Characterization of single nucleotide polymorphism markers for the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) based on RAD sequencing

We developed single nucleotide polymorphism (SNP) markers for the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) using restriction site-associated DNA sequencing (RAD-seq) genotyping on the Illumina HiSeq4000 platform. In total, we sequenced 44 individuals from seven populations occurring in the Caspian Sea basin. Of the 86 SNP loci, 43 loci were found to be polymorphic and bi-allelic. The minor allele frequency (MAF) of these SNPs varied from 0.112 to 0.444. The observed heterozygosity per locus ranged from 0.165 to 0.603, while the expected heterozygosity per locus was from 0.202 to 0.506. Among these SNP loci, 14 loci deviated significantly from the Hardy–Weinberg equilibrium after Bonferroni correction ( p < 0.05).These SNP markers provide a valuable resource for future population genomics and conservation genetics in the narrow-clawed crayfish.