Selection of epigenetic variation in Arabidopsis [SNP data]. Arabidopsis thaliana

In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. Selected populations exerted significant differences in flowering time and the number of branches and fruits, differences that were maintained over two to three generations in the absence of selection. We identified 4,629 and 5,158 differentially methylated cytosines which were overrepresented in genes that regulate flowering time, epigenetic processes, development and morphogenesis. Differentially methylated genes were enriched in differentially expressed genes. Thus, epigenetic variation is subject to selection and may play an important role in the adaptive response of populations in rapidly changing natural environments. Overall design: Genomic DNA was extracted from whole-plant above-ground tissue of individual 25-day-old plants with the Qiagen DNeasy kit (Qiagen). DNA from two randomly chosen CVL39 individuals from ancestral (A3) lines and from 7 selected (S3) lines that had experienced 5 generations of selection in the three replicated dynamic landscapes (2xD1, 3xD5,2xD6) was sequenced (paired-end, 100 bp) using the Illumina Highseq 2000 Instrument. Single nucleotide polymorphisms and TE insertions were mapped with respect to the recombinant reference genome and compared between selected and ancestral lines.

在拟南芥（Arabidopsis thaliana）中，无遗传变异与选择的条件下，其DNA甲基化组可发生高频自发表观遗传变异。长期以来，学界对自然表观遗传变异是否受选择作用、是否有助于种群在选择环境中获得适合度与适应性这一问题抱有极大研究兴趣。
本研究对两个拟南芥重组自交系的选择性状、全基因组胞嘧啶DNA甲基化及基因表达变异进行了比较分析，这两个株系经实验景观下五代选择后，与其遗传一致的祖先株系形成对照。经选择的种群在开花时间、分枝数与果实数上呈现显著差异，且该差异在无选择的情况下可维持2至3代。
本研究共鉴定出4629个和5158个差异甲基化胞嘧啶，它们在调控开花时间、表观遗传过程、发育及形态建成的基因中显著富集；且差异甲基化基因在差异表达基因中同样存在富集现象。综上，表观遗传变异受选择作用，或在种群应对快速变化的自然环境的适应性响应中发挥关键作用。
实验设计概况：采用Qiagen DNeasy试剂盒（Qiagen）提取25日龄单株整株地上组织的基因组DNA。从祖先株系（A3）的2株随机选取的CVL39单株，以及经3组重复动态景观（2xD1、3xD5、2xD6）完成5代选择的7个选择株系（S3）中提取的DNA，使用Illumina Highseq 2000测序仪进行双端100bp测序。以重组参考基因组为参照，对单核苷酸多态性与转座因子（Transposable Element, TE）插入变异进行定位，并在选择株系与祖先株系间开展比较分析。