Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat
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RESEARCH ARTICLE
Open Access
Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat Jingya Yuan1, Wu Jiao1, Yanfeng Liu1, Wenxue Ye1, Xiue Wang1, Bao Liu2, Qingxin Song1* and Z. Jeffrey Chen1,3*
Abstract Background: Wheat is a powerful genetic model for studying polyploid evolution and crop domestication. Hexaploid bread wheat was formed by two rounds of interspecific hybridization and polyploidization, processes which are often accompanied by genetic and epigenetic changes, including DNA methylation. However, the extent and effect of such changes during wheat evolution, particularly from tetraploid-to-hexaploid wheat, are currently elusive. Results: Here we report genome-wide DNA methylation landscapes in extracted tetraploid wheat (ETW, AABB), natural hexaploid wheat (NHW, AABBDD), resynthesized hexaploid wheat (RHW, AABBDD), natural tetraploid wheat (NTW, AABB), and diploid (DD). In the endosperm, levels of DNA methylation, especially in CHG (H=A, T, or C) context, were dramatically decreased in the ETW relative to natural hexaploid wheat; hypo-differentially methylated regions (DMRs) (850,832) were 24-fold more than hyper-DMRs (35,111). Interestingly, those demethylated regions in ETW were remethylated in the resynthesized hexaploid wheat after the addition of the D genome. In ETW, hypo-DMRs correlated with gene expression, and TEs were demethylated and activated, which could be silenced in the hexaploid wheat. In NHW, groups of TEs were dispersed in genic regions of three subgenomes, which may regulate the expression of TEassociated genes. Further, hypo-DMRs in ETW were associated with reduced H3K9me2 levels and increased expression of histone variant genes, suggesting concerted epigenetic changes after separation from the hexaploid. Conclusion: Genome merger and separation provoke dynamic and reversible changes in chromatin and DNA methylation. These changes correlate with altered gene expression and TE activity, which may provide insights into polyploid genome and wheat evolution. Keywords: Extracted tetraploid wheat, DNA methylation, Transposon, Genomics, Polyploidy, Wheat evolution
Background Polyploidy is a prominent feature for the evolution of some animals and all flowering plants, including most important crops such as wheat, cotton, and canola [1–3]. The common occurrence of polyploidy suggests an advantage for having additional genetic materials for diversification of polyploid plants and domestication of polyploid crops. * Correspondence: [email protected]; [email protected] 1 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China Full list of author information is available at the end of the article
Interspecific hybridization in cotton is accompanied with genetic and epigenetic changes including DNA methylation, many of which are maintained as stable epialleles among five allotetraploid cotton species during evolution and two cultivated cottons during dom
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