Improved genomic prediction accuracy by genetic relatedness using a crossbred pig population

Genomic prediction is crucial in animal breeding because it facilitates the selection of superior individuals based on genotype data. The success of genomic prediction is determined by its accuracy, which depends on the size of the reference population and relatedness between the reference and test populations. However, not all populations have large, highly genetically related reference populations. In this study, we evaluated the genomic prediction accuracy of three crossbreds and seven purebred populations using crossbred animals as a reference population and determined whether crossbred could be used as a reference population for small purebred populations. Genomic prediction accuracy was assessed using the genomic best linear unbiased prediction (GBLUP) for backfat thickness and carcass weight traits. Data from 29 Bisaro, 91 Duroc, 50 Duroc × Korean Native Pig (DK), 36 Iberian, 34 Korean Native Pig (KNP), 85 Landrace, 50 Landrace × Korean Native Pig (LK), 50 Landrace × Yorkshire × Duroc (LYD), 37 Meishan, and 49 Yorkshire pigs were used as test populations, whereas data from 245 DK, 964 LK, and 967 LYD crossbreds were used as the reference population. The findings indicated that the prediction accuracy of purebreds was higher when they were genetically related to the crossbred population, with accuracies ranging from 0.36 to 0.53 for backfat thickness and from 0.26 to 0.46 for carcass weight. In contrast, unrelated breeds showed lower accuracies, ranging from 0.16 to 0.48 for backfat thickness and from 0.13 to 0.40 for carcass weight. These results suggest that using crossbred populations related to the purebred population being predicted can improve prediction accuracy, especially for breeds with limited data. The prediction accuracy increased as the size of the reference population increased, regardless of genetic relatedness. Notably, small reference populations yielded higher accuracy when they were genetically related to the target animals, underscoring the importance of genetic similarity in addition to population size. These results highlight that using crossbred animals for reference populations is advantageous for genomic predictions because large populations can be rapidly established.