Data from: The multivariate association between genome-wide DNA methylation and climate across the range of Arabidopsis thaliana

Epigenetic changes can occur in response to extracellular environmental conditions. Consequently, epigenetic mechanisms can play an intermediate role to translate environmental signals to intracellular changes. This role might be particularly important in plants, which often show strong local adaptation and can have heritable epigenetic states. However, little is currently known about the role of epigenetic variation in the ecological mechanisms of adaptation.
Here, we used multivariate redundancy analyses to examine genome-wide associations between DNA methylation polymorphisms and climate variation in two independent panels of Arabidopsis accessions, including 122 Eurasian accessions as well as a regional panel of 148 Swedish accessions. At the single nucleotide methylation level, climate and space (geographic spatial structure) explain small yet significant amount of variation in both panels. In contrast, when viewed as genomic clusters of methylated and unmethylated cytosines, climate and space variables explain much greater amounts of variation in DNA methylation than those explained by variation at the nucleotide level.
We found that the single nucleotide methylation polymorphisms with the strongest associations with climate were enriched in transposable elements and potentially RNA-directed methylation contexts. When viewed in the context of genomic clusters, variation of DNA methylation at different sequence contexts exhibit distinctive segregation along different axes of variation in the redundancy analyses. Genome-wide methylation showed much stronger associations with climate within the regional panel (Sweden) compared to the global (Eurasia). Together, these findings indicate that genetic and epigenetic variation across the genome may play a role in response to climate conditions and local adaptation.