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Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.)

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Abstract

Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.

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Acknowledgments

The present work was financially supported by the Council of Scientific and Industrial Research, New Delhi (CSIR under NMITLI, SIP 005).

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Authors and Affiliations

  1. Plant Molecular Biology and Genetic Engineering Laboratory, National Botanical Research Institute, Rana Pratap Marg, Lucknow, India

    Satya Narayan Jena, Anukool Srivastava, Krishan Mohan Rai, Alok Ranjan, Sunil K. Singh, Tarannum Nisar, Meenal Srivastava, Sumit K. Bag, Mehar Hasan Asif, Hemant Kumar Yadav & Samir V. Sawant

  2. National Agri-Food Biotechnology Institute, Mohali, Punjab, India

    Shrikant Mantri & Rakesh Tuli

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  1. Satya Narayan Jena
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  2. Anukool Srivastava
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  3. Krishan Mohan Rai
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  5. Sunil K. Singh
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Correspondence to Samir V. Sawant.

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Communicated by P. Heslop-Harrison.

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Jena, S.N., Srivastava, A., Rai, K.M. et al. Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.). Theor Appl Genet 124, 565–576 (2012). https://doi.org/10.1007/s00122-011-1729-y

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