A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle

Genome-wide association study (GWAS) is a powerful approach to identify genomic regions and genetic variants associated with phenotypes. However, only limited mutual confirmation from different studies is available. We conducted a large-scale GWAS using 294,079 first-lactation Holstein cows and identified new additive and dominance effects on five production traits, three fertility traits, and somatic cell score. Four chromosomes had the most significant SNP effects on the five production traits, a Chr14 region containing DGAT1 mostly had positive effects on fat yield and negative effects on milk and protein yields, the 88.07–89.60 Mb region of Chr06 with SLC4A4, GC, NPFFR2, and ADAMTS3 for milk and protein yields, the 30.03–36.67 Mb region of Chr20 with C6 and GHR for milk yield, and the 88.19–88.88 Mb region with ABCC9 as well as the 91.13–94.62 Mb region of Chr05 with PLEKHA5, MGST1, SLC15A5, and EPS8 for fat yield. For fertility traits, the SNP in GC of Chr06, and the SNPs in the 65.02–69.43 Mb region of Chr01 with COX17, ILDR1, and KALRN had the most significant effects for daughter pregnancy rate and cow conception rate, whereas SNPs in AFF1 of Chr06, the 47.54–52.79 Mb region of Chr07, TSPAN4 of Chr29, and NPAS1 of Chr18 had the most significant effects for heifer conception rate. For somatic cell score, GC of Chr06 and PRLR of Chr20 had the most significant effects. A small number of dominance effects were detected for the production traits with far lower statistical significance than the additive effects and for fertility traits with similar statistical significance as the additive effects. Analysis of allelic effects revealed the presence of uni-allelic, asymmetric, and symmetric SNP effects and found the previously reported DGAT1 antagonism was an extreme antagonistic pleiotropy between fat yield and milk and protein yields among all SNPs in this study.