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

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 31, 2009
Publication Date: January 9, 2010
Citation: Cole, J.B., Sonstegard, T.S., Ma, L., Wiggans, G.R., Crooker, B.A., Van Tassell, C.P., Yang, J., Matukumalli, L., Da, Y. 2010. High Resolution QTL Map Of Net Merit Component Traits And Calving Traits From Genome-Wide Association Analysis In Contemporary U.S. Holstein Cows. Plant and Animal Genome Conference Proceedings. San Diego, Ca, Jan. 9-13, abstr. P565.

Technical Abstract: 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.