A Comparative Study of Optimizing Genomic Prediction Accuracy in Commercial Pigs

Genomic prediction (GP), which uses genome-wide markers to estimate breeding values, is a crucial tool for accelerating genetic progress in livestock and plant breeding. The accuracy of GP depends on several factors, including the statistical model, marker density, and cross-validation strategy. This study evaluated these factors to optimize GP accuracy for eight economically important carcass and body traits in a Duroc × (Landrace × Yorkshire) (DLY) pig population. This study used 50 K SNP chip data from 1494 DLY pigs, which were imputed to the whole genome sequence (WGS) level. Seven different models were compared, including GBLUP, ssGBLUP, and five Bayesian models. The ssGBLUP model consistently outperformed other models across all traits, with prediction accuracies ranging from 0.371 to 0.502. Further analyses showed that prediction accuracy improved with increasing cross-validation folds and marker density, particularly in the low-density panel. However, the improvement plateaued in medium-to-high-density scenarios. These findings underscore the importance of carefully selecting the model, marker density, and cross-validation strategy to optimize GP accuracy for carcass and body traits in commercial pigs. The insights from this study can guide breeders and researchers in maximizing genetic progress in pig breeding programs.