Establishment and population genetic analysis of SNP fingerprinting of Chinese soft-shelled turtle (Pelodiscus sinensis)

Chinese soft-shelled turtle ( Pelodiscus sinensis ) is an important aquaculture species in China. However, with the continuous development of P. sinensis cultures, problems related to germplasm degradation and population mixing have become increasingly prominent. This has seriously affected the protection and utilization of germplasm resources by P. sinensis . To broaden the understanding of the germplasm resources of P. sinensis and improve the efficiency of germplasm identification, Super-GBS sequencing technology was used to conduct population genetic analysis of P. sinensis samples from six different populations distributed in five provinces. As a result, 1464,488 SNPs were identified. Genetic structure analysis revealed that the six P. sinensis populations could be divided into three sub-populations. The genetic differentiation coefficient of the DT and CY populations was very low (Fst=0.0088), indicating that differentiation had not yet occurred. Additionally, 15 KASP core markers for the identification of P. sinensis populations were developed using KASP typing technique for the first time. Genetic information can lay a foundation for the protection and utilization of germplasm resources by P. sinensis , and the fingerprinting database developed in this study provides a practical tool for authenticating P. sinensis . • The genetic differences and species identification of 6 populations of P.sinensis were analyzed based on large-scale genome-wide genotyping. • The 6 populations of P.sinensis were divided into 3 subgroups. • We identified 15 SNP loci for P. sinensis germplasm identification, converted them into KASP markers, and created SNP fingerprinting maps.