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Development and characterization of 26 SNP markers in Ochetobius elongatus based on restriction site-associated DNA sequencing (RAD-seq)

  • Jiping Yang
  • Yuefei Li
  • Shuli Zhu
  • Weitao Chen
  • Jie Li
  • Huimin Xue
  • Xinhui LiEmail author
Technical Note

Abstract

Ochetobius elongatus (Cyprinidae, Leuciscinae) was once an endemic species and widely distributed in numbers of rivers throughout South China. Nevertheless, the wild population of O. elongatus reduced dramatically in recent years due to anthropogenic impacts and it has been listed as a critically endangered species by IUCN. In this study, 26 novel single nucleotide polymorphism (SNP) markers were developed based on Restriction-site associated DNA sequencing. The results showed that the minor allele frequency varied from 0.071 to 0.500, the observed heterozygosity and expected heterozygosity ranged from 0.093 to 0.964 and 0.133 to 0.505, respectively. The PIC ranged from 0.124 to 0.375. Six loci showed significant deviations from the HWE after Bonferroni correction (p < 0.05), but no significant linkage disequilibrium was found. These SNP markers will provide valuable information for future population and conservation genetics of this germplasm resource.

Keywords

Conservation genetics Ochetobius elongates SNP marker RAD-seq 

Notes

Acknowledgements

This work was supported by The Public Sector (agriculture) Special Scientific Research Projects (201303048) and Central Public-interest Scientific Institution Basal Research Fund, CAFS (2017HY-ZD0103).

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Jiping Yang
    • 1
  • Yuefei Li
    • 1
  • Shuli Zhu
    • 1
  • Weitao Chen
    • 1
  • Jie Li
    • 1
  • Huimin Xue
    • 1
    • 2
  • Xinhui Li
    • 1
    Email author
  1. 1.Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
  2. 2.College of Marine SciencesShanghai Ocean UniversityShanghaiChina

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