Population specific methylome remodeling in high and low elevation populations of Indian west Himalayan Arabidopsis thaliana in response to elevated CO2

Unravelling the plants responses towards rising atmospheric [CO2] have largely been explored in genetical and morpho-physiological contexts. However, epigenetic factors including DNA methylation which play critical roles in adaptation are largely unexplored. Here we investigated the methylome, transcriptome and morpho-physiological responses of the two Arabidopsis thaliana populations evolved at high (3400 m amsl) and low elevation (700 m amsl) zones to elevated [CO2] (e[CO2]). We show that depending on the origin of the population, there were local level variations in DNA methylation when exposed to e[CO2], but global methyl cytosine (mC) content remained unchanged. Further, there was loss of methylation and more protein coding genes were differentially methylated than transposable elements and non-coding RNA genes, in both the populations but more so in the low elevation one. The differentially methylated genes of the two populations belonged to distinct functional categories. More genes related to methylation machinery were down-regulated in the high elevation population than the low elevation one. Although there was no correlation between methylation and gene expression at the global scale but a few genes exhibited methylation dependent expression level. Finally the hyper- and hypo-methylated status of a few genes due to e[CO2] treatment were validated. Overall, our data suggested the two populations responded differently towards e[CO2] with respect to methylome remodeling, phenotypic and molecular plasticity. However, methylome remodeling and molecular plasticity were more prominent in the low elevation population. Understanding the evolution of epigenetic response towards e[CO2] may help in future crop improvement strategies.