Genome-wide assessment and characterization of simple sequence repeats (SSRs) makers for Capoeta aculeata (Valenciennes, 1844) using NGS data
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Abstract
The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater endemic species of Iran. However, investigation of the population genetic structure of this species is limited by the low number of molecular markers currently described. In this study, next-generation sequencing technology was implemented to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. Sixty individuals from three populations occurring in the Zagros basin were sequenced. A total of 36 novel polymorphic microsatellite markers were characterized and developed, and these loci were examined in 120 individuals from the same 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 SSR loci varied from 0.254 to 0.888. The observed heterozygosity (Ho) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (He) per locus ranged 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). These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeata populations and other closely related species.
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