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Development of EST derived SSRs and SNPs as a genomic resource in Indian catfish, Clarias batrachus

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Abstract

Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential cultivable species. The genomic resources in C. batrachus in the form of ESTs containing microsatellite repeats (EST-SSR) and single nucleotide polymorphisms (SNPs) that are associated with the expressed genes from spleen were mined. From a total of 1,937 ESTs generated, 1,698 unique sequences were obtained, out of which 221 EST-SSRs were identified and 54% could be functionally annotated by similarity searches. A total of 23 contigs containing 3 or more ESTs were found to contain 31 SNP loci, out of which 8 ESTs showed similarity to genes of known function and 1 for hypothetical protein. Nine ESTs with SSRs and/or SNPs identified in this study were reported to be associated with diseases in human and animals. These identified loci can be developed into markers in C. batrachus, which can be useful in linkage mapping, comparative genomics studies and for its genetic improvement programmes.

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Acknowledgments

Financial support received from the Department of Biotechnology, Government of India, for this study is thankfully acknowledged. Excellent technical assistance provided by Mr. R. S. Sah, Mr. Rajesh Kumar and Mr. Sree Ram is duly acknowledged.

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Authors and Affiliations

  1. National Bureau of Fish Genetic Resources, Canal Ring Road, PO Dilkusha, Lucknow, 226 002, UP, India

    Vindhya Mohindra, Akanksha Singh, A. S. Barman, Ratnesh Tripathi, Neeraj Sood & Kuldeep K. Lal

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  1. Vindhya Mohindra
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  2. Akanksha Singh
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Correspondence to Vindhya Mohindra.

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Mohindra, V., Singh, A., Barman, A.S. et al. Development of EST derived SSRs and SNPs as a genomic resource in Indian catfish, Clarias batrachus . Mol Biol Rep 39, 5921–5931 (2012). https://doi.org/10.1007/s11033-011-1404-z

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  • DOI: https://doi.org/10.1007/s11033-011-1404-z

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