Isolation and characterization of 41 SNP markers in Coilia nasus

Abstract

Coilia nasus is an important economic fish species in China due to its excellent meat quality and wonderful flavor. The germplasm resources of C. nasus have recently been seriously degraded by human activities. It is urgent to develop the genetic markers of C. nasus in order to apply to conservation of this species. In this study, we used C. nasus transcriptomic data from GENBANK to identify single nucleotide polymorphism (SNP) markers for this species. From 148,156 unigenes with functional annotations, 85,454 putative SNPs were identified. Forty-one of the 61 SNP loci (including 31 loci that were associated with osmoregulation-related genes and 10 loci associated with other functions) were successfully validated and showed bi-allelic polymorphism in three rivers. Nine, six and eleven of these SNP loci deviated significantly from Hardy–Weinberg equilibrium (P < 0.05) in Yangtze River, Yellow River and Huai River. The average observed and expected heterozygosities ranged from 0.136827 to 0.289015, and 0.148122 to 0.314441 in three rivers, respectively. The SNP markers identified here will be useful in population conservation and management, construction of genetic linkage maps, and in molecular breeding of C. nasus.