Development of microsatellite markers and genetic diversity in wild and cultured populations of black carp (Mylopharyngodon piceus) along the Yangtze River

Black carp (Mylopharyngodon piceus) is one of traditionally important aquaculture fishes in China; however, population genetic studies are relatively rare for this species. In the present study, we developed a set of microsatellite markers by FIASCO method and used ten of these polymorphic markers to evaluate genetic diversity of black carp (three wild populations and six cultured populations including larvae from fish seed farms and adults from fish markets, n = 269) along the Yangtze River basin. Among these samples, mean number of alleles (Na) and effective number of alleles (Ne) were 14 and 6, respectively. Genetic diversities of wild populations were higher than that of cultured populations, represented by Ho of 0.767 vs 0.730, He of 0.806 vs 0.722, and polymorphism information content of 0.767 vs 0.6731, respectively, although a few cultured populations were exceptional. Fst from 0.010 to 0.159 showed a moderate level of population differentiations, and Bayesian and clustering analysis consistently supported that these populations could be divided into 7 clusters. This study generated novel microsatellites and new evidence of genetic differentiation between wild and cultured populations of black carp, which are useful for conservation and sustainable utilization of fishery resources.