Publication Date:
2017-01-17
Description:
Understanding the causes ofcis-regulatory variation is a long-standing aim in evolutionary biology. Althoughcis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standingcis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shapingcis-regulatory variation in the outcrossing plantCapsella grandiflora. We first identified a set of 1,010 genes with commoncis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with commoncis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants ofcis-regulatory variation. Gene body methylation (gbM) was a major factor constrainingcis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most commoncis-regulatory variation inC. grandiflorais under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance ofcis-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 evidence for a link between gbM andcis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor ofcis-regulatory variation in a wide range of plant species.
Print ISSN:
0027-8424
Electronic ISSN:
1091-6490
Topics:
Biology
,
Medicine
,
Natural Sciences in General
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