Optimal Combination of Different Selection and Mating Strategies on Exploiting Genetic Diversity and Genetic Gain in Small Pig Conservation Populations

Abstract

Both selection and mating systems are essential tools for breeders to conserve the genetic variance and improve the performance of livestock animals. How to effectively balance the genetic gain and inbreeding has always been an important issue in quantitative genetics research. In this study, a total of 11 selection methods, including random and truncation selection, six conventional selection methods, three different optimal contribution selection (OCS) methods and three mating strategies including random mating, minimum-coancestry mating based on pedigree (MCPed) and genomic information (MCmarker), were performed using stochastic simulations. The long-term effects of different combinations of selection and mating strategies on the genetic gain, the rate of inbreeding and genetic diversity in the small-scale pig conservation populations were investigated. The results showed that different strategies of selection and mating methods had different effects on genetic gain and inbreeding rate. For maintaining additive genetic variance, the optimal strategy was random selection with random mating, followed by SIREhalf-DAMfullRandom selection (which means selecting dams randomly from each full-sib family) and random mating. For mainting the number of common ancestors, the optimal strategy was SIREhalf-DAMfull selection (which means selecting dams with the highest estimated breeding value within each full-sib family) and random mating, followed by SIREhalf-DAMfullRandom selection and random mating, OCS and MCPed mating. For genetic diversity metrics, taking He and Ho as an example, the optimal strategy was GOCS (optimal contribution selection based on genomic information) with MCmarker mating. For genetic gain, the optimal strategy was truncation selection and MCmarker mating, followed by POCS (optimal contribution selection based on pedigree information) and MCmarker mating, truncation selection and MCPed mating. For the rate of inbreeding, the optimal strategy was SIREhalf-DAMfull selection and MCPed mating. Our findings can help breeding managers and farmers choose a more suitable and sustainable strategy for maintaining the genetic diversity and improving the genetic gain of local pig breeds.