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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 that 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 to 90% of the heritability for two complex traits, flowering time and primary root length. These QTLepi are reproducible and can be subjected to artificial selection. Many of the experimentally induced DMRs are also variable in natural populations of this species and may thus provide an epigenetic basis for Darwinian evolution independently of DNA sequence changes.
Plant Epigenetics
Quantitative trait loci (QTLs) are genetic regions associated with phenotypic traits that help to determine the underlying genetics controlling the magnitude of a specific trait. Cortijo et al. (p. 1145, published online 6 February; see the Perspective by Schmitz) identified epigenetic QTLs associated with differences in methylation marks (epiQTLs) controlling flowering time and root length in the model plant Arabidopsis. These epiQTLs were mapped in genetically identical lines that differ only in their methylation marks. A small number of QTLs were able to explain up to 90% of the heritable variation in these traits. Thus, in plants, the heritability of some complex traits can be determined by epigenetic variation.
