Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

Authors: Cole, John; Wiggans, George; MA, LI - University Of Minnesota; Sonstegard, Tad; LAWLOR, THOMAS - Holstein Association Usa, Inc; CROOKER, BRIAN - University Of Minnesota; Van Tassell, Curtis - Curt; YANG, JING - University Of Minnesota; WANG, SHENGWEN - University Of Minnesota; MATUKUMALLI, LAKSHMI - US Department Of Agriculture (USDA); DA, YANG - University Of Minnesota

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/11/2011
Publication Date: 8/11/2011
Citation: Cole, J.B., Wiggans, G.R., Ma, L., Sonstegard, T.S., Lawlor, T.J., Crooker, B.A., Van Tassell, C.P., Yang, J., Wang, S., Matukumalli, L.K., Da, Y. 2011. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. Biomed Central (BMC) Genomics. Online, 12:408.

Interpretive Summary: Genome-wide association analysis is used to link phenotypic effects with regions of the bovine genome, and knowledge of genes and chromosomal regions associated with dairy phenotypes is useful for genome and gene-based selection. On this paper, a genome-wide analysis of 31 production, health, reproduction and body conformation traits in contemporary Holstein cows was conducted. A number of candidate genes and chromosome regions associated with these traits were identified. In addition to confirming results from previous studies, this analysis identified several new associations among phenotypes and genomic regions that need to be investigated. The results of this study should significantly contribute to the process of building consensus of dairy QTL effects. The results support the hypothesis that most traits are controlled by a large number of genes, each of which has a small effect on the phenotype. Production, health and reproduction traits involved more gene clusters of tightly linked genes than body conformation traits, indicating that genetic mechanisms of production, health and reproduction were more complex than those of body conformation traits.

Technical Abstract: Background Genome-wide association analysis is a powerful tool for annotating phenotypic effects on the genome and knowledge of genes and chromosomal regions associated with dairy phenotypes is useful for genome and gene-based selection. Here, we report results of a genome-wide analysis of predicted transmitting ability (PTA) of 31 production, health, reproduction and body conformation traits in contemporary Holstein cows. Results Genome-wide association analysis identified a number of candidate genes and chromosome regions associated with 31 dairy traits in contemporary U.S. Holstein cows. Highly significant genes and chromosome regions include: BTA13's GNAS region for milk, fat and protein yields; BTA7's INSR region and BTAX's LOC520057 and GRIA3 for daughter pregnancy rate, somatic cell score and productive life; BTA2's LRP1B for somatic cell score; BTA14's DGAT1-NIBP region for fat percentage; BTA1's FKBP2 for protein yields and percentage, BTA26's MGMT and BTA6's PDGFRA for protein percentage; BTA18's 53.9-58.7 Mb region for service-sire and daughter calving ease and service-sire stillbirth; BTA18's PGLYRP1-IGFL1 region for a large number of traits; BTA18's LOC787057 for service-sire stillbirth and daughter calving ease; BTA15's CD82, BTA23's DST and the MOCS1-LRFN2 region for daughter stillbirth; and BTAX's LOC520057 and GRIA3 for daughter pregnancy rate. For body conformation traits, BTA11, BTAX, BTA10, BTA5, and BTA26 had the largest concentrations of SNP effects, and PHKA2 of BTAX and REN of BTA16 had the most significant effects for body size traits. For body shape traits, BTAX, BTA19 and BTA3 were most significant. Udder traits were affected by BTA16, BTA22, BTAX, BTA2, BTA10, BTA11, BTA20, BTA22 and BTA25, teat traits were affected by BTA6, BTA7, BTA9, BTA16, BTA11, BTA26 and BTA17, and feet/legs traits were affected by BTA11, BTA13, BTA18, BTA20, and BTA26. Conclusions Genome-wide association analysis identified a number of genes and chromosome regions associated with 31 production, health, reproduction and body conformation traits in contemporary Holstein cows. The results provide useful information for annotating phenotypic effects on the dairy genome and for building consensus of dairy QTL effects.