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

Epigenetic changes can occur due to extracellular environmental
conditions. Consequently, epigenetic mechanisms can play an intermediate
role to translate environmental signals to intracellular changes. Such a
role might be particularly important in plants, which often show strong
local adaptation and have the potential for 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 genomewide associations between DNA
methylation polymorphisms and climate variation in two independent panels
of Arabidopsis accessions, including 122 Eurasian accessions as well as in
a regional panel of 148 accessions in Sweden. At the single-nucleotide
methylation level, climate and space (geographic spatial structure)
explain small yet significant amount of variation in both panels. On the
other hand, when viewed in a context of 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 single-nucleotide level. We found that the single-nucleotide
methylation polymorphisms with the strongest associations with climate
were enriched in transposable elements and in 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. Genomewide 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.