Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844)

Abstract

Background: The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of the population genetic structure of this species is limited by the low number of molecular markers currently described.

Methods and results: In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16 (average = 7.89). The results showed that, the polymorphism information content (PIC) of these simple sequence repeat (SSR) loci varied from 0.254 to 0.888. The observed heterozygosity (H_O) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (H_E) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05).

Conclusions: These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate and other closely related species.

Keywords: Capoeta aculeata; Genetic structure; Microsatellite markers; Next generation sequencing (NGS).