Fig. 2

Schematic summary of a methylation quantitative trait locus (meQTL) mapping study in A. thaliana natural accessions. In the cis-trans plot (top middle panel), each dot represents a significant association between a single nucleotide polymorphism (SNP) and a differentially methylated region (DMR). All cis associations map along the diagonal, while trans associations are visible as vertical bands. An example of a commonly detected cis association is shown in the left panel. The SNP-DMR association is a byproduct of linkage disequilibrium (LD) between the SNP and an often undetected transposable element (TE) insertion that has spread methylation into its flanking region. An example of a commonly detected trans- association is shown in the right panel, where a SNP is associated with multiple DMRs across the genome. Such pleiotropic effects can be the result of SNPs in transcription factor genes or methyltransferase genes