A genome‐wide survey reveals abundant rice blast R genes in resistant cultivars

Summary Plant resistance genes (R genes) harbor tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens. Nevertheless, few functional R genes have been identified for even the best‐studied pathosystems. Does this limited repertoire reflect specificity, with most R genes having been defeated by former pests, or do plants harbor a rich diversity of functional R genes, the composite behavior of which is yet to be characterized? Here, we survey 332 NBS‐LRR genes cloned from five resistant Oryza sativa (rice) cultivars for their ability to confer recognition of 12 rice blast isolates when transformed into susceptible cultivars. Our survey reveals that 48.5% of the 132 NBS‐LRR loci tested contain functional rice blast R genes, with most R genes deriving from multi‐copy clades containing especially diversified loci. Each R gene recognized, on average, 2.42 of the 12 isolates screened. The abundant R genes identified in resistant genomes provide extraordinary redundancy in the ability of host genotypes to recognize particular isolates. If the same is true for other pathogens, many extant NBS‐LRR genes retain functionality. Our success at identifying rice blast R genes also validates a highly efficient cloning and screening strategy. Significance Statement Resistance genes (R‐genes) provide protection against pathogens, but relatively few have been characterized. Here we surveyed the rice genome and identified 98 R‐genes capable of recognizing one or more isolates of rice blast, nearly twice the number previously identified against any pathogen. These results provide the most comprehensive picture to date of the architecture of resistance and overturn the perception that most R‐genes in genomes are relics that have been overcome by pathogens.