John B. Cole,1 Tad S. Sonstegard,2 Li Ma,3 George R. Wiggans,1 Brian A. Crooker,3 Curt P. Van Tassell,1,2 Jing Yang,3 Lakshmi K. Matukumalli,2 and Yang Da3
1Animal Improvement Programs and
2Bovine Functional Genomics Laboratories, Agricultural Research
Service, USDA, Beltsville, Maryland; and
3Department of Animal
Science, University of Minnesota, St. Paul, Minnesota
© 2010 the American Physiological Society
Genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped for 45,878 single nucleotide polymorphisms (SNPs) was used to detect quantitative trait loci (QTLs) associated with predicted transmitting abilities for 13 production, health, and reproduction traits. The top 100 effects for each trait explained 40 to 56% of trait variation. Across the 13 traits, the top 100 included 725 unique SNPs that were used for QTL detection. Those 725 SNPs were distributed across all chromosomes, but localized concentrations differed among traits: BTA13 for milk and fat yields; BTA7 for somatic cell score and daughter pregnancy rate; BTA14 for fat percentage; BTA18 for service-sire and daughter calving ease and service-sire stillbirth; BTA23 for daughter stillbirth; and BTAX for daughter pregnancy rate, productive life, and protein percentage. Over 20 gene clusters of 1 Mb with >850 genes were associated with significant SNPs, including a 55-gene cluster on BTA14 with DGAT1 and a cluster on BTA7 near INSR. Genes with or near the most significant SNPs included BTA7's INSR for somatic cell score, daughter pregnancy rate, and productive life; BTA13's GNAS for milk, fat, and protein yields; BTA14's DGAT1 and NIBP for fat percentage; BTA15's CD82 for daughter stillbirth; BTA18's PGLYRP1-IGFL1 region for all traits except somatic cell score, daughter pregnancy rate, and daughter stillbirth; BTA23's GPR110-GPR116 region for protein yield and DST for daughter stillbirth; BTA26's MGMT for protein yield and percentage, net merit, service-sire and daughter calving ease, and service-sire stillbirth; and BTAX's LOC616260 for protein yield.
dairy traits, single nucleotide polymorphism, quantitative trait loci, net merit, dairy cattle