China has rich and vast genetic resources of indigenous pig breeds. Currently, great attention is paid to either crossbreeding or conservation of these indigenous pig breeds, and insufficient attention is paid to the combination of conservation and breeding along with their long-term effects on genetic diversity. The genetic diversity of livestock is essential to increase productivity and respond to future challenges such as climate change. The genetic stability and product consistency of these indigenous pig breeds should be focused on and further improved. Therefore, the objective of this study is to compare the long-term effects of using conventional conservation and optimal contribution selection methods on genetic gain and genetic diversity.
A total of 11 different methods including conventional conservation and optimal contribution selection methods were investigated using stochastic simulations with a population size of 600 animals in each generation. Each scenario was run for 20 generations and 100 replicates. The long-term effects of using these methods were evaluated in terms of rate of genetic gain, rate of true inbreeding based on genome-wide identity-by-descient (IBD) markers and various genetic diversity metrices such as expected heterozygosity (He). The results indicated that the rates of true inbreeding in these conventional conservation methods were maintained at around 0.01. The optimal contribution selection methods based either on the pedigree (POCS) or genome (GOCS) information showed more genetic gain than conventional methods, and POCS achieved the largest gentic gain. Furthermore, the effect of using GOCS methods on most of the genetic diversity metrics was slightly better than the conventional conservation methods when the the rate of true inbreeding was the same, but this also required more sires used in OCS methods. According to the rate of true inbreeding, there was no significant difference among these conventional methods.
In conclusion, there is no significant difference in different ways of selecting sows on inbreeding when we use different conventional conservation methods. Compared with conventional methods, POCS method could achieve the most genetic gain. However, GOCS methods can not only achieve higher genetic gain, but also maintain a relatively high level of genetic diversity. Therefore, GOCS is a better choice if we want to combine conservation and breeding in actual production in the Chinese national-level conservation farms.