Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle

The accuracy of DGEBV increased significantly (p < 0.05) with the increase in the number of bulls in the TS (480, 960 or 1920), trait h2 (0.10, 0.25 or 0.40) and marker densities (40 k or 800 k). Increasing the number of animals in the TS by 4-fold and using their phenotypes to estimate marker effects was not sufficient to maintain or increase the accuracy of DGEBV obtained using estimated breeding values (EBVs) when the trait h2 was lower than 0.40 for both marker densities. Comparing to expected accuracies of parent average (PA), the gains by using DGEBV would be of 27%, 13% and 10% for trait h2 equal to 0.10, 0.25 and 0.40, respectively, considering the scenario with 40 k markers and 1920 bulls in TS.As reported in dairy cattle, the size of the TS and the extent of LD have major impact on the accuracy of DGEBV. Based on the findings of this simulation study, large TS, as well as dense marker panels, aiming to increase the level of LD between markers and QTL, will likely be needed in beef cattle for successful implementation of genomic selection.Genomic selection is a method of marker-assisted selection based on LD that potentially explores all QTL in the genome [1]. The breeding value (BV) is estimated by the sum of the effects of marker alleles or haplotypes covering the entire genome and its accuracy could be as high as 0.85 [1].The BV calculated from the estimated effects of markers is often called DGEBV and the blended value between DGEBV and traditional EBV is often called Genomic Estimated Breeding Value (GEBV). The accuracy of DGEBV and GEBV depends on: 1) the level of LD between markers and QTL; 2) the number of animals in the TS; 3) the heritability of the trait and 4) the distribution of QTL effects [2].Since 2009, national evaluations of Holstein bulls are being performed in the USA and Canada based on GEBV. Before that, a comprehensive study evaluating the reliability of GEBV of many economic traits in thousands of Holstein bulls genotyped with the Il