Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development

Although genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection on miRNA-associated motifs. Here, we performed a genome-wide dissection of nucleotide variation and selection of miRNA targets associated with rice flower development. By sampling and resequencing 26 miRNA targets for globally diverse representative populations of Asian cultivated rice and wild relatives, we found that purifying selection has reduced genetic variation at the conserved miRNA binding sites on the whole, and highly conserved miRNA binding sequences were maintained in the studied rice populations. Conversely, non-neutral evolution of positive and/or artificial selection accelerates the elevated variations at nonconserved binding sites in a population-specific behavior which may have contributed to flower development-related phenotypic variation. Taken together, our results elucidate that miRNA targets involved in flower development are under distinctive selection regimes during rice evolution.