Restructuring breeding programs 2: Assortative mating for improved commercial genetic gain when using optimum contribution selection and diversity introduction

BACKGROUND: Commercial breeding programs have two goals: genetic gain in the breeding population and delivering competitive genetic products, like semen, to production farms. Breeding programs must also manage genetic diversity, which reduces short-term genetic gain. Our study aimed to investigate the use of assortative mating to increase the genetic variance of the next generation. The resulting higher genetic variance is expected to increase the genetic level of the best animals of which semen can be sold to producers. We are here particularly interested in applying this strategy in breeding programs that invest in diversity introduction by bringing lost or lowly related alleles from lower-performing sources into the elite nucleus breeding population. We test two assortative mating strategies. The first, 'maximum assortative mating', aimed to increase the genetic variance as much as possible by mating the best male with the best female, second best with second best and so on. The second, 'tuned assortative mating', aimed to increase the genetic variance as much as needed to make the same gain as a hypothetical competitor that uses random mating. The motivation for the tuned strategy was to limit anticipated negative effects of assortative mating on genomic prediction accuracies. RESULTS: The 'tuned' strategy was outperformed by the 'maximum' strategy, and no negative effects on prediction accuracy or biases due to the mating strategy were found. With truncation selection, i.e., no control of the inbreeding rate, assortative mating led to a faster decrease of genetic diversity over time compared to random mating. Assortative mating combined with optimum contribution selection (OCS) showed a comparable inbreeding rate to random mating, and led to higher variance of breeding values. While achieving the same genetic gain of the population average, OCS with assortative mating thus led to a higher genetic level of the elite boars from which semen was marketed. CONCLUSIONS: Assortative mating improves the genetic level of outputs of breeding programs but this effect was not large enough to overcome the lower competitiveness associated with diversity introduction. To limit the accelerated loss of diversity, assortative mating should only be used when selection considers diversity, as in OCS.