Aquac Fish 2:103–111
Gui JF, Zhou L (2010) Genetic basis and breeding application of clonal diversity and dual reproduction modes in polyploid Carassius auratus gibelio. Sci China Life Sci 53:409–415
Lien S, Koop BF, Sandve SR et al (2016) The Atlantic salmon genome provides insights into rediploidization. Nature 533:200–205
Luo J, Chai J, Wen Y et al (2020) From asymmetrical to balanced genomic diversification during rediploidization: subgenomic evolution in allotetraploid fish. Sci Adv 6:eaaz7677
Chen D, Zhang Q, Tang W et al (2020) The evolutionary origin and domestication history of goldfish (Carassius auratus). Proc Natl Acad Sci 117:29775–29785
Li XY, Zhang XJ, Li Z et al (2014) Evolutionary history of two divergent Dmrt1 genes reveals two rounds of polyploidy origins in gibel carp. Mol Phylogenet Evol 78:96–104
Zhu HP, Ma DM, Gui JF (2006) Triploid origin of the gibel carp as revealed by 5S rDNA localization and chromosome painting. Chromosom Res 14:767–776
Zhou L, Gui JF (2002) Karyotypic diversity in polyploid gibel carp, Carassius auratus gibelio Bloch. Genetica 115:223–232
Soltis PS, Soltis DE (2016) Ancient WGD events as drivers of key innovations in angiosperms. Curr Opin Plant Biol 30:159–165
Liu S, Li Z, Gui JF (2009) Fish-specific duplicated dmrt2b contributes to a divergent function through Hedgehog pathway and maintains left-right asymmetry establishment function. PLoS One 4:e7261
Gan RH, Wang Y, Li Z et al (2021) Functional divergence of multiple duplicated Foxl2 homeologs and alleles in a recurrent polyploid fish. Mol Biol Evol 38:1995–2013
Ren F, Lin Q, Gong G et al (2020) Igf2bp3 maintains maternal RNA stability and ensures early embryo development in zebrafish. Commun Biol 3:94
Jiang D, Chen J, Fan Z et al (2017) CRISPR/Cas9-induced disruption of wt1a and wt1b reveals their different roles in kidney and gonad development in Nile tilapia. Dev Biol 428:63–73
Wang H, Yang H, Shivalila CS et al (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153:910–918
Liu D, Wang Z, Xiao A et al (2014) Efficient gene targeting in zebrafish mediated by a zebrafish-codon-optimized cas9 and evaluation of off-targeting effect. J Genet Genomics 41:43–46
Chang N, Sun C, Gao L et al (2013) Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res 23:465–472
Zhang J, Sun M, Zhou L et al (2015) Meiosis completion and various sperm responses lead to unisexual and sexual reproduction modes in one clone of polyploid Carassius gibelio. Sci Rep 5:10898
Vandesompele J, De Preter K, Pattyn F et al (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:RESEARCH0034
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402–408
Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14:988–995
Acknowledgments
This work was supported by the National Key Research and Development Program of China (2018YFD0900204), the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000), the Key Program of Frontier Sciences of the Chinese Academy of Sciences (QYZDY-SSW-SMC025), and China Agriculture Research System of MOF and MARA.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Gan, RH., Zhou, L., Gui, JF. (2023). Efficiently Editing Multiple Duplicated Homeologs and Alleles for Recurrent Polyploids. In: Van de Peer, Y. (eds) Polyploidy. Methods in Molecular Biology, vol 2545. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2561-3_26
Download citation
DOI: https://doi.org/10.1007/978-1-0716-2561-3_26
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-2560-6
Online ISBN: 978-1-0716-2561-3
eBook Packages: Springer Protocols