Skip to main content
Log in

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

  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • E. Ablett G. Seaton K. Scott D. Shelton M.W. Graham P. Baverstock S.L. Lee R.J. Henry (2000) Plant Sci. 159 87–95 Occurrence Handle10.1016/S0168-9452(00)00335-6 Occurrence Handle1:CAS:528:DC%2BD3cXmslOqu7o%3D Occurrence Handle11011096

    Article  CAS  PubMed  Google Scholar 

  • J.A. Anderson G.A. Churchill J.E. Sutrique S.D. Tanksley M.E. Sorrels (1993) ArticleTitleOptimizing parental selection for genetic linkage maps Genome 36 181–186 Occurrence Handle1:CAS:528:DyaK3sXit1Kktrs%3D

    CAS  Google Scholar 

  • A. Badr R. Schafer-Pregl H.E. Rabey (2000) ArticleTitleOn the origin and domestication history of barley (Hordeum vulgare) Mol. Biol. Evol. 17 499–510 Occurrence Handle1:CAS:528:DC%2BD3cXisVSgt7w%3D Occurrence Handle10742042

    CAS  PubMed  Google Scholar 

  • Y.G. Cho T. Ishii S. Temmykh X. Chen L. Lipovich S.R. McCouch W.D. Park N. Ayres S. Cartinhour (2000) ArticleTitleDiversity of microsatellites derived from genomic libraries and genebank sequences in rice (Oryza sativa L.) Theor. Appl. Genet. 100 713–722 Occurrence Handle10.1007/s001220051343 Occurrence Handle1:CAS:528:DC%2BD3cXjt1Kjsr0%3D

    Article  CAS  Google Scholar 

  • G.M. Cordeiro R. Casu C.L. McIntyre J.M. Manners R.J. Henry (2001) ArticleTitleMicrosatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to Erianthus and Sorghum Plant Sci. 160 1115–1123 Occurrence Handle10.1016/S0168-9452(01)00365-X Occurrence Handle1:CAS:528:DC%2BD3MXjtFGjurw%3D Occurrence Handle11337068

    Article  CAS  PubMed  Google Scholar 

  • M. Delseny M. Cooke M. Raynal F. Grellet (1997) ArticleTitleThe Arabidopsis thaliana cDNA sequencing projects FEBS Lett. 405 129–132 Occurrence Handle10.1016/S0014-5793(97)00184-1 Occurrence Handle1:CAS:528:DyaK2sXitVKkur8%3D Occurrence Handle9089275

    Article  CAS  PubMed  Google Scholar 

  • I. Eujayl M.E. Sorrels M. Baum P. Wolters W. Powel (2002) ArticleTitleIsolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat Theor. Appl. Genet. 104 399–407 Occurrence Handle10.1007/s001220100738 Occurrence Handle1:CAS:528:DC%2BD38XislOgt74%3D Occurrence Handle12582712

    Article  CAS  PubMed  Google Scholar 

  • T.A. Holton J.T. Christopher L. McClure N. Harker R.J. Henry (2002) ArticleTitleIdentification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat Mol. Breed. 9 63–71 Occurrence Handle10.1023/A:1026785207878 Occurrence Handle1:CAS:528:DC%2BD38XltlemsL4%3D

    Article  CAS  Google Scholar 

  • V. Ivandic C.A. Hackett E. Nevo R. Keit W.T. Thomas B.P. Forster (2002) ArticleTitleAnalysis of simple sequence repeats (SSRs) in wild barley from the Fertile Crescent: associations with ecology, geography and flowering time Plant Mol. Biol. 48 511–527 Occurrence Handle10.1023/A:1014875800036 Occurrence Handle1:CAS:528:DC%2BD38XjsFWrtr4%3D Occurrence Handle11999832

    Article  CAS  PubMed  Google Scholar 

  • R.V. Kantety M. La Rota D.E. Matthews M. Sorrels (2002) ArticleTitleData mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat Plant Mol. Biol. 48 501–510 Occurrence Handle10.1023/A:1014875206165 Occurrence Handle1:CAS:528:DC%2BD38XjsFWrsbc%3D Occurrence Handle11999831

    Article  CAS  PubMed  Google Scholar 

  • R. Kota R.K. Varshney T. Thiel K.J. Dehmer A. Graner (2001) ArticleTitleGeneration and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.) Hereditas 135 145–151 Occurrence Handle10.1111/j.1601-5223.2001.00145.x Occurrence Handle1:CAS:528:DC%2BD38XmsFaisL0%3D Occurrence Handle12152327

    Article  CAS  PubMed  Google Scholar 

  • S. LevYadun A. Gropher S. Abbo (2000) ArticleTitleThe cradle of agriculture Science 288 1602–1603 Occurrence Handle1:CAS:528:DC%2BD3cXjvVGks7c%3D

    CAS  Google Scholar 

  • M. Macaulay L. Ramsay W. Powel R. Waugh (2001) ArticleTitleA representativehighly informative genotyping set of barley SSRs Theor. Appl. Genet. 102 801–809 Occurrence Handle10.1007/s001220000487 Occurrence Handle1:CAS:528:DC%2BD3MXlt1SktLs%3D

