Establishing a base population for a breeding program in aquaculture, from multiple subpopulations, differentiated by genetic drift: I. Effects of the number of subpopulations, heritability and mating strategies using optimum contribution selection

Guidelines for constructing base populations in fish were examined using a drift model. A large number of drift differentiated, wild subpopulations, with inbreeding Fwild (Fwild ∈ [0.05–0.20]), and a trait with heritability htot2 (htot2 ∈ [0.10–0.30]), were assumed. A base population was generated by sampling 2N fish from each of nsub subpopulations (nsub ∈ [1–8]), and then mated to produce 160 or 240 families per generation. The matings were either at random, in a structured diallel-cross, or within subpopulations to produce generation 1. Optimal contribution selection on phenotype was applied from generation 1 to11, with a rate of inbreeding of 0.5% per generation. Genetic gain (Δg) improved with nsub, the improvement being largest when going from one to two subpopulations, with diminishing returns. Most of the potential improvement was obtained with nsub = 4, and was well predicted by ΔgnsubΔg1≈(1−Fwild/nsub)(1−Fwild). Initial matings across subpopulations improved Δg from the second round of selection compared to within. Consequently the effect of the mating strategy were first observed 3 generation after decisions were made and persisted over subsequent generations, but with minimal effect on the accumulated additive genetic gain in generation 11. It was concluded that sampling from at least four subpopulations was beneficial and that mating across subpopulations should start as early as possible.