Multibreed genomic prediction using summary statistics and a breed-origin-of-alleles approach

Because of an increasing interest in crossbreeding between dairy breeds in dairy cattle herds, farmers are requesting breeding values for crossbred animals. However, genomically enhanced breeding values are difficult to predict in crossbred populations because the genetic make-up of crossbred individuals is unlikely to follow the same pattern as for purebreds. Furthermore, sharing genotype and phenotype information between breed populations are not always possible, which means that genetic merit (GM) for crossbred animals may be predicted without the information needed from some pure breeds, resulting in low prediction accuracy. This simulation study investigated the consequences of using summary statistics from single-breed genomic predictions for some or all pure breeds in two- and three-breed rotational crosses, rather than their raw data. A genomic prediction model taking into account the breed-origin of alleles (BOA) was considered. Because of a high genomic correlation between the breeds simulated (0.62–0.87), the prediction accuracies using the BOA approach were similar to a joint model, assuming homogeneous SNP effects for these breeds. Having a reference population with summary statistics available from all pure breeds and full phenotype and genotype information from crossbreds yielded almost as high prediction accuracies (0.720–0.768) as having a reference population with full information from all pure breeds and crossbreds (0.753–0.789). Lacking information from the pure breeds yielded much lower prediction accuracies (0.590–0.676). Furthermore, including crossbred animals in a combined reference population also benefitted prediction accuracies in the purebred animals, especially for the smallest breed population.