DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

Li, Ning
Xu, Chunming
Wendel, Jonathan
Zhang, Ai
Lv, Ruili
Meng, Xinchao
Lin, Xiuyun
Gong, Lei
Wendel, Jonathan
Liu, Bao
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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.

<p>This is the peer reviewed version of the following article: Li, Ning, Chunming Xu, Ai Zhang, Ruili Lv, Xinchao Meng, Xiuyun Lin, Lei Gong, Jonathan F. Wendel, and Bao Liu. "DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids." <em>New Phytologist </em>(2019), which has been published in final form at doi: <a href="https://doi.org/10.1111/nph.15820">10.1111/nph.15820</a>. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. </p>
DNA methylation, homoeologous exchange, homolog copy number variation, gene expression, segmental allopolyploidy, sustained epigenetic diversity