Genetic origin and differentiation of ten paddy field–farmed Cyprinus carpio strains in China

Abstract

The common carp Cyprinus carpio has three subspecies, C. c. haematopterus, C. c. rubrofuscus, and C. c. carpio, and is also the main aquaculture species kept in paddy fields, known as paddy field carp (PFC). Many aquaculture strains of PFC have been developed worldwide. However, the contributions of each subspecies to the genetic material of many strains remain poorly understood. Moreover, the levels of genetic differentiation among these strains were defectively investigated due to limited sample coverage and molecular loci in previous reports. In this study, we collected 10 PFC strains in China, and used two mitochondrial loci (cytochrome b oxidase and the control region) and six microsatellite loci to trace their genetic origin and assess genetic differentiation among these strains. A constructed haplotype network provided evidence that PFC strains contained matrilineal genetic material from two common carp subspecies, C. c. haematopterus and C. c. rubrofuscus. The matrilineal genetic origin of cultivated strains could be traced to C. c. rubrofuscus in most cases. Genetic diversity calculations and Bayesian cluster analysis found that the Ruyuan Shili carp showed lower genetic diversity than the other strains and harbored simplex genetic resources, which was likely a result of inbreeding, intensive selection or a lack of systematic selection. Analysis of molecular variance and pairwise FST comparisons revealed statistically significant genetic differentiation among the analyzed PFC strains, and between populations within Heibei carp and Jinbei carp strains, suggesting that different PFC strains or localities may possess endemic genetic properties. Taken together, the present study provides important implications for the management of PFC, and could assist in improving monitoring programs for this historically significant aquaculture species.