ARS | Publication request: High-density SNP Scan of Production and Product Quality Traits in Beef Cattle

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: February 9, 2009
Publication Date: July 12, 2009
Citation: Thallman, R.M., Snelling, W.M., Allan, M.F., Ferrell, C.L., Freetly, H.C., Jenkins, T.G., Wheeler, T.L., Shackelford, S.D., King, D.A., Kuehn, L.A., Keele, J.W., Bennett, G.L. 2009. High-density SNP Scan of Production and Product Quality Traits in Beef Cattle [abstract]. Journal of Animal Science Supplement. 87(E-Suppl. 2):532. Abstract #626.

Technical Abstract: Genotypes from the BovineSNP50 BeadChip (50K) were obtained on animals derived from 150 AI sires from seven breeds (22 sires per breed; Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental) as either progeny (F1; 590 steers) or grandprogeny (F1 x F1 = F1**2; 1,306 steers and 707 females). Single SNP associations were conducted for each of the 44,163 SNP with minor allele frequency > 0.05 in the F1**2 generation. Records analyzed included birth weight (BWT), weaning weight (WWT) and postweaning gain (PWG) of 2,540 to 2,578 F1 and F1**2 steers and heifers; hot carcass weight (HCW), fat thickness (FT), ribeye area (REA), marbling score (MARB) and 14 d Warner-Bratzler shear force (WBS) of 1,667 to 1,693 F1 and F1**2 steers; and residual feed intake (RFI) and flight speed (FLS) of 1,187 to 1,192 F1**2 steers. Models included fixed effects for additive substitution effect of the SNP as well as sex, age of dam, contemporary group (year-season-location), covariates for calf breed composition and heterosis, and random direct additive polygenic effects. Models for BWT, WWT, and PWG also included fixed dam SNP substitution effects, covariates for dam breed composition and heterosis, and random maternal additive polygenic and permanent environment effects. The number of SNP nominally significant at P<0.001 and the false discovery rate (FDR), respectively, for each trait were BWT: 638, 0.07, WWT: 273, 0.16, WWT – maternal: 376, 0.12, PWG: 670, 0.07, PWG – maternal: 717, 0.06, FT: 115, 0.38, REA: 120, 0.37, MARB: 113, 0.39, HCW: 166, 0.27, WBS: 48, 0.92, RFI: 116, 0.38, and FLS: 51, 0.87. The number of SNP nominally significant at P<0.0001 and their FDR, respectively, were BWT: 308, 0.01, WWT: 103, 0.04, WWT-maternal: 79, 0.06, PWG: 226, 0.02 and PWG – maternal: 192, 0.02. For FT, REA, MARB, HCW, and RFI, 29-37% of SNP significant at P<0.001 are expected to be spurious. Many SNP could be identified with high confidence (0.01<FDR<0.06) for BWT, WWT, and PWG, the traits for which the greatest number of 50K genotypes and phenotypes were available. Only 7-16% of the many additional SNP significant for these traits at P<0.001 are expected to be spurious associations.