Abstract：The application of microsatellite markers for parentage determination has been approved in aquaculture which not only can maintain the parentage information, but also greatly reduce the cost in space and man-power and greatly improve breeding selection effect in communal environment, especially in the process of selective breeding. In this study, two selected cross-breeding families (the 49 full-sib families: 7 of Cyprinus carpio var. mirror♀×7 of C. carpio var. wuyuanensis♂and the 24 full-sib families: 3 of C. carpio var. wuyuanensis♀×8 of C. carpio var. mirror♂) were evaluated for genetic diversity and inheritance characteristics by 21 microsatellites loci, and examined several properties of microsatellites which could be considered to affect the accuracy of loci in parentage assignment. Finally, 13 suitability loci were obtained for parentage assignment, and performance of them showed that: (1) These 13 screened loci were high polymorphic. Mean number of alleles (K), mean expected heterozygosity (He), mean observed heterozygosity (Ho) and mean polymorphic information content (PIC) were respectively 0.505, 0.648, 0.791 and 0.5889 in the 49 full-sib families and 0.548, 0.670, 0.819 and 0.6138 in the 24 full-sib families. (2) 13 screened loci were of high discriminatory power. The combined exclusion probability (CPE) was 0.999997978 in the 49 full-sib families and 0.999999583 in the 24 full-sib families. (3) High efficiency of the loci subset was obtained. The CPE of 4 core microsatellite loci (MFW29, HLJ392, HLJ044 and HLJ855) could be accurate to more than 99% in the two cross-breeding groups.(4) Combined non-exclusion probabilities when the first parent was available (NE-1P), the second parent was available (NE-2P) and parent pairs were available (NE-PP) were respectively 1.34E-02, 3.91E-04 and 2.02E-06 in the 49 full-sib families, and were respectively 1.34E-02, 3.91E-04 and 2.02E-06 in the 24 full-sib families. (5) The simulations with 99% confidence indicated that 100% offspring of 49 full-sib families could be assigned to a parent pair using the 11 most polymorphic loci or more loci, 99% offspring of 24 full-sib families could be assigned to a parent pair using the best 9 or more loci. (6) The distance-based method of cluster analysis showed that: the set of 13 loci could clearly distinguished between the offspring of cross-breeding and the unrelated family in the polyculture. Based on these results, a suitable microsatellite-based tool for parentage assignment in cross-breeding carp is obtained, and displays a reliability and high efficacy alternative to physical tagging in subsequently selecting program.
