Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle

Results were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle.This research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.The advent of national genetic evaluation in beef cattle was made possible by the formulation of best linear unbiased prediction (BLUP) via the mixed model equations [1] and most livestock species now use BLUP for the evaluation of additive genetic merit and selection of parents to produce the next generation of progeny. However, most traits for which estimated breeding values or expected progeny differences (EPDs) are computed measure animal outputs rather than inputs. Because of the increased cost of production system inputs, interest has recently been stimulated for the development of efficient methods for producing phenotypes and EPDs for the efficiency of feed utilization. Feed costs in calf feeding and yearling finishing systems account for approximately 66% and 77% of total costs, respectively [2] and while increasing growth rate by 10% has been estimated to increase profitability by 18%, increasing the efficiency of growth of feedlot cattle by 10% is expected to increase profitability by 43% [3]. Other studies have suggested that increasing the feed efficiency of feedlot cattle has seven t