Genotyping strategies for genomic selection in small dairy cattle populations

This study evaluated different female-selective genotyping strategies to increase the predictive accuracy of genomic breeding values (GBVs) in populations that have a limited number of sires with a large number of progeny. A simulated dairy population was utilized to address the aims of the study. The following selection strategies were used: random selection, two-tailed selection by yield deviations, two-tailed selection by breeding value, top yield deviation selection and top breeding value selection. For comparison, two other strategies, genotyping of sires and pedigree indexes from traditional genetic evaluation, were included in the analysis. Two scenarios were simulated, low heritability (h² = 0.10) and medium heritability (h² = 0.30). GBVs were estimated using the Bayesian Lasso. The accuracy of predicted GBVs using the two-tailed strategies was better than the accuracy obtained using other strategies (0.50 and 0.63 for the two-tailed selection by yield deviations strategy and 0.48 and 0.63 for the two-tailed selection by breeding values strategy in low- and medium-heritability scenarios, respectively, using 1000 genotyped cows). When 996 genotyped bulls were used as the training population, the sire’ strategy led to accuracies of 0.48 and 0.55 for low- and medium-heritability traits, respectively. The Random strategies required larger training populations to outperform the accuracies of the pedigree index; however, selecting females from the top of the yield deviations or breeding values of the population did not improve accuracy relative to that of the pedigree index. Bias was found for all genotyping strategies considered, although the Top strategies produced the most biased predictions. Strategies that involve genotyping cows can be implemented in breeding programs that have a limited number of sires with a reliable progeny test. The results of this study showed that females that exhibited upper and lower extreme values within the distribution of yield deviations may be included as training population to increase reliability in small reference populations. The strategies that selected only the females that had high estimated breeding values or yield deviations produced suboptimal results.