The impact of training strategies on the accuracy of genomic predictors in United States Red Angus cattle.

Genomic selection (GS) has become an integral part of genetic evaluation methodology and has been applied to all major livestock species, including beef and dairy cattle, pigs, and chickens. Significant contributions in increased accuracy of selection decisions have been clearly illustrated in dairy cattle after practical application of GS. In the majority of U.S. beef cattle breeds, similar efforts have also been made to increase the accuracy of genetic merit estimates through the inclusion of genomic information into routine genetic evaluations using a variety of methods. However, prediction accuracies can vary relative to panel density, the number of folds used for folds cross-validation, and the choice of dependent variables (e.g., EBV, deregressed EBV, adjusted phenotypes). The aim of this study was to evaluate the accuracy of genomic predictors for Red Angus beef cattle with different strategies used in training and evaluation. The reference population consisted of 9,776 Red Angus animals whose genotypes were imputed to 2 medium-density panels consisting of over 50,000 (50K) and approximately 80,000 (80K) SNP. Using the imputed panels, we determined the influence of marker density, exclusion (deregressed EPD adjusting for parental information [DEPD-PA]) or inclusion (deregressed EPD without adjusting for parental information [DEPD]) of parental information in the deregressed EPD used as the dependent variable, and the number of clusters used to partition training animals (3, 5, or 10). A BayesC model with π set to 0.99 was used to predict molecular breeding values (MBV) for 13 traits for which EPD existed. The prediction accuracies were measured as genetic correlations between MBV and weighted deregressed EPD. The average accuracies across all traits were 0.540 and 0.552 when using the 50K and 80K SNP panels, respectively, and 0.538, 0.541, and 0.561 when using 3, 5, and 10 folds, respectively, for cross-validation. Using DEPD-PA as the response variable resulted in higher accuracies of MBV than those obtained by DEPD for growth and carcass traits. When DEPD were used as the response variable, accuracies were greater for threshold traits and those that are sex limited, likely due to the fact that these traits suffer from a lack of information content and excluding animals in training with only parental information substantially decreases the training population size. It is recommended that the contribution of parental average to deregressed EPD should be removed in the construction of genomic prediction equations. The difference in terms of prediction accuracies between the 2 SNP panels or the number of folds compared herein was negligible.