Genomic selection of purebreds for crossbred performance

Results demonstrate that crossbred data can be used to evaluate purebreds for commercial crossbred performance. Accuracies based on crossbred data were generally not much lower than accuracies based on pure breed data and almost identical when the breeds crossed were closely related breeds. The accuracy of both models (ASGM and BSAM) increased with marker density and size of the training data. Accuracies of both models also tended to decrease with increasing distance between breeds. However the effect of marker density, training data size and distance between breeds differed between the two models. BSAM only performed better than AGSM when the number of markers was small (500), the number of records used for training was large (4000), and when breeds were distantly related or unrelated.In conclusion, GS can be conducted in crossbred population and models that fit breed-specific effects of SNP alleles may not be necessary, especially with high marker density. This opens great opportunities for genetic improvement of purebreds for performance of their crossbred descendents in the field, without the need to track pedigrees through the system.One of the main limitations of many livestock breeding programs is that selection is in purebred nucleus lines or breeds that are housed in high-health environments but the goal of selection is to improve crossbred performance under field conditions. Due to genetic differences between purebreds and crossbreds and environmental differences between nucleus and field conditions, performance of purebred parents can be a poor predictor of performance of their crossbred descendants [1]. Furthermore, some important traits such as disease resistance cannot be measured in nucleus lines. In order to avoid these problems, it has been proposed to select purebred relatives based on crossbred performance using combined crossbred and purebred selection or CCPS [2-6]. This approach can increase response to selection for crossbred performance relat