Abstract: Cultivation and breeding of cold resistant varieties are very important for carp farming in the Three-North Region, meanwhile, genetic analysis of cultivars is helpful to the sustainable utilization of the germplasm resources.Comparative analysis of genetic diversity was conducted using microsatellite markers on three cold-resistant varieties of common carp with similar genetic background, Cyprinuscarpio L. (GG), Cyprinuscarpio var. wuyuanensis (HH), and Cyprinuscarpio var. Songpu(SS).The results showed as following: (1) The average effective number of alleles of three cold-resistant varieties of common carp (GG, HH, SS) were 4.392, 4.501 and 4.518, respectively. Average observed heterozygosities were 0.801, 0.815 and 0.809, respectively. The average polymorphism information contents were 0.720 and 0.717, 0.720, respectively. Three cold-resistant varieties of common carp were of highly polymorphic level. Three populations deviated from the Hardy-Weinberg equilibrium and the population structure were reasonable. (2) A tree diagram was constructed by clustering analysis according to genetic distance of three breeding carp. The results indicated that SS clustering was a separate branch firstly, followed by GG and HH. In accordance with the results of Structure analysis, HH separated as a group alone, GG and SS clustered together for the model K=2.Whereas GG, HH, and SS were clustered into 3 different groups for the model K=3.(3)seventy-three specific alleles were detected from 26 markers, of which 41 specific alleles frequency reached more than 10%. There were 161 specific genotypes with genotypic frequencies over 10%, which can be used for germplasm identification of 3 varieties of cold resistant carp. The purpose of this study was to provide a beneficial reference bases for the breeding and germplasm identification of common carp.

Key words: common carp, microsatellite, germplasm identification, genetic diversity