Functional & Integrative Genomics

, Volume 4, Issue 2, pp 74–83 | Cite as

An integrated approach for comparative mapping in rice and barley with special reference to the Rph16 resistance locus

  • Dragan Perovic
  • Nils Stein
  • Hangning Zhang
  • Anke Drescher
  • Manoj Prasad
  • Raja Kota
  • Doris Kopahnke
  • Andreas GranerEmail author
Original Paper


The accumulated sequence information of the almost completed rice genome and the transcriptome of other cereals provide an excellent starting point for comparative genome analysis. We performed targeted synteny-based marker saturation for the Rph16 leaf rust resistance locus in barley by extensively exploiting these newly available resources. Out of a collection of over 320,000 public barley ESTs 309 non-redundant candidate syntenic clones have been identified for this region in a two-step in silico selection procedure. For mapping, 54 barley cDNA-clones were selected due to the even distribution of their homologs on a putatively collinear 3-Mb rice BAC contig. Out of these, 97% (30) of the polymorphic markers could be genetically assigned in collinearity to the target region in barley and a set of 11 markers was integrated into an rph16 high-resolution map. Although, the collinear target region of rice does not contain an obvious candidate gene for rph16 the results demonstrate the potential of the presented procedure to efficiently utilize EST resources for synteny-based marker saturation. The systematic genome-wide exploitation of the increasing sequence data resources will strongly improve our current view of genome conservation and likely facilitate a synteny-based isolation of genes conserved across cereal species.


Synteny EST High resolution map Leaf rust 



The presented work was supported by grant no. Gr.1317/4-3 of the Deutsche Forschungsgemeinschaft (DFG), Germany. The authors would like to thank A. Kleinhofs, Washington State University, United States and P. Hayes, Oregon State University, United States for kindly providing seeds of the S × M and OWB D × R mapping populations. We would also like to thank D. Smilde, JIC, Norwich, United Kingdom for helpful comments on the manuscript and S. Stegmann, B. Hoppe and J. Perovic for technical assistance.


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Dragan Perovic
    • 1
  • Nils Stein
    • 1
  • Hangning Zhang
    • 1
  • Anke Drescher
    • 1
    • 3
  • Manoj Prasad
    • 1
  • Raja Kota
    • 1
  • Doris Kopahnke
    • 2
  • Andreas Graner
    • 1
    Email author
  1. 1.Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  2. 2.Federal Centre for Breeding Research on Cultivated PlantsInstitute for Epidemiology and ResistanceAscherslebenGermany
  3. 3.Allgemeine Genetik/ZMBPUniversität TübingenTübingenGermany

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