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.