Selection of epigenetic variation in Arabidopsis [Expression]

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. Whole plant tissue from 25-day old plants was used for RNA extractions. RNA was extracted from 4 plants of each genotype (CVL39 and CVL125) from ancestral lines (A2) = Reference sample (4 biological replicates), and lines that had experienced 5 generations of selection in dynamic landscapes (S2) = Test sample (4 biological replicates); average signal ratios were compared.