Genetic Resources and Crop Evolution

, Volume 52, Issue 7, pp 903–909 | Cite as

EST versus Genomic Derived Microsatellite Markers for Genotyping Wild and Cultivated Barley

  • K. Chabane
  • G. A. Ablett
  • G. M. Cordeiro
  • J. Valkoun
  • R. J. Henry


Genetic variation present in wild and cultivated barley populations was investigated using two sources of microsatellite also known as simple sequence repeat (SSR) markers. EST-SSRs are derived from expressed sequences and genomic SSRs are isolated from genomic DNA. Genomic SSR markers detected a higher level of polymorphism than those derived from ESTs. Polymorphism information content was higher in genomic SSRs than EST-derived SSRs. This study showed that the EST-SSR markers developed in cultivated barley are polymorphic in wild and cultivated varieties and produced high quality markers. Ten of these functional markers were polymorphic across the accessions studied. EST markers indicated clearer separation between wild and cultivated barley than genomic SSRs. The EST-SSRs are a valuable source of new polymorphic markers and should be highly applicable to barley genetic resources, providing a direct estimate of functional biodiversity.


Barley Expressed sequence tags derived microsatellites (EST-SSRs) Genetic diversity Simple sequence repeats (SSRs) 


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  1. Ablett, E., Seaton, G., Scott, K., Shelton, D., Graham, M.W., Baverstock, P., Lee, S.L., Henry, R.J. 2000Plant Sci.1598795CrossRefPubMedGoogle Scholar
  2. Anderson, J.A., Churchill, G.A., Sutrique, J.E., Tanksley, S.D., Sorrels, M.E. 1993Optimizing parental selection for genetic linkage mapsGenome36181186Google Scholar
  3. Badr, A., Schafer-Pregl, R., Rabey, H.E. 2000On the origin and domestication history of barley (Hordeum vulgare)Mol. Biol. Evol.17499510PubMedGoogle Scholar
  4. Cho, Y.G., Ishii, T., Temmykh, S., Chen, X., Lipovich, L., McCouch, S.R., Park, W.D., Ayres, N., Cartinhour, S. 2000Diversity of microsatellites derived from genomic libraries and genebank sequences in rice (Oryza sativa L.)Theor. Appl. Genet.100713722CrossRefGoogle Scholar
  5. Cordeiro, G.M., Casu, R., McIntyre, C.L., Manners, J.M., Henry, R.J. 2001Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to Erianthus and SorghumPlant Sci.16011151123CrossRefPubMedGoogle Scholar
  6. Delseny, M., Cooke, M., Raynal, M., Grellet, F. 1997The Arabidopsis thaliana cDNA sequencing projectsFEBS Lett.405129132CrossRefPubMedGoogle Scholar
  7. Eujayl, I., Sorrels, M.E., Baum, M., Wolters, P., Powel, W. 2002Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheatTheor. Appl. Genet.104399407CrossRefPubMedGoogle Scholar
  8. Holton, T.A., Christopher, J.T., McClure, L., Harker, N., Henry, R.J. 2002Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheatMol. Breed.96371CrossRefGoogle Scholar
  9. Ivandic, V., Hackett, C.A., Nevo, E., Keit, R., Thomas, W.T., Forster, B.P. 2002Analysis of simple sequence repeats (SSRs) in wild barley from the Fertile Crescent: associations with ecology, geography and flowering timePlant Mol. Biol.48511527CrossRefPubMedGoogle Scholar
  10. Kantety, R.V., La Rota, M., Matthews, D.E., Sorrels, M. 2002Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheatPlant Mol. Biol.48501510CrossRefPubMedGoogle Scholar
  11. Kota, R., Varshney, R.K., Thiel, T., Dehmer, K.J., Graner, A. 2001Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.)Hereditas135145151CrossRefPubMedGoogle Scholar
  12. LevYadun, S., Gropher, A., Abbo, S. 2000The cradle of agricultureScience28816021603Google Scholar
  13. Macaulay, M., Ramsay, L., Powel, W., Waugh, R. 2001A representativehighly informative genotyping set of barley SSRsTheor. Appl. Genet.102801809CrossRefGoogle Scholar
  14. Marmiroli, N., Maestri, E., Liviero, L., Massari, A., Malcevschi, A., Monciardini, P. 1999Application of genomic in assessing biodiversity in wild and cultivated barleyMol. Ecol.8S95S106CrossRefGoogle Scholar
  15. McDermott, J.M., McDonald, B.A. 1993Gene flow in plant pathosystemsAnnu. Rev. Phytopathol.31353373CrossRefGoogle Scholar
  16. Michalek, V., Weschke, W., Pleisner, K.P., Graner, A. 2002EST analysis in barley defines a unigene set comprising 4000 genesTheor. Appl. Genet.10497103CrossRefPubMedGoogle Scholar
  17. Nei, M. 1978Estimation of average heterozygosity and genetic distance from small number of individualsGenetics89583590Google Scholar
  18. Qingyand, H., Beharav, A., Li, Y., Kizhner, V., Nevo, E. 2002Mosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneumat Neve Yarr, IsraelGenome4512161229Google Scholar
  19. Ramsay, L., Macaulay, M., Mclean, K., Fuller, J., Edwards, K., Turesson, S., Morgante, M., Degli-Ivanissivich, S., Marmoroli, N., Maestri, E., Massari, A., Powel, W., Waugh, R. 2000A simple sequence repeat-based linkage map of barleyGenetics15619972005PubMedGoogle Scholar
  20. Röder, M.S., Plaske, J., Konig, S.U., Börner, A., Sorells, M.E., Tanksley, S.D., Ganal, M.W. 1995Abundance, variability and chromosomal location of microsatellites in wheatMol. Gen. Genet.246327333CrossRefPubMedGoogle Scholar
  21. Röder, M.S., Korzun, V., Wendehake, K., Plaske, J., Tixier, M., Leroy, P., Ganal, M. 1998A microsatellite map of wheatGenetics14920072023PubMedGoogle Scholar
  22. Russel, J., Fuller, J., Young, G. 1997Discriminating between barley genotypes using microsatellite markersGenome40442450Google Scholar
  23. Scott, K.D., Eggler, P., Seaton, G., Rossetto, E.M., Ablett, E.M., Lee, L.S., Henry, R.J. 2000Analysis of SSRs derived from grape ESTsTheor. Appl. Genet.100723726CrossRefGoogle Scholar
  24. Struss, D., Pleiske, J. 1998The use of microsatellite markers for detection of genetic diversity in barley populationsTheor. Appl. Genet.97308315CrossRefGoogle Scholar
  25. Thiel, T., Michalek, R.K., Varshney, R.K., Graner, A. 2003Exploiting EST databases for the development and characterization of gene-derived SSR markers in barley (Hordeum vulgare L.)Theor. Appl. Genet.106411422PubMedGoogle Scholar
  26. Turpeinen, T., Tenhola, T., Manninen, O., Nevo, E., Nissilä, E. 2002Microsatellite diversity associated with ecological factors in Hordeum spontaneum populations in IsraelMol. Ecol.1015771591Google Scholar
  27. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., Zabeau, M. 1995AFLP a new technique for DNA fingerprintingNucleic Acids Res.2344074414PubMedGoogle Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  • K. Chabane
    • 1
  • G. A. Ablett
    • 2
  • G. M. Cordeiro
    • 2
  • J. Valkoun
    • 1
  • R. J. Henry
    • 2
  1. 1.International Center for Agricultural Research in the Dry Areas (ICARDA)AleppoSyria
  2. 2.Centre for Plant Conservation GeneticsSouthern Cross UniversityLismoreAustralia

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