Data from: Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations

Background: The genetic structure and differentiation of wild emmer wheat suggests that genetic diversity is eco-geographically structured. However, very little is known about the structure and extent of the heritable epigenetic variation and its influence on local adaptation in natural populations. Results: The structure and extent of the heritable methylation-based epigenetic variation were assessed within and among natural populations of Triticum turgidum ssp. dicoccoides. We used methylation sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) techniques, to assess the methylation status of random genomic CCGG sites and CCGG sites flanking transposable elements (TEs), respectively. Both techniques were applied to the DNA of 50 emmer accessions which were collected from five different geographically isolated regions. In order to ensure the assessment of heritable epigenetic variation, all accessions were grown under common garden conditions for two generations. In all accessions, the difference in methylation levels of CCGG sites, including CCGG sites that flanked TEs, were not statistically significant and relatively high, ranging between 46 and 76 %. The pattern of methylation was significantly different among accessions, such that clear and statistically significant population-specific methylation patterns were observed. Conclusion: In this study, we have observed population-unique heritable methylation patterns in emmer wheat accessions originating from five geographically isolated regions. Our data indicate that methylation-based epigenetic diversity might be eco-geographically structured and might be partly determined by climatic and edaphic factors.

背景：野生二粒小麦的遗传结构与分化特征表明，其遗传多样性呈现生态地理分区结构。然而，目前学界对自然种群中可遗传表观遗传变异的结构、范围及其对本地适应的影响仍知之甚少。
结果：本研究针对野生二粒小麦（Triticum turgidum ssp. dicoccoides）自然种群内部及种群间的基于甲基化的可遗传表观遗传变异的结构与范围展开评估。我们分别采用甲基化敏感扩增多态性（methylation sensitive amplified polymorphism, MSAP）与转座子甲基化展示（transposon methylation display, TMD）技术，对随机基因组CCGG位点以及转座因子（Transposable Elements, TEs）侧翼的CCGG位点的甲基化状态进行检测。上述两种技术均应用于从5个地理隔离区域采集的50份二粒小麦种质的基因组DNA。为确保所评估的为可遗传表观遗传变异，所有材料均在同质园栽培条件下种植两代。对所有材料的分析显示，包含转座因子侧翼CCGG位点在内的CCGG位点的甲基化水平差异无统计学显著性，但整体甲基化水平相对较高，介于46%至76%之间。不同材料间的甲基化模式存在显著差异，可观测到清晰且具有统计学显著性的种群特异性甲基化模式。
结论：本研究在源自5个地理隔离区域的二粒小麦种质中，发现了种群特有的可遗传甲基化模式。研究数据表明，基于甲基化的表观遗传多样性可能具有生态地理分区结构，且可能部分由气候与土壤因子决定。