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Background  Utilization of broad-spectrum resistance ( R ) genes is an effective and economical strategy to control the fungal pathogen  Magnaporthe oryzae , the causal agent of the rice blast disease. Among the cloned blast resistance genes,  Pi9 ,  Pi2  and  Piz-t  confer broad-spectrum resistance to diverse  M. oryzae  isolates and were isolated from the  Pi2/9  locus on chromosome 6. Identification and isolation of additional  R  genes with different resistance spectra from this locus will provide novel genetic resources for better control of this important rice disease.    Results  In this study, we identified a dominant  R  gene,  Pi2-2,  at the  Pi2/9  locus from Jefferson, an elite U.S. rice cultivar, through genetic and physical mapping. Inoculation tests showed that Jefferson has different resistant specificities to  M. oryzae  isolates compared rice lines with the  Pi9 ,  Pi2  and  Piz-t  genes .  Fine mapping delimited  Pi2-2  to a 270-kb interval between the markers AP5659-3 and RM19817, and this interval contains three nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in the Nipponbare genome. Five bacterial artificial chromosome (BAC) clones spanning the region were identified, and a BAC contig covering the  Pi2-2  locus was constructed.    Conclusions  We identified a new allelic gene at the  Pi2/9  locus and fine-mapped the gene within a 270-kb region. Our results provide essential information for the isolation of the  Pi2-2  gene and tightly linked DNA markers for rice blast resistance breeding.    Electronic supplementary material  The online version of this article (doi:10.1186/1939-8433-5-29) contains supplementary material, which is available to authorized users.

Molecular mapping of the Pi2/9 allelic gene Pi2-2 conferring broad-spectrum resistance to Magnaporthe oryzae in the rice cultivar Jefferson