Evidence for Selection on Gene Expression in Cultivated Rice (Oryza sativa)

Artificial selection has been used throughout plant domestication and breeding to develop crops that are adapted to diverse environments. Here, we investigate whether gene regulatory changes have been widespread targets of lineage-specific selection in cultivated lines Minghui 63 and Zhenshan 97 of rice, Oryza sativa. A line experiencing positive selection for either an increase or a decrease in genes' transcript abundances is expected to have an overabundance of expression quantitative trait locus (eQTL) alleles that increase or decrease those genes' expression, respectively. Results indicate that several genes that share Gene Ontology terms or are members of the same coexpression module have eQTL alleles from one parent that consistently increase gene expression relative to the second parent. A second line of evidence for lineage-specific selection is an overabundance of cis-trans pairs of eQTL alleles that affect gene expression in the same direction (are reinforcing). Across all cis-trans pairs of eQTL, including pairs that both weakly and strongly affect gene expression, there is no evidence for selection. However, the frequency of genes with reinforcing eQTL increases with eQTL strength. Therefore, there is evidence that eQTL with strong effects were positively selected during rice cultivation. Among 41 cis-trans pairs with strong trans eQTL, 31 have reinforcing eQTL. Several of the candidate genes under positive selection accurately predict phenotypic differences between Minghui 63 and Zhenshan 97. Overall, our results suggest that positive selection for regulatory alleles may be a key factor in plant improvement.