State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100039, China.
Genome Biol. 2018 Sep 10;19(1):128. doi: 10.1186/s13059-018-1516-z.
In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored.
To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways.
This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.
除了遗传变异外，表观遗传变异在决定各种生物过程中也起着重要作用。自然遗传变异对作物驯化和改良的重要性已经得到了广泛的研究。然而，在群体水平上，表观遗传变异在作物驯化中的贡献却很少被探索。
为了了解表观遗传学对作物驯化的影响，我们通过对 45 个大豆品种（包括野生大豆、地方品种和栽培品种）进行全基因组亚硫酸氢盐测序，研究了大豆驯化和改良过程中 DNA 甲基化的变化。通过甲基组分析，我们鉴定出了 5412 个差异甲基化区域（DMRs）。这些 DMRs 表现出与遗传选择区域不同的特征。特别是，它们具有显著更高的遗传多样性。关联分析表明，只有 22.54%的 DMR 可以用局部遗传变异来解释。有趣的是，与任何遗传变异都没有关联的 DMR 中的基因在碳水化合物代谢途径中富集。
本研究提供了一个在不同品种中广泛的 DNA 甲基化图谱，并剖析了大豆驯化过程中 DNA 甲基化变异与遗传变异之间的关系，从而扩展了我们对大豆驯化和改良的理解。
