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Development of SNP in spotted steed (Hemibarbus maculatus Bleeker) using GBS sequencing

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Abstract

Spotted steed (Hemibarbus maculatus) is a native freshwater fish widely distributed in China, but data regarding its genetic markers are scarce. In this study, we used genotyping by sequencing (GBS) to develop single nucleotide polymorphisms (SNPs) from 56 individuals. We discovered a total of 57,523 genome-wide SNP markers. After applying strict filtering criteria, 166 high-qualified SNPs were obtained. Among these SNPs markers, 42 polymorphic markers were identified and characterized. The observed and expected heterozygosity ranged from 0.063 to 0.479 and 0.100 to 0.500, respectively. Polymorphic information content ranged from 0.094 to 0.372. Among these markers, no loci were significantly deviated from Hardy–Weinberg equilibrium. This study indicated that GBS sequencing allowed fast and efficient isolation of SNPs, and these results could provide a useful resource in further population genetic studies and genetic mapping in spotted steed.

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Acknowledgements

This work was supported by the Innovation Scientists and Technicians Troop Construction Projects of Henan Province (Grant no. CXTD2016043), and Henan Science and Technology Program (182102110383).

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Authors and Affiliations

  1. College of Fisheries, Henan Normal University, Xinxiang, 453007, People’s Republic of China

    Liu Huifen, Wang Jing, Zhang Limin, Fang Fugui, Zhang Meng, Ma Xiao, Tian Xue, Li Xuejun & Nie Guoxing

  2. College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People’s Republic of China

    Liu Huifen, Wang Jing, Zhang Limin, Zhang Meng, Ma Xiao, Tian Xue, Li Xuejun & Nie Guoxing

Authors
  1. Liu Huifen
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  2. Wang Jing
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  3. Zhang Limin
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  4. Fang Fugui
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  5. Zhang Meng
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  6. Ma Xiao
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  7. Tian Xue
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  8. Li Xuejun
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  9. Nie Guoxing
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Corresponding authors

Correspondence to Li Xuejun or Nie Guoxing.

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Huifen, L., Jing, W., Limin, Z. et al. Development of SNP in spotted steed (Hemibarbus maculatus Bleeker) using GBS sequencing. Conservation Genet Resour 12, 379–383 (2020). https://doi.org/10.1007/s12686-019-01123-w

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  • DOI: https://doi.org/10.1007/s12686-019-01123-w

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