Compensatory -regulatory alleles minimizing variation in expression are common within .

Heritable variation in gene expression is common within species. Much of this variation is due to genetic differences outside of the gene with altered expression and is -acting. This -regulatory variation is often polygenic, with individual variants typically having small effects, making the genetic architecture and evolution of -regulatory variation challenging to study. Consequently, key questions about -regulatory variation remain, including the variability of -regulatory variation within a species, how selection affects -regulatory variation, and how -regulatory variants are distributed throughout the genome and within a species. To address these questions, we isolated and measured -regulatory differences affecting promoter activity among 56 strains of , finding that -regulatory backgrounds varied approximately twofold in their effects on promoter activity. Comparing this variation to neutral models of -regulatory evolution based on empirical measures of mutational effects revealed that despite this variability in the effects of -regulatory backgrounds, stabilizing selection has constrained regulatory differences within this species. Using a powerful quantitative trait locus mapping method, we identified ∼100 -acting expression quantitative trait locus in each of three crosses to a common reference strain, indicating that regulatory variation is more polygenic than previous studies have suggested. Loci altering expression were located throughout the genome, and many loci were strain specific. This distribution and prevalence of alleles is consistent with recent theories about the genetic architecture of complex traits. In all mapping experiments, the nonreference strain alleles increased and decreased promoter activity with similar frequencies, suggesting that stabilizing selection maintained many -acting variants with opposing effects. This variation may provide the raw material for compensatory evolution and larger scale regulatory rewiring observed in developmental systems drift among species.