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Background  The rice  Pi2/9  locus harbors multiple resistance ( R ) genes each controlling broad-spectrum resistance against diverse isolates of  Magnaporthe oryzae , a fungal pathogen causing devastating blast disease to rice. Identification of more resistance germplasm containing novel  R  genes at or tightly linked to the  Pi2/9  locus would promote breeding of resistance rice cultivars.    Results  In this study, we aim to identify resistant germplasm containing novel  R  genes at or tightly linked to the  Pi2/9  locus using a molecular marker, designated as Pi2/9-RH ( Pi2/9  resistant haplotype), developed from the 5′ portion of the  Pi2  sequence which was conserved only in the rice lines containing functional  Pi2/9  alleles. DNA analysis using Pi2/9-RH identified 24 positive lines in 55 shortlisted landraces which showed resistance to 4 rice blast isolates. Analysis of partial sequences of the full-length cDNAs of  Pi2/9  homologues resulted in the clustering of these 24 lines into 5 haplotypes each containing different  Pi2/9  homologues which were designated as  Pi2/9-A5 , − A15 , − A42 , − A53 , and - A54 . Interestingly,  Pi2/9-A5  and  Pi2/9-A54  are identical to  Piz-t  and  Pi2 , respectively. To validate the association of other three novel  Pi2/9  homologues with the blast resistance, monogenic lines at BC 3 F 3  generation were generated by marker assisted backcrossing (MABC). Resistance assessment of the derived monogenic lines in both the greenhouse and the field hotspot indicated that they all controlled broad-spectrum resistance against rice blast. Moreover, genetic analysis revealed that the blast resistance of these three monogenic lines was co-segregated with Pi2/9-RH, suggesting that the  Pi2/9  locus or tightly linked loci could be responsible for the resistance.    Conclusion  The newly developed marker Pi2/9-RH could be used as a potentially diagnostic marker for the quick identification of resistant donors containing functional  Pi2/9  alleles or unknown linked  R  genes. The three new monogenic lines containing the  Pi2/9  introgression segment could be used as valuable materials for disease assessment and resistance donors in breeding program.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-017-0176-z) contains supplementary material, which is available to authorized users.

rice

Identification of resistant germplasm containing novel resistance genes at or tightly linked to the Pi2/9 locus conferring broad-spectrum resistance against rice blast