Genetic and Epigenetic Control of DNA Methylation Variation in Maize

DNA methylation is a chromatin mark that can play a role in silencing transposons and in some cases, genes. While DNA methylation is often considered an epigenetic modification, it is a chromatin mark that may be caused by genetic variation or can be independent of genetic variation resulting in true ‘epialleles’ that may impact heritable variation regardless of genetic state. This distinction is important as genetically-controlled methylation variants will be accounted in GWAS approaches while epialleles are likely to be missed. Genome-wide profiling of DNA methylation in diverse maize lines has identified several thousand differential methylation regions (DMRs) across the studied genotypes. There are examples of methylation states that are common across multiple genotypes while others are rare, with a single genotype displaying an altered DNA methylation state. In some cases DNA methylation changes are strongly associated with local genetic variation while many other DMRs are not associated with local sequence variation providing evidence for genetic and epigenetic DNA methylation variation. Detailed inspection of some genetically controlled DMRs provides evidence that polymorphic transposable element insertions resulted in DMRs in flanking genomic regions. This study provides evidence for numerous examples of DNA methylation variation caused by both genetic and epigenetic variation.