Theoretical and Applied Genetics

, Volume 124, Issue 3, pp 565–576 | Cite as

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

  • Satya Narayan Jena
  • Anukool Srivastava
  • Krishan Mohan Rai
  • Alok Ranjan
  • Sunil K. Singh
  • Tarannum Nisar
  • Meenal Srivastava
  • Sumit K. Bag
  • Shrikant Mantri
  • Mehar Hasan Asif
  • Hemant Kumar Yadav
  • Rakesh Tuli
  • Samir V. Sawant
Original Paper

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.

Keywords

Simple Sequence Repeat Marker Polymorphism Information Content Repeat Motif Genomic SSRs Simple Sequence Repeat Motif 

Notes

Acknowledgments

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

Supplementary material

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Supplemental Table S1 (XLS 126 kb)
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Supplemental Table S2 (XLS 443 kb)
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Supplemental Table S3 (XLS 136 kb)
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Supplemental Fig. S4 (DOC 119 kb)
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Supplemental Table S5 (XLS 192 kb)
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Supplemental Fig. S6 (PPT 1101 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Satya Narayan Jena
    • 1
  • Anukool Srivastava
    • 1
  • Krishan Mohan Rai
    • 1
  • Alok Ranjan
    • 1
  • Sunil K. Singh
    • 1
  • Tarannum Nisar
    • 1
  • Meenal Srivastava
    • 1
  • Sumit K. Bag
    • 1
  • Shrikant Mantri
    • 2
  • Mehar Hasan Asif
    • 1
  • Hemant Kumar Yadav
    • 1
  • Rakesh Tuli
    • 2
  • Samir V. Sawant
    • 1
  1. 1.Plant Molecular Biology and Genetic Engineering LaboratoryNational Botanical Research InstituteLucknowIndia
  2. 2.National Agri-Food Biotechnology InstituteMohaliIndia

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