Rice is the staple food for more than half people of the world, and the demand is increasing because of the expanding rice-eating population, particularly in many developing countries in Africa and Asia. However, rice production is severely affected by various biotic and abiotic stresses ([Khush and Jena 2009]). Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the major limitations, and usually causes 10-30% yield loss in rice production when a rice blast epidemic occurs ([Talbot 2003];[Skamnioti and Gurr 2009]). Use of host resistance is an effective and economical way to control the blast disease ([Khush and Jena 2009]). To date, over 80 blast resistance genes have been identified, and are distributed on 11 rice chromosomes except chromosome 3 ([Liu et al. 2010];[Yang et al. 2009]). So far, 21 have been cloned (Pib, Pita, Pi9, Pi2, Piz-t, Pid2, Pi36, Pi37, Pik-m, Pit, Pi5, Pid3, pi21, Pb1, Pish, Pik, Pik-p, Pi54, Pia, NLS1 and Pi25). Interestingly, most of them are NBS-LRR genes except Pi-d2 and pi21 ([Wang et al. 1999];[Bryan et al. 2000];[Qu et al. 2006];[Zhou et al. 2006];[Chen et al. 2006];[Liu et al. 2007];[Lin et al. 2007];[Ashikawa et al. 2008];[Hayashi and Yoshida. 2009];[Lee et al. 2009];[Shang et al. 2009];[Fukuoka et al. 2009];[Hayashi et al. 2010];[Takahashi et al. 2010];[Zhai et al. 2011];[Yuan et al. 2011];[Sharma et al. 2005];[Okuyama et al. 2011];[Tang et al. 2011];[Chen et al. 2011]). Pi-d2 encodes a receptor-like kinase protein with a predicted extracellular domain of a bulb-type mannose-specific binding lectin (B-lectin) and an intracellular serine-threonine kinase domain ([Chen et al. 2006]). Pi21 encodes a proline-rich protein that includes a putative heavy metal-binding domain and protein-protein interaction motifs. The resistant allele pi21 carrying deletions in the proline-rich motif can reduce blast infection rate ([Fukuoka et al. 2009]). Pik, Pik-m and Pik-p are located at the locus of Pik on chromosome 11, and interestingly, each of them requires two independent NBS-LRR genes for the blast resistance ([Zhai et al. 2011];[Ashikawa et al. 2008];[Yuan et al. 2011]). Similarly, both Pi5 and Pia also require two NBS-LRR members for their resistance function ([Lee et al. 2009];[Okuyama et al. 2011]).
At least eight blast resistance genes were identified from the Pi2/9 locus, which is located on the short arm and near the centromere of chromosome 6. Among them, Pi9, Pi2 and Piz-t were successfully cloned ([Qu et al. 2006];[Zhou et al. 2006]). Pi26(t) ([Wu et al. 2005]), Pigm(t) ([Deng et al. 2006]), Piz(t) ([Fjellstrom et al. 2006]), Pi40(t) ([Jeung et al. 2007]) and Pi50(t) ([Zhu et al. 2012]) are in the process of being cloned by different laboratories. Interestingly, most of them confer broad-spectrum resistance to diverse M. oryzae races or isolates. The near isogenic line C101A51 carrying Pi2 is resistant to 455 isolates collected from Philippines and most of the 792 isolates from China ([Chen et al. 1996, 1999]). The Pi9-bearing line, 75-1-127, is resistant to 43 isolates collected from 13 different countries ([Liu et al. 2002]). Piz-t and Pigm from Toride and Gumei4, respectively, are resistant to more than 90% of tested isolates from China and Thailand ([Shen et al. 2003]). The near-isogenic line containing Pi50(t) is incompatible to 97.7% of the 523 isolates from different regions of China ([Zhu et al. 2012]). However, the underlying mechanism of broad-spectrum resistance of these genes is still not well understood.
Jefferson, a long-grain tropical japonica cultivar grown in the southern U.S., has retained its resistance to blast since its first use in 1997 ([McClung et al. 1997];[Skamnioti and Gurr 2009]). It was reported that Jefferson possesses three blast resistance genes, Piz(t), Pi-d(t) and Pi-k
(t), based on its disease reactions ([McClung et al. 1997]). Our preliminary observation showed that Jefferson was immune in the blast nursery of Taojiang County, Hunan Province, China, which contained 11 major M. oryzae races including ZC9, ZC11, ZE3, ZB29, ZG1, ZB25, ZB31, ZB13, ZC7, ZA9, and ZF1 (unpublished). To determine the genetic basis of broad-spectrum resistance in Jefferson, we performed greenhouse inoculations with individual isolates and genetic analysis using an F2 population derived from a cross between Jefferson and the susceptible cultivar CO39. We identified a dominant R gene in Jefferson on chromosome 6 at the Pi2/9 locus, named Pi2-2. Allelism analysis indicated that Pi2-2 is tightly linked or allelic to Pi9. We constructed a BAC contig in the genomic region and fine-mapped the gene within a region approximately 270 kb. These data will facilitate both the positional cloning of the R gene and molecular breeding programs of rice blast resistance.