Development and characterization of 40 SNP markers of endangered species Cuora flavomarginata by whole-genome resequencing

Abstract

Cuora flavomarginata is an endangered and protected species in China as well as listed as endangered under the criteria of the IUCN. Single nucleotide polymorphisms (SNPs) are an important component of animal genomic diversity, and are invaluable as genetic markers in the fields of evolutionary and conservation genetics. In this study, a total of 40 novel SNP markers were developed based on whole-genome resequencing. The analysis of the 40 SNP genotypes in 56 turtles showed that the observed heterozygosity and expected heterozygosity ranged from 0.1786 to 0.6071 and 0.1641 to 0.5043, respectively. The minor allele frequency ranged from 0.1161 to 0.911, and the polymorphism information content ranged from 0.252 to 0.455. Among these SNPs, only one SNP was found to deviate from Hardy-Weinberg equilibrium significantly after Bonferroni correction (P < 0.01). These SNP markers could be a valuable tool for genetic management and population conservation in this endangered species.