Genetic diversity and population structure of bighead carp (Hypophthalmichthys nobilis) from the middle and lower reaches of the Yangtze River revealed using microsatellite markers

The bighead carp, Hypophthalmichthys nobilis, is one of the most economically important freshwater fish species native to China. In recent decades, fishery resources of the bighead carp in the Yangtze River have been severely depleted, and there is limited information on the genetic features of the bighead carp in the Yangtze River. In this study, we analyzed the genetic divergence and population structure of bighead carps from 8 populations in the middle and lower reaches of the Yangtze River by using 15 microsatellite DNA markers. A relatively high genetic diversity was detected in the populations, with similar Ho and He (0.694–0.769 and 0.706–0.734, respectively). Weak genetic differentiation was found among the populations (Fst = 0.02, p < 0.01); and admixture of genetic clusters was generally present at the individual level. The Mantel test demonstrated a low correlation between genetic and geographic distances (r = 0.442, p < 0.01), implying admixture was partly due to dispersal between contiguous populations. Different relative directional migration rates (0.23–1.00) were inferred between population pairs, indicating the presence of both directional gene flows (dispersals). In addition, no significant heterozygosity excess was found in any of the populations (p > 0.05), and normal distribution of allele frequency indicated that no recent genetic bottleneck had occurred in any population. In summary, we found high diversity and weak genetic structuring within bighead carp populations in the middle and lower reaches of the Yangtze River, suggesting that genetic connectivity exists across these sections and the decline in fishery resource in the recent decades has not resulted in a bottleneck effect in this fish species. These findings provide vital genetic information on the bighead carp as well as a baseline for future conservation and breeding programs.