Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
Nat Commun. 2020 Nov 2;11(1):5539. doi: 10.1038/s41467-020-19333-4.
DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
DNA 甲基化是一种普遍存在的染色质特征，存在于玉米基因组中 25%的胞嘧啶中，但在玉米驯化过程中，甲基化景观的变异和进化在很大程度上仍然未知。在这里，我们利用现代玉米、地方品种和类蜀黍（Zea mays ssp. parviglumis）群体的全基因组测序（WGS）和全基因组亚硫酸氢盐测序（WGBS）数据，估计了表观突变率和选择系数。我们发现，在任何情况下，DNA 甲基化都没有直接选择的弱证据，但在全人群中鉴定出了数千个与近期选择相关的差异甲基化区域（DMRs）。对于两个与性状相关的 DMR，vgt1-DMR 和 tb1-DMR，HiChIP 数据表明，DMR 和各自下游基因之间的交互环存在于现代玉米系 B73 中，但不存在于类蜀黍中。我们的结果使人们更好地理解了作用于 DNA 甲基化模式的进化力量，并表明了甲基化变异在适应性进化中的作用。
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