The conservation of genetic diversity in traditional agricultural systems and the underlying mechanism are increasingly concerned. The rice-fish co-culture system, which has been practiced for more than a thousand years, is a typical traditional agricultural system in southern China. Here, we present a study on the genetic diversity of local carp populations (referred to as paddy field carp) in the rice-fish co-culture system using microsatellite analysis.
We investigated the carp populations in three rice growing areas in southern China, i.e. Qingtian county (120.31E, 27.99N) of Zhejiang Province, Congjiang county (108.68E, 25.63N) of Guizhou Province and Wuyishan city (118.13E, 27.14N) of Fujian Province. All of these sites had a long history of rice-fish co-culture. Thirty carp individuals were collected from each site. The tail fin of each individual carp was clipped and preserved in 95% ethanol, and stored under 4℃ temporarily. Genomic DNA was extracted from carp samples using a DNA extraction kit (E-Zup kit, Sangon, China). Microsatellite polymorphism of DNA samples was analyzed by using 20 pairs of microsatellite primers. The sequences were performed on ABI3730xl platform by Sangon Biotech (Shanghai, China).
The Microsatellite analysis indicated that the genetic diversity of paddy field carp was high across the three sampling sites. The number of alleles (Na) ranged from 9.56 to 11.67, and the expected heterozygosity (He) was between 0.78 and 0.80, both higher than the average level of wild carp populations (Na=7.71, He=0.71). The inbreeding coefficient (Fis) of the paddy field carp was between -0.02 and 0.07, suggesting a low risk of inbreeding depression. The analysis of molecular variance (AMOVA) showed that 92% of the genetic variation was within populations, with only 8% explained by differences among populations (P=0.001). Pairwise genetic differentiation (Fst) was relatively small. The principal coordinate analysis (PCoA) revealed that the three populations were clearly separated, but historical germplasm exchange might have occurred between Wuyishan and Qingtian since they are geographically close. Bayesian modeling (K=3) also showed that 90% of individuals from Congjian and Qingtian could be clustered into one population. The proportion for Wuyishan population, however, was only 70%, suggesting multiple origins. The above results indicated that the genetic diversity was maintained at a relatively high level across the three rice-fish systems, and the three carp populations were genetically separated from each other. Our study suggests that traditional agricultural systems would be important sites for genetic diversity conservation.