Genome-Wide Association Study of Daughter Pregnancy Rate in Crossbred Dairy Cows

A genome-wide association study (GWAS) of daughter pregnancy rate (DPR) was conducted using 75,133 SNPs and 40,203 first lactation crossbred dairy cows mostly from Jersey-Holstein crosses. The GWAS analysis detected 6528 additive effects, 65 dominance effects, 1638 additive × additive (A × A) effects, 3 additive × dominance effects, and 18 intra-chromosome dominance × dominance (D × D) effects. Of the 1638 A × A effects, 1634 were intra-chromosome and four were inter-chromosome A × A effects. The distance between two SNPs with intra-chromosome epistasis effects was in the range of 3.61 Kb to 2.68 Mb, and many interacting SNP pairs were within the same genes. The additive and A × A effects were distributed on all chromosomes showing genome-wide involvement in DPR heterosis. The dominance and D × D effects all had homozygous advantages and heterozygous disadvantages. The GWAS results identified four genetic mechanisms underlying DPR heterosis in crossbred dairy cows: complementary additive effects from different breeds and new additive effects due to cross breeding, two-locus allelic interactions between loci and between breeds, within-locus allelic interactions between breeds, and genotype × genotype interactions enabled by allelic interactions between breeds. Results in this study provided a novel understanding about the genetic factors and mechanisms underlying DPR heterosis in crossbred dairy cows.