Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

High Resolution QTL Map Of Net Merit Component Traits And Calving Traits From Genome-Wide Association Analysis In Contemporary U.S. Holstein Cows

John B. Cole¹ , Tad S. Sonstegard² , Li Ma³ , George R. Wiggans¹ , Brian A. Crooker³ , Curt P. Van Tassell^1,2 , Jing Yang³ , Lakshmi K. Matukumalli² , Yang Da³

¹  Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350, USA

²  Bovine Functional Genomics Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350, USA

³  Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA

A QTL map of 725 SNPs affecting 13 dairy traits (top 100 effects per trait) was constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with 45,878 SNPs. The 13 traits were net merit (NM$), its 8 component traits and 4 calving traits. The top 100 effects of each trait explained 40-56% of the phenotypic variation. The 725 SNPs were distributed across all chromosomes but had different local concentrations for different traits. The following chromosomes had concentrations of significant effects: BTA13 for milk yield (MY), fat yield (FY); BTA7 for somatic cell score (SCS), daughter pregnancy rate (DPR); BTA14 for fat percent (FPC); BTAX for DPR, productive life (PL), protein percent (PPC); BTA18 for sire calving ease (SCE), sire still birth (SSB), daughter calving ease (DCE); and BTA23 for daughter still birth (DSB). Of the 725 SNPs, 36% (258 SNPs) were in 217 genes while the 45,878 SNPs also had 36% SNPs (16,516 SNPs) in 7,434 genes. Over 20 1-Mb gene clusters had significant SNPs, including a BTA14 cluster of 55 genes containing DGAT1 and 9 BTA7 clusters with SNP effects on SCS, DPR and PL. Genes with or near most significant SNPs include: GNAS of BTA13 for MY, FY, PY; DGAT1 and NIBP of BTA14 for FPC; PGLYRP1 and IGFL1 of BTA18 for 10 traits (other than SCS, DPR and DSB); MGMT of BTA26 for PPY, PY, NM$, SCE, DCE, SSB; INSR of BTA7 for SCS, DPR, PL; and DST of BTA23 for DSB.