A Million-Cow Genome-Wide Association Study of Three Fertility Traits in U.S. Holstein Cows

A genome-wide association study (GWAS) of the daughter pregnancy rate (DPR), cow conception rate (CCR), and heifer conception rate (HCR) using 1,001,374-1,194,736 first-lactation Holstein cows and 75,140-75,295 SNPs identified 7567, 3798, and 726 additive effects, as well as 22, 27, and 25 dominance effects for DPR, CCR, and HCR, respectively, with log (1/p) > 8. Most of these effects were new effects, and some new effects were in or near genes known to affect reproduction including , , and , and a gene cluster of pregnancy-associated glycoproteins. The confirmed effects included those in or near the and regions of Chr06 and the region of Chr01. Eleven SNPs in the region of Chr18, the region of Chr06, and the region of Chr01 with sharply negative allelic effects and dominance values for the recessive homozygous genotypes were recommended for heifer culling. Two SNPs in and near the region of Chr04 that were sharply negative for HCR and age at first calving, but slightly positive for the yield traits could also be considered for heifer culling. The results from this study provided new evidence and understanding about the genetic variants and genome regions affecting the three fertility traits in U.S. Holstein cows.