Optimizing genomic reference populations to improve crossbred performance

Abstract

Background In pig and poultry breeding, the objective is to improve the performance of crossbred production animals, while selection takes place in the purebred parent lines. One way to achieve this is to use genomic prediction with a crossbred reference population. A crossbred reference population benefits from expressing the breeding goal trait but suffers from a lower genetic relatedness with the purebred selection candidates than a purebred reference population. Our aim was to investigate the benefit of using a crossbred reference population for genomic prediction of crossbred performance for: (1) different levels of relatedness between the crossbred reference population and purebred selection candidates, (2) different levels of the purebred-crossbred correlation, and (3) different reference population sizes. We simulated a crossbred breeding program with 0, 1 or 2 multiplication steps to generate the crossbreds, and compared the accuracy of genomic prediction of crossbred performance in one generation using either a purebred or a crossbred reference population. For each scenario, we investigated the empirical accuracy based on simulation and the predicted accuracy based on the estimated effective number of independent chromosome segments between the reference animals and selection candidates. Results When the purebred-crossbred correlation was 0.75, the accuracy was highest for a two-way crossbred reference population but similar for purebred and four-way crossbred reference populations, for all reference population sizes. When the purebred-crossbred correlation was 0.5, a purebred reference population always resulted in the lowest accuracy. Among the different crossbred reference populations, the accuracy was slightly lower when more multiplication steps were used to create the crossbreds. In general, the benefit of crossbred reference populations increased when the size of the reference population increased. All predicted accuracies overestimated their corresponding empirical accuracies, but the different scenarios were ranked accurately when the reference population was large. Conclusions The benefit of a crossbred reference population becomes larger when the crossbred population is more related to the purebred selection candidates, when the purebred-crossbred correlation is lower, and when the reference population is larger. The purebred-crossbred correlation and reference population size interact with each other with respect to their impact on the accuracy of genomic estimated breeding values.

Review: optimizing genomic selection for crossbred performance by model improvement and data collection

“…Testing PB animals in a CB environment may have an advantage over using a CB reference population because of differences in genetic relatedness with the selection candidates. For example, with a 4-way crossbreeding program without any multiplication steps, the available CB reference animals are separated by five generations from the selection candidates, whereas PB reference animals tested in a CB environment are separated by only two generations ( Wientjes et al, 2020 ). As a result, the genetic relatedness between the reference animals and selection candidates is stronger when PB are tested in a CB environment, compared with when CB information is used, resulting in a higher expected accuracy.…”

“…In addition, this strategy may improve genomic prediction accuracy, because predictions are based on actual genotypes of crossbreds, rather than on their genotype probabilities. Although the crossbreds with phenotypes and genotypes do not have to be closely related to the selection candidates, the accuracy is higher when this relationship is stronger ( Wientjes et al, 2020 ). Hence, the benefit of collecting CB information partly depends on the genetic relatedness of the available CB reference animals to the selection candidates.…”

“…Researchers that aim to compare such strategies, therefore, need to carefully scrutinize the differences between their study and the practical situation. For example, in practice it is likely that the PB selection candidates are more closely related to a PB reference population than to a CB reference population ( Wientjes et al, 2020 ). It is advisable to reflect this difference in the data used or simulated when studying the benefit of a CB over a PB reference population.…”

“…Finally, the authors simulated traits with a heritability in CB animals that was much smaller than in PB animals (0.05 vs. 0.20). For those traits, using two-way or four-way CB information resulted in higher accuracies than using PB information when was 0.50, but not when was 0.75 ( Wientjes et al, 2020 ).…”

“…The effect of differences in relatedness between the CB reference animals and selection candidates for the benefit of collecting CB information was studied by Wientjes et al (2020) , who simulated a pig breeding program. They compared the use of a PB reference population with the use of a CB reference population while considering the BOA, for two-way or four-way crossbreeding, and with or without multiplication steps to produce crossbreds.…”