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Characterization of single nucleotide polymorphism markers for the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) based on RAD sequencing

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Abstract

We developed single nucleotide polymorphism (SNP) markers for the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) using restriction site-associated DNA sequencing (RAD-seq) genotyping on the Illumina HiSeq4000 platform. In total, we sequenced 44 individuals from seven populations occurring in the Caspian Sea basin. Of the 86 SNP loci, 43 loci were found to be polymorphic and bi-allelic. The minor allele frequency (MAF) of these SNPs varied from 0.112 to 0.444. The observed heterozygosity per locus ranged from 0.165 to 0.603, while the expected heterozygosity per locus was from 0.202 to 0.506. Among these SNP loci, 14 loci deviated significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (p < 0.05).These SNP markers provide a valuable resource for future population genomics and conservation genetics in the narrow-clawed crayfish.

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Acknowledgements

This project was supported by Grants from the Iran National Science Foundation (INSF) (Contract No. 89004480).

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Authors and Affiliations

  1. Department of Fisheries, School of Natural Resources, University of Guilan, P.O. Box 1144, Sowmehsara, Iran

    Majidreza Khoshkholgh

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

    Sajad Nazari

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  1. Majidreza Khoshkholgh
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  2. Sajad Nazari
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Correspondence to Majidreza Khoshkholgh.

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Khoshkholgh, M., Nazari, S. Characterization of single nucleotide polymorphism markers for the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) based on RAD sequencing. Conservation Genet Resour 12, 549–553 (2020). https://doi.org/10.1007/s12686-020-01154-8

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