Development and characterization of 37 SNP markers in the ark shell Scapharca subcrenata using RAD sequencing and high resolution melting analysis

Abstract

The ark shell Scapharca subcrenata, an important fishery resource in Asian countries, has been suffering from severe population decline in recent years. To facilitate genetic conservation studies, novel single nucleotide polymorphisms (SNPs) markers were developed using next generation sequencing for this species, which yielded a total of 781,860 putative SNPs. To validate these markers, 96 SNP genotyping assays were designed to characterize polymorphisms using high resolution melting (HRM) analysis in 32 individuals from a wild population. As a result, 37 SNPs showed polymorphisms with MAF ranging from 0.0313 to 0.4844. The observed heterozygosity ranged from 0 to 0.8333, while the expected heterozygosity varied from 0.0605 to 0.4995. After the Bonferroni correction, 5 of the 37 loci showed significant departure from Hardy–Weinberg equilibrium. These novel SNP markers will be useful for future investigation of population structure and conservation genetics of the ark shell S. subcrenata.