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

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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 (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).

Conclusions

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

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Data availability

The datasets generated are available from the corresponding author upon request.

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Acknowledgements

This work was supported by the Research Fund for the department of Fisheries of the Islamic Azad University of Tehran, Iran.

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Authors and Affiliations

  1. Department of Fisheries, Science and Research Branch, Islamic Azad University, Tehran, Iran

    Habibollah Gandomkar, Seyed Pezhman Hosseini Shekarabi & Mehdi Shamsaie Mehrgan

  2. Agricultural Research, Education and Extension Organization (AREEO), Iranian Fisheries Sciences Research Institute, Tehran, Iran

    Hossein Ali Abdolhay

  3. Agricultural Research, Education and Extension Organization (AREEO), Shahid Motahary Cold-Water Fishes Genetic and Breeding Research Center, Iranian Fisheries Sciences Research Institute, Yasouj, Iran

    Sajad Nazari

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  1. Habibollah Gandomkar
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  2. Seyed Pezhman Hosseini Shekarabi
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  3. Hossein Ali Abdolhay
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  5. Mehdi Shamsaie Mehrgan
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Contributions

HG made the literature, sample collection, material preparation. SPHS has major contribution to the preliminary study design and interpretation of data. The first draft of the manuscript was written by HAA. SN designed the experiment, institutional support and supervision of the preliminary experiment and made the data analysis. MSM has significant contributions to the laboratory work and interpretation of the results. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Seyed Pezhman Hosseini Shekarabi.

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The authors declare that they have no conflict of interest.

Ethical approval

The main research project researcher of this work was approved for animal ethics by Iranian Fisheries Sciences Research Institute (IFSRI) for scientific purposes development, Iran. All applicable guidelines for the care and use of animals were followed by the authors. The experiment was approved for Animal Welfare by the Institutional Animal Welfare Committee of Agricultural Research, Education and Extension Organization (AREEO), Iran.

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Gandomkar, H., Shekarabi, S.P.H., Abdolhay, H.A. et al. Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844). Mol Biol Rep 48, 6471–6480 (2021). https://doi.org/10.1007/s11033-021-06653-x

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