Genetic and physical mapping of a rice blast resistance locus, Pi-CO39(t), that corresponds to the avirulence gene AVR1-CO39 of Magnaporthe grisea

R. Chauhan, M. Farman, H. B. Zhang, S. Leong

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92 Scopus citations


We have identified, genetically mapped and physically delineated the chromosomal location of a new rice blast resistance locus, designated Pi-CO39(t). This locus confers resistance to Magnaporthe grisea isolates carrying the AVR1-CO39 avirulence locus. The AVR1-CO39 locus is conserved in non-rice (cereals and grasses)-infecting isolates of M. grisea, making Pi-CO39(t) useful for engineering M. grisea resistance in rice and other cereals. The resistance in the rice line CO39 was inherited as a single dominant locus in segregating populations derived from F2 and F3 crosses between disease-resistant (CO39) and susceptible (51583) rice genotypes. Microsatellite, RFLP and resistance gene analog (RGA) markers were used to map the Pi-CO39(t) locus to a 1.2-cM interval between the probenazole-responsive (RPR1) gene (0.2 cM) and RFLP marker S2712 (1.0 cM) on the short arm of rice chromosome 11. RFLP markers G320 and F5003, and resistance gene analogs RGA8, RGA38 and RGACO39 were tightly linked to the Pi-CO39(t) locus (no recombination detected in a sample of ∼ 2400 gametes). A large-insert genomic library of CO39 was constructed in the binary plant transformation vector pCLD04541. A library screen using RGA8, RGA38 and probes derived from the ends of CO39 clones, as well as BAC end probes from the corresponding locus in the rice cv. Nipponbare, resulted in the assembly of three CO39 contigs of 180 kb, 110 kb and 145 kb linked to the Pi-CO39(t) locus. A 650-kb contig was also constructed representing the susceptible locus, pi-CO39(t), in the Nipponbare genome. The two genomes are highly divergent with respect to additions, deletions and translocations at the Pi-CO39(t) locus, as revealed by the presence or absence of mapping markers.

Original languageEnglish
Pages (from-to)603-612
Number of pages10
JournalMolecular Genetics and Genomics
Issue number5
StatePublished - 2002

Bibliographical note

Funding Information:
Acknowledgements Technical assistance by Jack Hirt and Joe Seals in the preparation of progeny DNAs and pathogen inoculations is acknowledged. Special thanks to Pam Ronald and Dahu Chen, Department of Plant Pathology, University of California at Davis, for making CO39·51583 crosses. RFLP markers used in the study were kindly provided by S. McCouch, Cornell University, and T. Sasaki, Japan Rice Genome Project. We acknowledge Rod Wing, Clemson University Genomics Institute, for providing Nipponbare BAC filters and clones. We are thankful to the Department of Biotechnology, Government of India for awarding a Long-Term Overseas Associateship to Dr. R. S. Chauhan to pursue research on rice blast resistance. Financial support to Dr. S. A. Leong and Dr. R. S. Chauhan from the USDA-ARS and The Graduate School of the University of Wisconsin, Madison is also acknowledged.


  • Bacterial artificial chromosome
  • Cereals
  • Disease resistance
  • Positional cloning
  • Restriction Fragment Length Polymorphisms (RFLPs)

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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