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

Abstract

Background: The success of genomic selection depends mainly on the extent of linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), the number of animals in the training set (TS) and the heritability (h2) of the trait. The extent of LD depends on the genetic structure of the population and the density of markers. The aim of this study was to calculate accuracy of direct genomic estimated breeding values (DGEBV) using best linear unbiased genomic prediction (GBLUP) for different marker densities, heritabilities and sizes of the TS in simulated populations that mimicked previously reported extent and pattern of LD in beef cattle.

Results: 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.

Conclusions: 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.

Figure 1

Schematic representation of the simulation steps.

Figure 2

Schematic representation of the simulated scenarios. n_TS: number of bulls in the training set. Accuracies of EBV for all n_TS were 0.79, 0.90 or 0.94 for heritability = 0.10, 0.25 or 0.40, respectively. The average progeny size was 73 for all n_TS and heritability levels.

Figure 3

Accuracy of Direct Genomic Estimated Breeding Value (DGEBV) for 40 k Scenario. DGEBV as a function of number of animals in the training set, considering three levels of heritability and 40 k markers. The results are presented as the average of 10 replicates.