AUTHOR=Jiang Jicai , Ma Li , Prakapenka Dzianis , VanRaden Paul M. , Cole John B. , Da Yang 

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

JOURNAL=Frontiers in Genetics

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.00412

DOI=10.3389/fgene.2019.00412

ISSN=1664-8021

ABSTRACT=<p>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 <italic>DGAT1</italic> 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 <italic>SLC4A4, GC, NPFFR2</italic>, and <italic>ADAMTS3</italic> for milk and protein yields, the 30.03–36.67 Mb region of Chr20 with <italic>C6</italic> and <italic>GHR</italic> for milk yield, and the 88.19–88.88 Mb region with <italic>ABCC9</italic> as well as the 91.13–94.62 Mb region of Chr05 with <italic>PLEKHA5, MGST1, SLC15A5</italic>, and <italic>EPS8</italic> for fat yield. For fertility traits, the SNP in <italic>GC</italic> of Chr06, and the SNPs in the 65.02–69.43 Mb region of Chr01 with <italic>COX17, ILDR1</italic>, and <italic>KALRN</italic> had the most significant effects for daughter pregnancy rate and cow conception rate, whereas SNPs in <italic>AFF1</italic> of Chr06, the 47.54–52.79 Mb region of Chr07, <italic>TSPAN4</italic> of Chr29, and <italic>NPAS1</italic> of Chr18 had the most significant effects for heifer conception rate. For somatic cell score, <italic>GC</italic> of Chr06 and <italic>PRLR</italic> 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 <italic>DGAT1</italic> antagonism was an extreme antagonistic pleiotropy between fat yield and milk and protein yields among all SNPs in this study.</p>