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

Research output: Contribution to journalArticlepeer-review

39 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)565-76
Number of pages12
JournalTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Issue number3
StatePublished - Feb 2012


  • Base Sequence
  • Cluster Analysis
  • Computational Biology
  • Data Mining
  • Gene Library
  • Genomics/methods
  • Gossypium/genetics
  • Microsatellite Repeats/genetics
  • Molecular Sequence Data
  • Phenotype
  • Polymorphism, Genetic
  • Sequence Analysis, DNA

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't


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