Comparison of breeding strategies for purging inbreeding depression via simulation

Purging deleterious genes in breeding programs, particularly with endangered species, has become of increased interest in recent years, but less attention has been paid to the effectiveness of alternative breeding schemes in these purging programs. We conducted a computer simulation to examine the relative effectiveness of purging deleterious genes in five breeding schemes: continuous selfing, half-sib mating, and three mixtures of selfing or half-sib mating alternating over generations. We considered a multiplicative fitness model of lethal, highly detrimental, and detrimental genes affecting viability. We simulated a diploid breeding population of progeny sizes (10, 50, 200) with initial lethal equivalents of 2, 4, 6, 8, and 10 in which each of the five breeding schemes was applied over 10 generations. The patterns of purging, progeny survival, and probability of population extinction were compared among the breeding schemes. Continuous selfing could quickly purge deleterious genes of large effect, especially for increasing progeny fitness, but not necessarily with a low probability of extinction. Continuous half-sib mating could be as effective in purging as continuous selling, especially after several generations, but generally with low risk of extinction. The breeding schemes of mixed selling and half-sib mating fall mostly between continuous selfing and half-sib mating schemes in the effectiveness of purging deleterious genes as well as progeny survival and probability of extinction. These results suggest that a mild inbreeding system such as half-sib mating might be the breeding scheme of choice in breeding programs of endangered species, especially for avoiding increases in extinction probability.