SNP discovery in spotted halibut (Verasper variegatus) using restriction site-associated DNA sequencing(RAD-seq)

Abstract

The spotted halibut (Verasper variegatus) is an important economic marine flatfish species in China and Japan. However, the wild population of V. variegatus has suffered a drastic decline in recent years. We implemented restriction site-associated DNA sequencing(RAD-seq) to develop SNP markers from 36 individuals. In total, 100 high quality SNPs were obtained after a stringent SNP filter process. The minor allele frequency of these SNPs ranged from 0.0455 to 0.5000. The range of observed heterozygosity and expected heterozygosity were from 0.0909 to 1.0000 and from 0.0881 to 0.5077, respectively. The inbreeding coefficient varied from −1.000 to 0.220. Among these SNPs, 16 loci deviated significantly from Hardy–Weinberg equilibrium after Bonferroni correction. These novel SNP markers will serve as a valuable tool for future population and conservation genetics studies for this species.