Identification and characterization of 76 SNP markers in the large-scale loach (Paramisgurnus dabryanus) by using SLAF sequencing

The large-scale loach, Paramisgurnus dabryanus , is a commercially important fish species in East Asia. However, little is known about the genetics of this species. In this study, a total of 715,539 putative single nucleotide polymorphism (SNP) loci from 157,274 sequences were identified using specific-locus amplified fragment sequencing with eight P. dabryanus specimens. Thirty-six SLAF sequences were randomly selected for the verification of SNP loci with 32 fin clips of P. dabryanus , and 76 SNP loci were identified from 22 SLAF sequences. The minor allele frequency, observed heterozygosity, expected heterozygosity, and polymorphic information content of these SNP loci ranged from 0.047 to 0.500, 0.094 to 0.969, 0.091 to 0.510, and 0.085 to 0.411, respectively. Ten loci deviated significantly from the Hardy–Weinberg equilibrium ( P < 0.05). The novel SNP loci identified and validated in this study will serve as valuable genomic resources for P. dabryanus .