Genome-wide association analysis of eighteen body confirmation traits in contemporary U.S. Holstein cows

George R. Wiggans,¹ Li Ma,³ Tad S. Sonstegard,² John B. Cole,¹ Tom Lawlor,⁴ 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; and ⁴Holstein Association USA, Brattleboro, Vermont

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 18 body conformation traits. The top 100 effects for each trait explained 38 to 56% of trait variation. Across the 18 traits, the top 100 included 1,005 unique SNPs that were used for QTL detection. The largest numbers of significant SNPs were located on BTA11, BTAX, BTA10, BTA5, and BTA26; localized concentrations were found on BTA2, BTA6, BTA8, BTA13, and BTA16-23. Of the 1,005 significant SNPs, 366 were located in 297 genes. The REN gene on BTA16 was highly significant for 12 traits. For body size traits, LOC515732 on BTAX was ranked first in significance for stature, strength, and body depth and second for rump width; REN was first for rump width, second for strength, and third for body depth. The most significant genes or chromosomes for other traits were BTAX, BTA3, BTA7, BTA17, and BTA10 for dairy form; BTA5 and BTA9 for rump angle; REN and LOC515732 for fore udder attachment; BTA2 and BTA10 for rear udder height; BTA25 and BTA22 for udder depth; BTA7, BTA19, and BTA6 for udder cleft; BTA6 for front teat placement; BTA7 for rear teat placement; BTA11, BTA26, BTA21, and BTA17 for teat length; MGMT on BTA26 for foot angle; BTA1 and BTA18 for rear legs (rear view); BTAX, BTA11, and BTA26 for rear legs (rear view); and BTA26, BTA13, and BTAX for feet/legs score.

type traits, single nucleotide polymorphism, quantitative trait loci, final score, dairy cattle