Abstract：Abstract The traditional rice-fish coculture system is considered a sustainable form of agriculture that provides rice grain and fish for farmers in the world. Cyprinus carpio rubrofuscus, as a high quality local varieties paddy field carp, has been cultured in paddy fields of the north region of Guangdong province with a long history. In order to understand the effect of artificial culture and selective breeding on the genetic diversity and genetic structure of C. carpio rubrofuscus and to provide the study basis for preservation of germplasm resources and utilization, 16 microsatellite markers were selected and used to compare the genetic diversity of one generation of selectively bred population (F5) and 2 landraces (Ruyuan population and Lechang population) in C. carpio rubrofuscus in this study. The results showed that all selected primers were polymorphic and 119 alleles were detected from these 3 populations. The number of alleles detected on each locus varied from 3 to 10 with 7.44 alleles per primer pair on an average. In the 3 populations, the average expected heterozygosity (He) were 0.636 0, 0.698 9 and 0.775 1; the Shannon's diversity index (I) were 1.206 3, 1.402 0 and 1.612 2; and the average polymorphism information content (PIC) were 0.570 1, 0.645 8 and 0.720 7，respectively. It is suggested that the genetic diversity level of all the 3 populations were high (PIC＞0.5000), but the level of genetic diversity of the tow landraces was higher than that in F5 generation of selectively bred population. The genetic differentiation index (Fst) among all the locus was 0.102 8 with the value ranged from 0.044 0 to 0.246 8 indicated a moderate level of differentiation in the 3 populations. Pairwise Fst values also indicated that the 3 populations had moderate genetic differentiation with the highest value (0.182) between the selectively bred population (F5) and the Lechang population indicating a greater level of differentiation. While the value between the Ruyuan population and Lechang population was lowest (0.058), indicating a moderate level of differentiation. Among the 3 populations, the genetic distance was 0.205 6~0.622 4 and the genetic identify index was 0.536 6~0.814 2. The selectively bred population (F5) was the furthest with the Lechang population (0.6224) and the Ruyuan population was nearest with the Lechang population in terms of genetic distance (0.2056), while the genetic identity between the selectively bred population (F5) and Lechang population was lowest (0.5366) and the highest between the Ruyuan population and the Lechang population (0.8142). The NJ clustering tree based on the genetic distance by using the unweighted pair group method with arithmetic (UPGMA) demonstrated that the 2 landraces (Ruyuan population and Lechang population) clustered together firstly and then clustered with the selectively bred population (F5). This study suggested that the selective breeding work was efficient and the artificial selection has enlarged genetic differentiation between the breeding and landraces populations while decreased the genetic diversity within the breeding populations, but the high genetic diversity and genetic potential were maintained in the breeding population, indicating that there is great potential for future selections of C. carpio rubrofuscus through selective breeding. This study would provide valuable information for genetically breeding in C. carpio rubrofuscus in the future.
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