Selection of epigenetic variation in Arabidopsis [Bisulfite-Seq]

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 four randomly chosen individuals was pooled from selected (S2) lines that had experienced 5 generations of selection in the three replicated dynamic landscapes (D1, D5, D6) and from the ancestrals (A2) for both CVL39 and CVL125 respectively, yielding eight samples for bisulfite sequencing. DNA was treated with bisulfite which converts unmethylated cytosines to thymines but leaves methylated cytosines unconverted. DNA was then sequenced using the SOLIDTM Life technologiesTM System. DNA cytosine methylation profiles of selected lines (S2) were compared to methylation profiles from ancestral (A2) lines.