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Characterization of 36 insert/deletion mutations by STR genotyping method in grass carp, Ctenopharyngodon idella

  • Meng Zhang
  • Yubang Shen
  • Xiaoyan Xu
  • Rongquan Wang
  • Xiangjun Leng
  • Jiale LiEmail author
Technical Note
  • 21 Downloads

Abstract

Grass carp is one of the most important freshwater aquaculture fish in China. Though a few molecular markers had been reported, it was not enough for grass carp germplasm improvement and protection. In order to verify the effectiveness and practicability of insert/deletion mutations reported in grass carp genome, 85 insert/deletion mutations were randomly selected and analyzed. After simple sequence analysis and attempting primer design, 49 markers were removed due to being simple sequence repeats or unable to design primer for them. Finally, 36 insert/deletion mutations were successfully characterized by STR genotyping method in 32 wild grass carp (collected from Pearl River). The mean effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) were 1.4976, 0.3190, 0.2970 and 0.2349, respectively. Among all the 36 insert/deletion mutations, three deviated significantly from Hardy–Weinberg equilibrium (P < 0.05). In addition, three pairs of loci (ID-13F with ID-24H, ID-20F with ID-21H and ID-39F with ID-64H) had significant linkage disequilibrium (P < 0.05). Those insert/deletion mutations may lay the foundation for germplasm improvement and protection in grass carp.

Keywords

Insert/deletion Mutation STR Grass carp 

Notes

Acknowledgements

This study was supported by the China’s Agricultural Research System (Grant No. CARS-45-03), Project of Shanghai Engineering and Technology Center for Promoting Ability (Grant No. 16DZ2281200) and National Natural Science Foundation of China Youth Project (Grant No. 31802285).

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Meng Zhang
    • 1
  • Yubang Shen
    • 1
    • 2
    • 3
  • Xiaoyan Xu
    • 1
    • 2
    • 3
  • Rongquan Wang
    • 4
  • Xiangjun Leng
    • 1
    • 2
    • 3
  • Jiale Li
    • 1
    • 2
    • 3
    Email author
  1. 1.Key Laboratory of Freshwater Aquatic Genetic ResourcesMinistry of Agriculture, Shanghai Ocean UniversityShanghaiChina
  2. 2.Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
  3. 3.National Demonstration Center for Experimental Fisheries Science EducationShanghai Ocean UniversityShanghaiChina
  4. 4.Key Laboratory of Conventional Freshwater Fish Breeding and Health Culture Technology Germplasm ResourcesSuzhou Shenhang Eco-technology Development Limited CompanySuzhouChina

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