Running head : Single - step genomic BLUP for Angus Genetic evaluation using single - step genomic BLUP in American Angus

Predictive ability of genomic EBV when using single-step genomic BLUP 1 (ssGBLUP) in Angus cattle was investigated. Over 6 million records were available on birth 2 weight (BW) and weaning weight (WW), almost 3.4 million on post-weaning gain (PWG), and 3 over 1.3 million on calving ease (CE). Genomic information was available on at most 51,883 4 animals, which included high and low EBV accuracy animals. Traditional EBV was computed 5 by BLUP and genomic EBV by ssGBLUP and indirect prediction based on SNP effects derived 6 from ssGBLUP; SNP effects were calculated based on the following reference populations: 7 ref_2k (high EBV accuracy sires and cows), ref_8k (ref_2k, plus all genotyped ancestors of 8 validation animals), and ref_33k (ref_8k, plus all remaining genotyped animals not in the 9 validation). Indirect prediction was obtained as direct genomic value (DGV) or as an index of 10 DGV and parent average (PA). Additionally, runs with ssGBLUP used the inverse of the 11 genomic relationship matrix calculated by an algorithm for proven and young animals (APY) 12 that uses recursions on a small subset of reference animals. An extra reference subset included 13 3872 genotyped parents of genotyped animals (ref_4k). Cross-validation was used to assess 14 predictive ability on a validation population of 18,721 animals born in 2013. Computations for 15 growth traits used multiple-trait linear model, and for CE, a bivariate CE-BW threshold-linear 16 model. With BLUP, predictivities were 0.29, 0.34, 0.23, and 0.12 for BW, WW, PWG, and CE, 17 respectively. With ssGBLUP and ref_2k (ref_33k), predictivities were 0.34, 0.35, 0.27, and 0.13 18 (0.39, 0.38, 0.29, and 0.13), respectively. Low predictivity for CE was due to low incidence rate 19 of difficult calving. Indirect predictions with ref_33k were as accurate as with full ssGBLUP. 20 Using APY and recursions on ref_4k (ref_8k) gave 88% (97%) gains of full ssGBLUP. 21 Genomic evaluation in beef cattle with ssGBLUP is feasible while keeping the models (maternal, 22 multiple trait, threshold) already used in regular BLUP. Gains in predictivity are dependent on 23 Page 2 of 28 Journal of Animal Science Journal of Animal Science Accepted paper, posted 04/06/2015. doi:10.2527/jas2014-8836