Isolation and characterization of gene-derived single nucleotide polymorphism (SNP) markers in Scylla paramamosain

Abstract

Single nucleotide polymorphisms (SNPs) are thought to be well suitable for genetic and evolutionary studies. In this study, we reported the first set of SNP markers in a commercially important crab species, Scylla paramamosain . A total of 12,500 base pairs high quality DNA sequences were obtained from 15 genes, and thirty-seven SNPs were identified, representing one SNP every 338 base pairs. Twenty-four SNPs were successfully genotyped in a single population. All loci had two alleles and the minor allele frequency ranged from 0.02 to 0.44. The observed and expected heterozygosity ranged from 0.04 to 0.59 and from 0.04 to 0.50, respectively. No significant departures from Hardy–Weinberg equilibrium at each locus was found. The linkage disequilibrium was detected in six loci pairs, but absent after sequential Bonferroni correction. These SNP markers will provide a useful addition to the genetic tools for genetic and evolutionary studies for S. paramamosain . ► We isolated and characterized the first set of SNPs in Scylla paramamosain . ► Thirty-seven SNPs were identified, of which twenty-four were genotyped successfully using SNaPshot. ► The total level of polymorphism of these SNP loci was relative low. ► No significant departures from HWE and no significant LD were found.