Genetic diversity and structural analysis of Chelydra serpentina based on whole genome resequencing

【Objective】The genetic diversity and genetic structure of the breeding population of Chelydra serpentina were analyzed from the whole genome level，and the germplasm resources of C. serpentina were evaluated，so as to provide reference for the development and utilization of germplasm resources of C. serpentina and promote the healthy development of the breeding industry of C. serpentina.【Method】A total of 30 C. serpentina were collected from Rongjie Turtle Breeding Professional Cooperative（RJ）in Huandao Town，Gaoyao City，Zhaoqing City，Ziyuan Turtle Breeding Professional Cooperative in Zhaoqing City（ZY）and Sihui Zhaoqing Shengke Agricultural Development Co.，Ltd. in Zhaoqing City（SK）respectively，and 90 samples from 3 C. serpentina groups were resequenced. Phylogenetic tree analysis and principal component analysis were conducted based on whole genome single nucleotide polymorphisms（SNP）to evaluate the genetic diversity and population genetic structure of cultured C. serpentina at the genome level.【Result】The results of cluster analysis based on morphological trait proportion parameters showed that the 3 groups were divided into 2 branches，SK group and RJ group were first clustered together，and then aggregated with ZY group. A total of 708112 SNPs loci were detected in the 3 groups，and 220950 high quality homozygous SNPs loci and 440435 high quality heterozygous SNPs loci were obtained after filtering. The single nucleotide density，single nucleotide polymorphism（π），polymorphism information content（PIC）and observed heterozygosity（H_o）of the 3 groups of C. serpentina were 0.01 SNP / kb，0.00166-0.00171，0.151-0.154 and 0.171-0.205. The inbreeding coefficient（F_HOM）ranged from 0.0571 to 0.1110. The coefficient of genetic differentiation（F_st）and gene flow（Nm）ranged from 0.0056 to 0.0138 and from -0.2486 to -0.2466. The phylogenetic tree constructed on the basis of the whole genome SNP showed that the 3 groups of C. serpentina could be divided into 2 branches as a whole. The first branch was mainly composed of RJ group and SK group，and the second branch was mainly composed of ZY group，which was basically consistent with the results of morphological cluster analysis. The principal component analysis also found that the distance between the 3 groups of C. serpentina was relatively close，and there was cross-over phenomenon.【Conclusion】The genetic polymorphism 3 groups of C. serpentina is low，the genetic background is not rich enough，and the degree of genetic differentiation between the groups is low，so it is presumed that they had similar genetic background and come from the same introduced population. Therefore，it is urgent to introduce new germplasm resources in future breeding work to provide a richer genetic basis for germplasm innovation.