Development of SNP markers for Xenocypris argentea based on transcriptomics

Xenocypris argentea is a cyprinid fish species and widely distributed in rivers and lakes within China. The germplasm resources of X. argentea have recently been seriously degraded by human activities. Thus, the development of sufficient molecular markers to inform conservation efforts of X. argentea is urgently needed. In this study, we used Illumina HiSeq high-throughput sequencing of X. argentea transcriptomic data to identify single nucleotide polymorphism (SNP) markers for X. argentea. From 43,346 unigenes with functional annotations, 462,621 putative SNPs were identified. Among these, we validated 32 polymorphic loci of 40 function-related SNPs from a Poyang Lake population of X. argentea. Six of these SNP loci deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). Observed and expected heterozygosities ranged from 0.0645 to 0.5806, and 0.0635 to 0.5062, respectively. The SNP markers identified here will be useful in population conservation and management, construction of genetic linkage maps, and in molecular breeding of X. argentea.