Improving Genomic Prediction Accuracy in the Chinese Holstein Population by Combining with the Nordic Holstein Reference Population

Simple Summary The size of the reference population is critical to the accuracy of genomic prediction. In addition, joining the reference populations from different breeding organizations is a convenient and effective method by which to enlarge reference populations. By adding the Nordic Holstein reference population to the Chinese Holstein reference population, we found that the accuracy of genomic prediction in the Chinese Holstein population was improved substantially for the traits with high or moderate genetic correlation between the two populations; however, the low-genetic-correlation traits did not improve. These findings are important for the purposes of multi-country joint genomic evaluation. The size of the reference population is critical in order to improve the accuracy of genomic prediction. Indeed, improving genomic prediction accuracy by combining multinational reference populations has proven to be effective. In this study, we investigated the improvement of genomic prediction accuracy in seven complex traits (i.e., milk yield; fat yield; protein yield; somatic cell count; body conformation; feet and legs; and mammary system conformation) by combining the Chinese and Nordic Holstein reference populations. The estimated genetic correlations between the Chinese and Nordic Holstein populations are high with respect to protein yield, fat yield, and milk yield-whereby these correlations range from 0.621 to 0.720-and are moderate with respect to somatic cell count (0.449), but low for the three conformation traits (which range from 0.144 to 0.236). When utilizing the joint reference data and a two-trait GBLUP model, the genomic prediction accuracy in the Chinese Holsteins improves considerably with respect to the traits with moderate-to-high genetic correlations, whereas the improvement in Nordic Holsteins is small. When compared with the single population analysis, using the joint reference population for genomic prediction in younger animals, results in a 2.3 to 8.1 percent improvement in accuracy. Meanwhile, 10 replications of five-fold cross-validation were also implemented in order to evaluate the performance of joint genomic prediction, thereby resulting in a 1.6 to 5.2 percent increase in accuracy. With respect to joint genomic prediction, the bias was found to be quite low. However, for traits with low genetic correlations, the joint reference data do not improve the prediction accuracy substantially for either population.

Automated summary

The size of the reference population is critical in improving the accuracy of genomic prediction. Combining reference populations from different breeding organizations has proven to be effective. Combining the Chinese and Nordic Holstein reference populations substantially improves genomic prediction accuracy for traits with high or moderate genetic correlations, but does not improve accuracy for traits with low genetic correlations in either population.