Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
New Phytol. 2019 Jul;223(2):979-992. doi: 10.1111/nph.15820. Epub 2019 Apr 30.
Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome-wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome-wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome-wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.
异源多倍化涉及种间杂交和全基因组加倍（WGD），与新兴的遗传和表观遗传不稳定性有关，这些不稳定性被认为有助于适应和进化。新生异源多倍化的一个常见的基因组后果是同源染色体交换（HE），它源于减数分裂保真度受损，并产生遗传和表型上可变的后代。在这里，我们使用遗传上可操作的合成水稻片段异源四倍体系统来研究全基因组 DNA 甲基化和基因表达对杂交、WGD 和 HE 的单独和联合作用的反应和结果。由于影响所有染色体的全基因组 HE，四倍体水稻的后代在基因组上是多样化的，但它们表现出整体甲基组稳定性。尽管如此，在四倍体中广泛存在胞嘧啶甲基化状态的区域变化。转录组分析揭示了全基因组基因表达的改变，这至少部分与 DNA 甲基化的改变有关。有趣的是，DNA 甲基化和基因表达的变化可以与杂交分离，并通过 HE 持续和放大。我们的结果表明，HE，新生异源多倍体的一个主要遗传后果，可以加剧、多样化和延续异源多倍化对表观遗传和基因表达变异的影响，因此可能有助于异源多倍体的进化。
