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Isolation and characterization of 48 SNP markers of sleepy cod, Oxyeleotris lineolata by whole-genome resequencing

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Abstract

The sleepy cod Oxyeleotris lineolata is native to northern Australia. At present, there is little information on the genome information of the sleepy cod. In this study, a total of 48 novel single nucleotide polymorphism (SNP) markers were developed based on whole-genome resequencing. The analysis of the 48 SNP genotypes in 58 fish showed that the observed heterozygosity and expected heterozygosity ranged from 0.3030 to 0.6667 and 0.2133 to 0.8541, respectively. The minor allele frequency ranged from 0.1211 to 0.4899, and the polymorphism information content ranged from 0.1902 to 0.3749. Among these SNPs, seven SNPs were found to deviate from Hardy–Weinberg equilibrium significantly (P < 0.05). These SNP markers could find application in genetic linkage maps and association analysis with growth traits of sleepy cod.

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Acknowledgements

This work was supported by the Science and Technology Program of Guangzhou, China (202201010745), Guangdong Provincial Special Fund for Modern Agriculture Industry Technology Innovation Teams (2023KJ150) and Central Public-interest Scientific Institution Basal Research Fund, CAFS (2023TD37).

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Authors and Affiliations

  1. Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No 1 Xingyu Road, Liwan District, 510380, Guangzhou, Guangdong Province, China

    Jiajia Fan, Dongmei Ma, Huaping Zhu, Minghui Lin, Huanhuan Su & Zaixuan Zhong

  2. Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, Guangdong Province, 510380, China

    Jiajia Fan, Dongmei Ma, Huaping Zhu, Minghui Lin, Huanhuan Su & Zaixuan Zhong

Authors
  1. Jiajia Fan
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  2. Dongmei Ma
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  3. Huaping Zhu
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  4. Minghui Lin
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  5. Huanhuan Su
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  6. Zaixuan Zhong
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Contributions

Dongmei Ma designed the study. Jiajia Fan wrote the final draft of the manuscript. All authors reviewed the manuscript.

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Correspondence to Dongmei Ma.

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The authors declare no competing interests.

Ethics statement

In this study, all experiments were conducted in accordance with the recommendations in the Guide for the Care and Use of Laboratory animals of Pearl River Fishery Research Institute. And this study was approved by the Committee on the Ethics of Animal Experiments of Pearl River Fishery Research Institute.

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Fan, J., Ma, D., Zhu, H. et al. Isolation and characterization of 48 SNP markers of sleepy cod, Oxyeleotris lineolata by whole-genome resequencing. Conservation Genet Resour 16, 73–78 (2024). https://doi.org/10.1007/s12686-023-01334-2

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  • DOI: https://doi.org/10.1007/s12686-023-01334-2

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