Comparison of the relative potential for epigenetic and genetic variation to contribute to trait stability

Epigenetic variation, both natural and induced, can influence heritable phenotypic variation of complex traits. Understanding the effect of epigenetic changes on trait variation is complicated by the confounding effects of DNA sequence polymorphisms. To overcome this complication, epigenetic recombinant inbred lines (epiRILs) have been developed from parental lines with little or no DNA sequence variation, but differing in DNA methylation patterns. Aller et al. used Arabidopsis epiRILs to compare the potential of epigenetic and genetic variation to influence adaptive traits. Specifically, they look at the correlation between DNA methylation changes and accumulation of glucosinolates, defense compounds produced by almost all plants of the order Brassicales. Potential epigenetic heritability (epi-heritability) of glucosinolate variation ranged from 10% – 13% in the epiRILS, much lower than estimates of 30% to 80% heritability in genetically diverse populations. Also, the authors found that glucosinolate epi-heritability was lower than the epi-heritability for flowering time (32%). The authors then identified epiQTLs containing differentially methylated regions (DMRs) correlating with variance in glucosinolate levels. They did not find any significant epiQTL overlapping known genes controlling glucosinolates, perhaps indicating that the DNA methylation differences affect loci with unknown causal effect or a different suite of genes with small effects on the trait. They also found DMRs linked to both increased and decreased glucosinolate levels compared to wild type. In contrast, for flowering time epiQTL, these were all skewed towards earlier flowering, highlighting fundamental differences in how DNA methylation variation influences different traits. For example, DNA methylation may act as an irreversible switch for traits like flowering, which cannot stop once the process is initiated; while for other traits like biosynthesis, genes in different steps can be affected to increase or decrease production, accumulation, transport etc. They conclude that the contribution of epigenetic variation to glucosinolate variation is much lower than the effect of genetic variation. They also suggest that DNA methylation changes may have an effect on trait stability for both glucosinolates and flowering time. G3