Asymmetric variation in DNA methylation during domestication and de-domestication of rice

文献类型： 外文期刊

第一作者： Cao, Shuai

作者： Cao, Shuai;Lu, Kening;Chen, Shiting;Zhang, Xiyu;Song, Qingxin;Cao, Shuai;Chen, Kai;Shen, Congcong;Zhu, Shuangbin;Niu, Yanan;Xu, Jianlong;Fan, Longjiang;Chen, Z. Jeffrey

作者机构：

期刊名称：PLANT CELL （ 影响因子：11.6； 五年影响因子：12.9 ）

ISSN： 1040-4651

年卷期： 2023 年

页码：

收录情况： SCI

摘要： Hundreds of plant species have been domesticated to feed human civilization, while some crops have undergone de-domestication into agricultural weeds, threatening global food security. To understand the genetic and epigenetic basis of crop domestication and de-domestication, we generated DNA methylomes from 95 accessions of wild rice (Oryza rufipogon L.), cultivated rice (Oryza sativa L.) and weedy rice (O. sativa f. spontanea). We detected a significant decrease in DNA methylation over the course of rice domestication but observed an unexpected increase in DNA methylation through de-domestication. Notably, DNA methylation changes occurred in distinct genomic regions for these 2 opposite stages. Variation in DNA methylation altered the expression of nearby and distal genes through affecting chromatin accessibility, histone modifications, transcription factor binding, and the formation of chromatin loops, which may contribute to morphological changes during domestication and de-domestication of rice. These insights into population epigenomics underlying rice domestication and de-domestication provide resources and tools for epigenetic breeding and sustainable agriculture. A pan-DNA methylome of rice uncovers reversal of DNA methylation changes during domestication and de-domestication.

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