Effect of assortative mating on genetic gain and inbreeding in aquaculture selective breeding programs

In this simulation study, the effect of the mating scheme on genetic gain and inbreeding has been explored for aquaculture selection programs where tank effects and large family sizes are common. Different selection methods were investigated (individual, family, sib, combined and within-family selection). Our results suggest that under family and sib selection, genetic gain was increased with assortative mating in comparison to random mating. The advantage of assortative mating increased when common environmental effects were present. Contrarily, a decrease in genetic gain was observed with disassortative mating, except for the case of within-family selection. The advantage of assortative mating over random mating was due to the increase in the between-family component of the additive genetic variance that was exacerbated with the presence of common environmental effects. Under family and sib selection, the join effect of assortative mating and common environmental effects produced an increase in genetic gain of around 80 and 40% at early generations, and around 10 and 60% at later generations, respectively. Inbreeding was low under family selection for all mating schemes but much higher under sib selection when assortative mating was performed. In fact, the inbreeding coefficient after 10 generations of selection was 300% higher when assortative matings were performed under sib selection, compared to random matings. This was due to the fact that under sib selection, matings were based on family means, leading to an increased frequency of within-family matings. To our knowledge, this is the first study that investigates the effect of the mating scheme on genetic gain and inbreeding in an aquaculture context where family sizes are large and tank effects are present, and shows that assortative mating can substantially enhance the response to selection, particularly when family selection methods are applied.Our article complies with the Policy Statement for submission of manuscripts to the Genetics Section, as it provides insight into the issue of breeding programs. Here, we have connected previous work in the field to address new questions, focusing on how the mating scheme may affect both genetic gain and inbreeding in aquaculture selection programs, where family sizes are typically large and tank effects are usually present.In fish species, it is possible to consider different mating schemes because fecundity is high and because in vitro fertilization is often possible. A particular problem in aquaculture breeding programs is the impossibility of tagging physically newborn individuals. Given this, a common practice in aquaculture is to rear families in separate tanks until the fish are large enough to be individually tagged. This introduces an environmental effect common to the members of the same family (tank effect) which can lead to a reduction of the response to selection that needs to be considered.We studied here the efficiency of different selection methods in terms of genetic gain and inbreeding and investigated the effect of the mating scheme to optimize breeding programs in aquaculture when tank effects are present. We have shown that assortative mating can substantially enhance the response to selection, particularly when family selection methods are applied and tank effects are present. To our knowledge, the effect of the mating scheme in an aquaculture context has never been addressed before. Our results suggest that assortative mating in the presence of common environmental variance may be considered in selection programs in aquaculture. Our conclusions will help breeders make optimal mating choices.