Simple sequence repeat-based analysis of the genetic diversity and population genetic structure of populations of Siniperca chuatsi

In order to provide genetic information for the selective breeding of Siniperca chuatsi, 14 microsatellite DNA loci were used to evaluate the genetic diversity and structure of four farmed populations and one wild population in China. The four cultivated populations were Foshan (FS), Jiangmen (JM), Nanjing (NJ), and Hongze Lake (HZL), and the wild population was collected from the Hubei HuangGang section of the Yangtze River (HG). All five populations exhibited high genetic diversity (H-E values of between 0.608 and 0.633); the highest was found in the wild population (H-E = 0.633). Genetic differentiation within the populations was relatively low (F-ST < 0.15); 5.44% of the genetic variation was between the populations and 94.56% was within the populations. The greatest genetic distance was between JM and HG (0.1894), which had the lowest genetic identity (0.8725). NJ and HG had the shortest genetic distance (0.0365) and the highest genetic identity (0.9641). A phylogenetic analysis revealed that FS, JM, and HZL were clustered into one group, while NJ and HG were in another group, suggesting that the wild and NJ populations were closely related. Our results demonstrate that although the farmed populations have maintained a relatively high genetic diversity, they exhibit lower genetic diversity and higher genetic differentiation than the wild population. These results provide evidence that wild resources should be used for breeding, in order to maintain genetic diversity and ensure sustainable S. chuatsi farming.