Molecular Genetics and Genomics

, Volume 271, Issue 6, pp 742–751 | Cite as

EST derived SSR markers for comparative mapping in wheat and rice

  • J.-K. Yu
  • M. La Rota
  • R. V. Kantety
  • M. E. Sorrells
Original Paper


Structural and functional relationships between the genomes of hexaploid wheat (Triticum aestivum L.) (2n=6x=42) and rice (Oryza sativa L.) (2n=2x=24) were evaluated using linkage maps supplemented with simple sequence repeat (SSR) loci obtained from publicly available expressed sequence tags (ESTs). EST-SSR markers were developed using two main strategies to design primers for each gene: (1) primer design for multiple species based on supercluster analysis, and (2) species-specific primer design. Amplification was more consistent using the species-specific primer design for each gene. Forty-four percent of the primers designed specifically for wheat sequences were successful in amplifying DNA from both species. Existing genetic linkage maps were enhanced for the wheat and rice genomes using orthologous loci amplified with 58 EST-SSR markers obtained from both wheat and rice ESTs. The PCR-based anchor loci identified by these EST-SSR markers support previous patterns of conservation between wheat and rice genomes; however, there was a high frequency of interrupted colinearity. In addition, multiple loci amplified by these primers made the comparative analysis more difficult. Enhanced comparative maps of wheat and rice provide a useful tool for interpreting and transferring molecular, genetic, and breeding information between these two important species. These EST-SSR markers are particularly useful for constructing comparative framework maps for different species, because they amplify closely related genes to provide anchor points across species.


Wheat Rice EST-SSR Comparative map 



We are grateful to Drs. Susan McCouch and Svetlana Temnykh for providing the DH lines of rice mapping population IR64 × Azucena and map data; Drs. Bikram Gill and Sukhwinder Singh for wheat EST-SSR primer sequences, and Doug Valenta for technical assistance. We thank Dr. David E. Matthews and Hugh Edwards for providing advice and information regarding integration of new maps and data into the GrainGenes database ( The present work was supported by grants from the USDA/NRI Project No. 2001-35301-10612 and Hatch Project 149419.


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • J.-K. Yu
    • 1
  • M. La Rota
    • 1
  • R. V. Kantety
    • 1
  • M. E. Sorrells
    • 1
  1. 1.Department of Plant BreedingCornell UniversityIthacaUSA

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