Enhancing Genomic Prediction Accuracy for Body Conformation Traits in Korean Holstein Cattle

Simple Summary The Holstein breed is crucial in the dairy industry in Korea. In this study, we focused on the accuracy of genomic predictions for 12 of 24 significant body conformation traits examined in Korean Holstein cattle. Employing various statistical methods and levels of genetic data, we assessed how accurately these traits could be predicted. The prediction accuracy increased notably when both offspring and parental genetic information were considered. We identified 18 key genetic regions, offering valuable insights for future research to identify specific genes related to these traits. This study highlights the potential of advanced genetic tools to improve breeding strategies for Korean Holstein cattle, in particular for enhancing traits with significant economic and health impacts.Abstract The Holstein breed is the mainstay of dairy production in Korea. In this study, we evaluated the genomic prediction accuracy for body conformation traits in Korean Holstein cattle, using a range of pi levels (0.75, 0.90, 0.99, and 0.995) in Bayesian methods (BayesB and BayesC). Focusing on 24 traits, we analyzed the impact of different pi levels on prediction accuracy. We observed a general increase in accuracy at higher levels for specific traits, with variations depending on the Bayesian method applied. Notably, the highest accuracy was achieved for rear teat angle when using deregressed estimated breeding values including parent average as a response variable. We further demonstrated that incorporating parent average into deregressed estimated breeding values enhances genomic prediction accuracy, showcasing the effectiveness of the model in integrating both offspring and parental genetic information. Additionally, we identified 18 significant window regions through genome-wide association studies, which are crucial for future fine mapping and discovery of causal mutations. These findings provide valuable insights into the efficiency of genomic selection for body conformation traits in Korean Holstein cattle and highlight the potential for advancements in the prediction accuracy using larger datasets and more sophisticated genomic models.