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.