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Isolation and characterization of 66 SNP markers in blotched snakehead (Channa maculata) using 2b-RAD sequencing

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Abstract

Blotched snakehead (Channa maculata) is an economically important aquaculture species in China and Southeast Asia, but wild blotched snakehead resources have declined sharply in recent years because of its overexploitation and habitat destruction. Thus, it is very urgent to develop genetic markers of blotched snakehead to investigate the natural resources. In this study, a total of 66 novel single nucleotide polymorphism (SNP) markers were developed based on 2b-RAD simplified genome sequencing. The results showed that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.130 to 0.667 and 0.112 to 0.502, respectively. The PIC ranged from 0.116 to 0.375. Two loci showed significant deviations from the HWE after Bonferroni correction (p < 0.05). These SNP markers will serve as a valuable tool for population genetic analysis, natural resource conservation and selective breeding of this blotched snakehead.

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Acknowledgements

This study was support by grants from the by China agriculture Research System (CARS-46), Central Public-interest Scientific Institution Basal Research Fund, CAFS (2020TD34, 2023TD37, 2021SJ-XT1, 2021SJ-XT2), Science and Technology Plan Project of Guangzhou (202102021070), Guangdong Agricultural Research System (2022KJ150), National Freshwater Genetic Resource Center (NFGR-2020) and Natural Science Foundation of Guangdong Province (2021A1515012075). We would like to thank all colleagues in our lab for sample preparation and laboratory technical assistance. We would like to thank all colleagues and postgraduate students in our lab for sample collection and laboratory technical assistance.

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Authors and Affiliations

  1. College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China

    Lan Liu & Weiwei Xia

  2. Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China

    Lan Liu, Haiyang Liu, Weiwei Xia, Kunci Chen, Qing Luo, Mi Ou & Jian Zhao

Authors
  1. Lan Liu
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  2. Haiyang Liu
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  3. Weiwei Xia
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  4. Kunci Chen
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  5. Qing Luo
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  6. Mi Ou
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  7. Jian Zhao
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Contributions

Jian Zhao conceived and guided the experiments; Lan Liu and Haiyang Liu carried out the experiments, performed bioinformatics analysis and wrote the manuscript; Weiwei Xia, Kunci Chen, Qing Luo and Mi Ou provided help in collecting samples. All authors reviewed and approved the final manuscript.

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Correspondence to Haiyang Liu or Jian Zhao.

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Liu, L., Liu, H., Xia, W. et al. Isolation and characterization of 66 SNP markers in blotched snakehead (Channa maculata) using 2b-RAD sequencing. Conservation Genet Resour 15, 215–220 (2023). https://doi.org/10.1007/s12686-023-01319-1

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