The quantitative genetics of gene expression in Mimulus guttatus.

Mimulus guttatus (yellow monkeyflower) is a model for the study of quantitative trait evolution in natural populations. Research has focused mainly on whole organism traits like flower size or herbivore resistance, but the level of expression of a gene is also a quantitative trait. In this study, we dissect leaf transcriptome variation using a breeding design that estimates the contribution of individual loci to expression variation (eQTLs). We find at least rough agreement to the "oligogenic model" where a major locus (the cis regulatory region) generates much of the genetic variation in the population. While associations studies routinely characterize genetic effects as binary (the two alternatives at a single nucleotide polymorphism or "SNP"), this description proves insufficient for Mimulus. Most loci exhibit multiple, and in some cases, a continuum of alleles. We find that trans eQTLs have different features than cis eQTLs, both in terms of the diversity and genetic dominance of alleles. These genetic features of eQTLs are critical determinants of the "G matrix", the genetic variances and covariances among all genes. The G matrix determines how gene expression will evolve under selection in response to changing environmental conditions. Our finding of large effect sizes and high allelic diversity suggests that the G matrix may be surprisingly malleable, even on ecological timescales.