Population structure of Caspian Kutum (Rutilus frisii, Nordmann, 1840) in the southern coast of Caspian Sea using Genome-wide single nucleotide polymorphism markers

The Caspian kutum (Rutilus frisii, Nordmann, 1840) is one of the most important semi-anadromous endemic fish species in the southern part of the Caspian Sea. The fisheries from wild populations of R. frisii are declined drastically due to variability of sea levels, overfishing, and illegal fishing. For this regard, genetic studies is very noticed to maintain of remained this endangered species. Here, we used restriction site-associated DNA sequencing (RAD-seq) approach to explore population structure, genetic variability, and single nucleotide polymorphisms (SNPs) from 146 individuals from eight rivers in Iran. In total 86,274 SNP loci were determined, and after filtering, 16,193 high-quality SNP markers were applied in statistical analyses. Twenty-eight percent of selected SNPs were located in genic regions and about 65% of these SNPs were in the coding sequence. Of the 102 SNP loci, 42 loci were found to be polymorphic and bi-allelic. The minor allele frequency (MAF) of these SNPs varied from 0.156 to 0.471. The observed heterozygosity (Ho) per locus ranged from 0.119 to 0.864, while the expected heterozygosity (He) per locus was from 0.142 to 0.569. Among these SNP loci, 22 SNP loci were significantly deviated from the Hardy–Weinberg equilibrium (P < 0.01) after Bonferroni correction. Both Principal coordinate analysis (PCA) and Bayesian clustering satisfyingly showed population genomic structure in Caspian kutum populations, indicating the description of distinct population segments. The first development of SNP markers in this study provides the better monitoring of population genetic variation in Caspian kutum at a more detailed level and in the scarce of genetic information about this species.