Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora

Understanding the causes of cis -regulatory variation is a long-standing aim in evolutionary biology. Although cis -regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis -regulatory variation. To address these questions, we studied the prevalence, genomic determinants and selective forces shaping cis -regulatory variation in the outcrossing plant Capsella grandiflora . We first identified a set of 1,010 genes with common cis -regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis -regulatory variation are 1) under weaker purifying selection and 2) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis -regulatory variation. Gene-body methylation (gbM) was a major factor constraining cis -regulatory variation, whereas presence of nearby TEs and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis -regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis -regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide novel evidence for a link between gbM and cis -regulatory constraint, possibly reflecting greater dosage-sensitivity of body-methylated genes. Given the extensive conservation of gene-body methylation in flowering plants, this suggests that gene-body methylation could be an important predictor of cis -regulatory variation in a wide range of plant species.