    Article  CAS  Google Scholar 

  • N. Marmiroli E. Maestri L. Liviero A. Massari A. Malcevschi P. Monciardini (1999) ArticleTitleApplication of genomic in assessing biodiversity in wild and cultivated barley Mol. Ecol. 8 S95–S106 Occurrence Handle10.1046/j.1365-294X.1999.00812.x Occurrence Handle1:CAS:528:DC%2BD3cXhtV2ksrg%3D

    Article  CAS  Google Scholar 

  • J.M. McDermott B.A. McDonald (1993) ArticleTitleGene flow in plant pathosystems Annu. Rev. Phytopathol. 31 353–373 Occurrence Handle10.1146/annurev.py.31.090193.002033

    Article  Google Scholar 

  • V. Michalek W. Weschke K.P. Pleisner A. Graner (2002) ArticleTitleEST analysis in barley defines a unigene set comprising 4000 genes Theor. Appl. Genet. 104 97–103 Occurrence Handle10.1007/s001220200011 Occurrence Handle12579433

    Article  PubMed  Google Scholar 

  • M. Nei (1978) ArticleTitleEstimation of average heterozygosity and genetic distance from small number of individuals Genetics 89 583–590

    Google Scholar 

  • H. Qingyand A. Beharav Y. Li V. Kizhner E. Nevo (2002) ArticleTitleMosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneumat Neve Yarr, Israel Genome 45 1216–1229

    Google Scholar 

  • L. Ramsay M. Macaulay K. Mclean J. Fuller K. Edwards S. Turesson M. Morgante S. Degli-Ivanissivich N. Marmoroli E. Maestri A. Massari W. Powel R. Waugh (2000) ArticleTitleA simple sequence repeat-based linkage map of barley Genetics 156 1997–2005 Occurrence Handle1:CAS:528:DC%2BD3MXjsFGgug%3D%3D Occurrence Handle11102390

    CAS  PubMed  Google Scholar 

  • M.S. Röder J. Plaske S.U. Konig A. Börner M.E. Sorells S.D. Tanksley M.W. Ganal (1995) ArticleTitleAbundance, variability and chromosomal location of microsatellites in wheat Mol. Gen. Genet. 246 327–333 Occurrence Handle10.1007/BF00288605 Occurrence Handle7854317

    Article  PubMed  Google Scholar 

  • M.S. Röder V. Korzun K. Wendehake J. Plaske M. Tixier P. Leroy M. Ganal (1998) ArticleTitleA microsatellite map of wheat Genetics 149 2007–2023 Occurrence Handle9691054

    PubMed  Google Scholar 

  • J. Russel J. Fuller G. Young (1997) ArticleTitleDiscriminating between barley genotypes using microsatellite markers Genome 40 442–450

    Google Scholar 

  • K.D. Scott P. Eggler G. Seaton E.M. Rossetto E.M. Ablett L.S. Lee R.J. Henry (2000) ArticleTitleAnalysis of SSRs derived from grape ESTs Theor. Appl. Genet. 100 723–726 Occurrence Handle10.1007/s001220051344 Occurrence Handle1:CAS:528:DC%2BD3cXjt1Kjsro%3D

    Article  CAS  Google Scholar 

  • D. Struss J. Pleiske (1998) ArticleTitleThe use of microsatellite markers for detection of genetic diversity in barley populations Theor. Appl. Genet. 97 308–315 Occurrence Handle10.1007/s001220050900 Occurrence Handle1:CAS:528:DyaK1cXlslais7o%3D

    Article  CAS  Google Scholar 

  • T. Thiel R.K. Michalek R.K. Varshney A. Graner (2003) ArticleTitleExploiting EST databases for the development and characterization of gene-derived SSR markers in barley (Hordeum vulgare L.) Theor. Appl. Genet. 106 411–422 Occurrence Handle1:CAS:528:DC%2BD3sXht1Cmurg%3D Occurrence Handle12589540

    CAS  PubMed  Google Scholar 

  • T. Turpeinen T. Tenhola O. Manninen E. Nevo E. Nissilä (2002) ArticleTitleMicrosatellite diversity associated with ecological factors in Hordeum spontaneum populations in Israel Mol. Ecol. 10 1577–1591

    Google Scholar 

  • P. Vos R. Hogers M. Bleeker M. Reijans T. Lee ParticleVan de M. Hornes A. Frijters J. Pot J. Peleman M. Kuiper M. Zabeau (1995) ArticleTitleAFLP a new technique for DNA fingerprinting Nucleic Acids Res. 23 4407–4414 Occurrence Handle1:CAS:528:DyaK2MXpslensbo%3D Occurrence Handle7501463

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to K. Chabane.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chabane, K., Ablett, G.A., Cordeiro, G.M. et al. EST versus Genomic Derived Microsatellite Markers for Genotyping Wild and Cultivated Barley. Genet Resour Crop Evol 52, 903–909 (2005). https://doi.org/10.1007/s10722-003-6112-7

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-003-6112-7

Keywords

Navigation