Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species

  • Ramesh K. Aggarwal
  • Prasad S. Hendre
  • Rajeev K. Varshney
  • Prasanna R. Bhat
  • V. Krishnakumar
  • Lalji Singh
Original Paper


Genic microsatellites or EST–SSRs derived from expressed sequence tags (ESTs) are desired because these are inexpensive to develop, represent transcribed genes, and often a putative function can be assigned to them. In this study we investigated 2,553 coffee ESTs (461 from the public domain and 2,092 in-house generated ESTs) for identification and development of genic microsatellite markers. Of these, 2,458 ESTs (all >100 bp in size) were searched for SSRs using MISA—search module followed by stackPACK clustering that revealed a total of 425 microsatellites in 331 (13.5%) non-redundant ESTs/consensus sequences suggesting an approximate frequency of 1 SSR/2.16 kb of the analysed coffee transcriptome. Identified microsatellites mainly comprised of di-/tri-nucleotide repeats, of which repeat motifs AG and AAG were the most abundant. A total of 224 primer pairs could be designed from the non-redundant SSR-positive ESTs (excluding those with only mononucleotide repeats) for possible use as potential genic markers. Of this set, a total of 24 (10%) primer pairs were tested and 18 could be validated as usable markers. Sixteen of these markers revealed moderate to high polymorphism information content (PIC) across 23 genotypes of C. arabica and C. canephora, while 2 markers were found to be monomorphic. All the markers also showed robust cross-species amplifications across 14 Coffea and 4 Psilanthus species. The apparent broad cross-species/genera transferability was further confirmed by cloning and sequencing of the amplified alleles. Thus, the study provides an insight about the frequency and distribution of SSRs in coffee transcriptome, and also demonstrates the successful development of genic-SSRs. It is expected that the potential markers described here would add to the repertoire of DNA markers needed for genetic studies in cultivated coffee and also related taxa that constitute the important secondary genepool for coffee improvement.


Simple Sequence Repeat Marker Polymorphism Information Content Genomic SSRs Simple Sequence Repeat Motif Coffea Species 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors thank the Department of Biotechnology, Government of India, New Delhi, India for the financial support to RKA, Director, CCMB, Hyderabad for the facilities to undertake the study, Dr R Naidu, Director Research, Coffee Board, Bangalore and Dr M. Udayakumar of University of Agricultural Sciences, Bangalore for the drought-stressed coffee leaf materials. PSH was supported by Senior Research Fellowship of Council of Scientific and Industrial Research, New Delhi.

Supplementary material

122_2006_440_MOESM1_ESM.doc (381 kb)
Supplementary material


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Ramesh K. Aggarwal
    • 1
    • 3
  • Prasad S. Hendre
    • 1
  • Rajeev K. Varshney
    • 1
    • 2
  • Prasanna R. Bhat
    • 1
  • V. Krishnakumar
    • 1
  • Lalji Singh
    • 1
  1. 1.Centre for Cellular and Molecular Biology (CCMB)HyderabadIndia
  2. 2.International Crops ResearchInstitute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  3. 3.Centre for Cellular and Molecular BiologyHyderabadIndia

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