Data from: Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages

DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.

DNA甲基化（DNA methylation）是表观遗传修饰（epigenetic modifications）的核心机制之一。环境因素可诱导DNA甲基化改变，且此类诱导产生的修饰有时可传递至子代世代。然而，目前仍无法确定这类环境诱导的跨代DNA甲基化变化的普遍性，以及其能否持续超过一个子代世代。
本研究将西洋蒲公英类群（Taraxacum officinale group）的两个不同无融合生殖蒲公英谱系的多个种质株系——翼柄蒲公英（Taraxacum alatum）与半环蒲公英（T. hemicyclum）——分别施加干旱胁迫与水杨酸（salicylic acid, SA）处理。研究采用甲基化敏感扩增多态性片段长度多态性标记（methylation-sensitive amplified fragment length polymorphism markers, MS-AFLPs），对胁迫处理后全基因组范围内CCGG限制性酶切位点处的非靶向甲基化变化进行了筛选，并评估了诱导的甲基化变化在后续两个未受胁迫的子代世代中的遗传稳定性。
无论初始胁迫处理类型如何，在三个世代中均观察到可遗传DNA甲基化变异的显著积累，这表明可遗传表观突变（heritable epimutations）存在相当高的本底发生率。而环境因素诱导的效应则证据较为有限：干旱胁迫仅在受胁迫的当代中表现出种质株系特异性的甲基化变化证据，但此类变化并未传递至子代；与之相反，水杨酸处理可导致处理植株的子代个体中甲基化变化频率升高，此类变化似乎无定向性，仅增加了子代个体间的跨代表观遗传变异，并未产生可预测的表观遗传变异体。
尽管本研究通过MS-AFLP检测到的DNA甲基化变化的功能效应仍有待验证，但本研究结果表明：（1）蒲公英中胁迫诱导的跨代DNA甲基化修饰具有基因型与环境背景特异性；（2）由环境诱导产生的DNA甲基化效应大多无定向性，并未靶向特定的基因组位点。