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Significance Despite long-standing interest in the contribution ofcis- regulatory changes to adaptation, we still have a limited understanding of the selective importance and genomic determinants ofcis -regulatory variation in natural populations. We use a combination of analyses of allele-specific expression and population genomic analyses to investigate the selective forces and genomic determinants ofcis- regulatory variation in the outcrossing plant speciesCapsella grandiflora . We conclude that gene-specific functional constraints shapecis- regulatory variation and that genes withcis- regulatory variation are under relaxed purifying selection compared with other genes. Finally, we identify a link between gene body methylation and the extent ofcis- regulatory constraint in natural populations.

Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora