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Molecular Biology Reports

, Volume 39, Issue 5, pp 5921–5931 | Cite as

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

  • Vindhya Mohindra
  • Akanksha Singh
  • A. S. Barman
  • Ratnesh Tripathi
  • Neeraj Sood
  • Kuldeep K. Lal
Article

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.

Keywords

Indian catfish Clarias batrachus Spleen cDNA library Expressed sequence tags Type I microsatellite Single nucleotide polymorphism 

Notes

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.

Supplementary material

11033_2011_1404_MOESM1_ESM.pdf (221 kb)
Supplementary material 1 (PDF 220 kb)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Vindhya Mohindra
    • 1
  • Akanksha Singh
    • 1
  • A. S. Barman
    • 1
  • Ratnesh Tripathi
    • 1
  • Neeraj Sood
    • 1
  • Kuldeep K. Lal
    • 1
  1. 1.National Bureau of Fish Genetic ResourcesLucknowIndia

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