Identification of novel rice blast resistance alleles through sequence-based allele mining

Background: As rice ( Oryza sativa ) is the staple food of more than half the world’s population, rice production contributes greatly to global food security. Rice blast caused by the fungus M agnaporthe oryzae is a devastating fungal disease of rice, affecting yield and grain quality and resulting in substantial annual economic losses. Because the fungus evolves rapidly,, resistance conferred by most of the single blast race resistance genes is often broken after a few years of intensive agricultural use. Effective resistance breeding in rice therefore requires continual enrichment of the reservoir of resistance genes and alleles. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles. Results: We carried out a large-scale screen for novel blast resistance alleles in 1883 rice varieties from major rice producing areas across China. Of these, 107 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. Using sequence-based allele mining to amplify and clone the allelic variants of major rice blast resistance genes at the Pi2/9/gm/zt locus of chromosome 6 from the 107 blast-resistant varieties, we identified 13 novel blast resistance alleles. We then used controlled infections to assess the resistance of rice varieties carrying the novel alleles to 34 single rice blast isolates from Hubei, Guangdong, Jiangsu, Hunan, Jangxi, Sichuan, Heilongjiang, and Fujin Provinces. The varieties identified as being resistant in the nursery trials showed varied disease responses when infected with the single blast isolates, suggesting that the novel Pi2/9/gm/zt alleles vary in their blast resistance spectra. Some of the newly identified alleles have unique single nucleotide polymorphisms (SNPs), insertions, or deletions, in addition to polymorphic residues that are shared between the different alleles. Conclusions: These alleles expand the allelic series of blast resistance genes, enriching the genetic resource for rice blast resistance breeding programs and for studies aimed at deciphering rice–rice blast molecular interactions. Key words : Pi9 , R-genes, Nucleotide diversity, Gene conversion, Resistance gene alleles, Rice blast