Theoretical and Applied Genetics

, Volume 113, Issue 2, pp 251–260 | Cite as

Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes

  • K. Hayashi
  • H. Yoshida
  • I. Ashikawa
Original Paper


Blast resistance is one of the most important traits in rice breeding, and application of molecular markers for blast resistance breeding is likely to allow the rapid screening for the trait during early growth stages, without the need for inoculation of pathogen and phenotyping. Allele-specific PCR markers and insertion/deletion (InDel) markers, which genotype single-nucleotide polymorphisms and InDel polymorphisms, respectively, are useful tools for marker-assisted selections. We developed sets of allele-specific PCR and InDel markers for nine rice blast resistance genes—Piz, Piz-t, Pit, Pik, Pik-m, Pik-p, Pita, Pita-2, and Pib—which are commonly used in Japanese blast resistance rice breeding programs. For each resistance gene, we used the segregation information from thousands of progeny in several crosses or published gene locations to generate a marker that cosegregated with the gene and markers that closely flanked the gene on either side. The developed cosegregating markers uniquely discriminated among each of the lines with the individual resistance genes (except for Pita and Pita-2). Therefore, these markers will likely facilitate the development of multiline cultivars carrying one or a combination of these nine blast resistance genes. In addition, the systems we developed may be valuable tools in the quality control of seed production from blast-resistant multiline cultivars.


Flank Marker Blast Resistance InDel Marker Target Gene Region Blast Resistance Gene 
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.



We thank Dr. M. Yano (National Institute of Agrobiological Sciences) for providing us with the seeds of 99SL-44 and OISL235. We also thank T. Nakajima, N. Yasuda, and M. Noguchi (National Agriculture Research Center) for their technical advice on assaying the blast resistance of the mapping population. This work was supported by a grant from the Japanese Ministry of Agriculture, Forestry and Fisheries under the project name “Development of DNA Marker-aided Selection Technology for Plants and Animals”.


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  1. 1.National Agricultural Research CenterJoetsuJapan
  2. 2.National Institute of Crop ScienceTsukubaJapan

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