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Genetic variation and population structure of endemic yellow catfish, Horabagrus brachysoma (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers

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Abstract

Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic and endangered yellow catfish, Horabagrus brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy and Nethravathi River systems. Of the 124 total RAPD fragments amplified, 49 (39.51%) were found to be shared by individuals of all 3 populations. The remaining 75 fragments were found to be polymorphic (60.48%). In microsatellites, six polymorphic microsatellite loci were identified by using primers developed for Pangasius hypophthalmus, Clarias macrocephalus and Clarias gariepinus. The identified loci were confirmed as microsatellite by sequencing after making a clone. The nucleotide sequences of 6 loci were published in NCBI genbank. The number of alleles across the six loci ranged from 4 to 7 and heterozygosities ranged from 0.07 to 0.93. The mean number of alleles and effective number of alleles per locus were 5.00 and 3.314, respectively. The average heterozygosity across all investigated samples was 0.72, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods reported a high degree of gene diversity and genetic distances depicted by UPGMA dendrograms among the populations of H. brachysoma.

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Acknowledgments

Indian Council of Agricultural Research-National Agricultural Technology Project (ICAR-NATP), which supported this study financially, is gratefully acknowledged. The authors are grateful to Dr. A. G. Ponniah and D. Kapoor (former Directors, NBFGR) and Dr. S. P. Singh (PI, NATP, NBFGR) for encouragement, support and guidance.

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Authors and Affiliations

  1. National Bureau of Fish Genetic Resources (NBFGR) Cochin Unit, CMFRI Campus, Cochin, Kerala, 682 018, India

    P. M. Abdul Muneer, A. Gopalakrishnan, K. K. Musammilu & V. S. Basheer

  2. Molecular Biology and Genetic Engineering Research Unit, School of Biosciences, Mar Athanasios College for Advanced Studies (MACFAST), Thiruvalla, Kerala, India

    P. M. Abdul Muneer

  3. NBFGR, Canal Ring Road, P.O. Dilkusha, Lucknow, Utter Pradesh, 226002, India

    Vindhya Mohindra, K. K. Lal & W. S. Lakra

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  1. P. M. Abdul Muneer
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Abdul Muneer, P.M., Gopalakrishnan, A., Musammilu, K.K. et al. Genetic variation and population structure of endemic yellow catfish, Horabagrus brachysoma (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers. Mol Biol Rep 36, 1779–1791 (2009). https://doi.org/10.1007/s11033-008-9381-6

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