DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.

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与气候相关的自然发生的表突变及其在拟南芥植物适应中的作用

DNA甲基化被认为是一种重要的机制，它使植物能够对环境做出反应，有时完全与遗传变异无关。为了了解拟南芥群体规模 DNA 甲基化的遗传基础、生物学功能和气候关系，我们利用高质量的单核苷酸多态性 (SNP) 进行了全基因组关联分析，发现平均约 56%特别是在 CHH 序列背景下 (71%)，差异甲基化区域 (DMR) 未用 SNP 标记。其中，共有3235个DMR与基因表达显着相关且具有潜在遗传性。 3235个DMR中有655个与气候变量相关，我们通过实验验证了其中之一，HEI10（人类细胞入侵增强剂10号）。这种表观遗传位点可能会受到自然选择的影响，从而影响植物的适应，并且有望成为面临风险的种质的指标。因此，我们将这些与气候相关的 DMR 纳入梯度森林模型，并发现南欧的天然拟南芥种质在未来气候变化下可能面临最大的风险。我们的研究结果强调了整合独立于遗传变异的 DNA 甲基化和气候数据的重要性，以预测植物对未来气候变化的脆弱性。