Classical mutations tend to be deleterious to traits and fitness. Is this the case for mutations with polygenic effects? Here, we infer ancestral and mutant alleles (MAs) for 8 million sequence variants in 113k cattle and quantify the effects of MA on 37 complex traits. Heterozygosity at sites conserved across 100 vertebrates increase fertility, stature, and milk production, positively associating these traits with fitness. MAs decrease fat and protein concentration in milk and stature but increase gestation length and somatic cell count in milk indicative of mastitis. However, the frequency of MAs that decrease fat and protein concentration and stature and increase gestation length and somatic cell count is lower than the frequency of MAs with the opposite effect. These results suggest bias in the direction of effect of mutation (e.g. towards reduced protein in milk), but selection operating to reduce the frequency of these MAs. MAs with a large-effect decrease protein and milk yield, while small-effect MAs increase the two traits. These results imply two classes of genomic sites subject to long-term selection: sites conserved across vertebrates show hybrid vigour while sites subject to less long-term selection show a bias in mutation towards alleles that are selected against.
Hybrid Vigour and Fibre Production
