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Identification and characterization of SSRs in Clarias batrachus and their application in population study

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  • Biology
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Abstract

Magur Clarias batrachus is an indigenous catfish, commonly found in India, Nepal, Bhutan and Bangladesh. Presently, the populations of magur have declined rapidly in their natural habitat mainly due to overexploitation and habitat degradation. Understanding the population genetic structure of the species has significance in improvement of stocks and in conservation of the species. In the present study, simple sequence repeat (SSR) markers were used to differentiate the populations of magur, collected from three geographic locations. For this, a total of 31,814 SSRs were mined from the de novo assembled pooled of whole genome sequence data of C. batrachus. A bioinformatics pipeline with stringent criteria was applied to analyze the data which resulted in selection of 30,142 microsatellite loci falling in the intergenic region. Out of the 25 loci selected for primer development, 16 loci were successfully amplified and 9 loci were found to be polymorphic in this species. The average observed as well as expected heterozygosity in the loci across different stocks varied from 0.652 to 0.688 and 0.864 to 0.873, respectively. These three populations were further segregated into two clusters based on the NJ genetic distance. The Lucknow population formed one cluster, while the Bhubaneswar and Kolkata populations constituted another cluster. A comparable finding was also deduced from the STRUCTURE analyses. The results revealed significant variation among the populations of C. batrachus under study.

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Acknowledgements

Funding was provided by the Department of Biotechnology, New Delhi Government of India (grant no. BT/PR3688/AAQ/3/571/2011 dated 10.09.2013).

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Authors and Affiliations

  1. Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, 226 002, India

    Shreya Srivastava, Basdeo Kushwaha, Manmohan Pandey, Suyash Agarwal, Ravindra Kumar, Mahender Singh & Joy Krushna Jena

  2. AMITY Institute of Biotechnology, AMITY University, Lucknow Campus, Lucknow, Uttar Pradesh, 226 028, India

    Jyoti Prakash

  3. Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, Odisha, 751 002, India

    Paramananda Das

  4. Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India

    Chaitanya Joshi

  5. Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Mumbai, 400 061, India

    N. S. Nagpure

Authors
  1. Shreya Srivastava
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  2. Basdeo Kushwaha
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  3. Jyoti Prakash
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  9. Paramananda Das
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Correspondence to Basdeo Kushwaha.

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Srivastava, S., Kushwaha, B., Prakash, J. et al. Identification and characterization of SSRs in Clarias batrachus and their application in population study. Fish Sci 83, 265–272 (2017). https://doi.org/10.1007/s12562-017-1066-4

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  • DOI: https://doi.org/10.1007/s12562-017-1066-4

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