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Identification of novel Est-ssr markers by transcriptome sequencing in ridgetail white prawn Exopalaemon carinicauda

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Abstract

The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of 14273 SSR loci were identified from 130,082 assembled transcripts, with 6590 pairs of PCR primers designed. A total of 12,155 sequences containing SSR were predicted; and 2764 (22.74%) transcripts had significant matches to the NCBI non redundant protein (Nr) database. 11,563 transcripts were assigned into gene ontology (GO) categories. A set of 200 primers selected randomly were synthesized, of which 152 (76.0%) were successfully amplified. Further test with 60 pairs of polymorphic SSR primers to evaluate the genetic diversity of 30 wild populations and 43 loci were polymorphic, which had a polymorphic information content between 0.204 and 0.911. The results enriched genomic resources of E. carinicauda and provided powerful information for future conservation and breeding researches.

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Acknowledgements

This project was financially supported by the earmarked fund for Modern Agro-industry Technology Research System (No. CARS-48), The Program of Shandong Leading Talent (No. LNJY2015002), National Natural Science Foundation of China (No. 31472275) and Qingdao Industrial Development Program Science and Technology Benefit Special Project (17-3-3-62-nsh).

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Authors and Affiliations

  1. Fisheries College, Ocean University of China, Qingdao, 266003, People’s Republic of China

    Jiajia Wang

  2. Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People’s Republic of China

    Jiajia Wang, Qianqian Ge, Jitao Li, Haiyu Gao, Jian Li & Fazhen Zhao

  3. Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People’s Republic of China

    Jian Li & Fazhen Zhao

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  1. Jiajia Wang
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  2. Qianqian Ge
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  3. Jitao Li
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  4. Haiyu Gao
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  5. Jian Li
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Correspondence to Jian Li.

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Conflict of interest

Jiajia Wang declares that he/she does not have conflict of interests. Qianqian Ge declares that he/she does not have conflict of interests. Jitao Li declares that he/she does not have conflict of interests. Haiyu Gao declares that he/she does not have conflict of interests. Jian Li declares that he/she does not have conflict of interests. Fazhen Zhao declares that he/she does not have conflict of interests.

Ethical approval

This article does not contain any studies with human participants performed by any of the authors. The study protocol was approved by the Experimental Animal Ethics Committee, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, China.

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Wang, J., Ge, Q., Li, J. et al. Identification of novel Est-ssr markers by transcriptome sequencing in ridgetail white prawn Exopalaemon carinicauda . Genes Genom 40, 207–215 (2018). https://doi.org/10.1007/s13258-017-0571-2

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  • DOI: https://doi.org/10.1007/s13258-017-0571-2

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