Mapping the epigenetic basis of complex traits

Quantifying the impact of heritable epigenetic variation on complex traits is an emerging challenge in population genetics. Here we analyze a population of isogenic Arabidopsis lines which segregate experimentally-induced DNA methylation changes at hundreds of regions across the genome. We demonstrate that several of these differentially methylated regions (DMRs) act as bona fide epigenetic quantitative trait loci (QTLepi), accounting for 60-90% of the observed heritability for two complex traits, flowering time and primary root length. These QTLepi are reproducible and can be subjected to artificial selection. Most of the DMRs in the QTL intervals are also variable in natural populations of this species and may thus provide a basis for Darwinian evolution independently of DNA sequence changes.