Most nonsynonymous mutations are thought to be deleterious because of their effect on protein sequence and are expected to be removed or kept at low frequency by the action of natural selection. Nonetheless, the effect of positive selection on linked sites or drift in small or inbred populations may also impact the evolution of deleterious alleles. Despite their potential to affect complex trait phenotypes, deleterious alleles are difficult to study precisely because they are often at low frequency. Here, we made use of genome-wide genotyping data to characterize deleterious variants in a large panel of maize inbred lines. We show that, despite small effective population sizes and inbreeding, most putatively deleterious SNPs are indeed at low frequencies within individual genetic groups. We find that genes associated with a number of complex traits are enriched for deleterious variants. Together, these data are consistent with the dominance model of heterosis, in which complementation of numerous low-frequency, weak deleterious variants contribute to hybrid vigor.
Keywords: Deleterious mutations; GBS SNPs; Heterosis; Maize; Quantitative traits.