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

Habibollah Gandomkar,Seyed Pezhman Hosseini Shekarabi,Mehdi Shamsaie Mehrgan,Hossein Ali Abdolhay,Sajad Nazari

doi:10.1007/s11033-021-06653-x

Abstract

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. 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 (HO) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (HE) 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). These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate and other closely related species.

Highlights

The genus Capoeta is a herbivorous cyprinid genus and highly diversified with 14 species and widely distributed in water bodies of Western Iran
The results showed that, the polymorphism information content (PCI) of these Simple sequence repeat (SSR) loci varied from 0.254 to 0.888
For non-model organisms, microsatellite loci were generally identified by 5̕ anchor polymerase chain reaction (PCR) (Ling et al 2013), transcriptome sequence analysis (Ariede et al 2018; Han et al 2018), and microsatellite library screening (Bazsalovicsová et al 2018) and development of microsatellite loci through cross-species amplification of closely related species (Gravley et al 2018)

Summary

Introduction

The genus Capoeta is a herbivorous cyprinid genus and highly diversified with 14 species and widely distributed in water bodies of Western Iran. Kohgiluyeh and Boyer-Ahmad Province in the southwest part of Iran is a region with high number of endemism in some freshwater fish species including Capoeta aculeata (Valenciennes, 1844) (Zareian et al, 2016). Populations of this species have experienced significant declines over the last 20 years, due primarily to habitat loss and fragmentation caused by water storage and land clearing. Microsatellite loci have not been reported in this species (Gandomkar et al, 2020)

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Conclusion