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Identification and characterization of 76 SNP markers in the large-scale loach (Paramisgurnus dabryanus) by using SLAF sequencing

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Abstract

The large-scale loach, Paramisgurnus dabryanus, is a commercially important fish species in East Asia. However, little is known about the genetics of this species. In this study, a total of 715,539 putative single nucleotide polymorphism (SNP) loci from 157,274 sequences were identified using specific-locus amplified fragment sequencing with eight P. dabryanus specimens. Thirty-six SLAF sequences were randomly selected for the verification of SNP loci with 32 fin clips of P. dabryanus, and 76 SNP loci were identified from 22 SLAF sequences. The minor allele frequency, observed heterozygosity, expected heterozygosity, and polymorphic information content of these SNP loci ranged from 0.047 to 0.500, 0.094 to 0.969, 0.091 to 0.510, and 0.085 to 0.411, respectively. Ten loci deviated significantly from the Hardy–Weinberg equilibrium (P < 0.05). The novel SNP loci identified and validated in this study will serve as valuable genomic resources for P. dabryanus.

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Fig. 1

Data availability

The sequencing raw data of SLAF-seq have been submitted to the Sequence Read Archive (SRA) database of NCBI with the accession code: PRJNA739518 (Release data: 2022-06-20).

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Funding

This study was supported by the Open Fund of Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs (No. FBB2020-02).

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Authors and Affiliations

  1. Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China

    Jianjun Fu, Wenbin Zhu, Lanmei Wang, Mingkun Luo & Zaijie Dong

  2. Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China

    Shunpeng Wan

  3. Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China

    Xianhu Zheng

Authors
  1. Jianjun Fu
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  2. Shunpeng Wan
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  3. Wenbin Zhu
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  4. Lanmei Wang
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  5. Mingkun Luo
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  6. Xianhu Zheng
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  7. Zaijie Dong
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Corresponding authors

Correspondence to Xianhu Zheng or Zaijie Dong.

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Fu, J., Wan, S., Zhu, W. et al. Identification and characterization of 76 SNP markers in the large-scale loach (Paramisgurnus dabryanus) by using SLAF sequencing. Conservation Genet Resour 14, 137–141 (2022). https://doi.org/10.1007/s12686-021-01251-2

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  • DOI: https://doi.org/10.1007/s12686-021-01251-2

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