Natural variation in the atypical resistance gene Ptr confers broad‐spectrum neck blast resistance in rice

Abstract

Neck blast (NB), caused by Magnaporthe oryzae , infects rice ( Oryza sativa L.) and reduces yield. Knowledge of NB resistance remains limited due to the lack of reliable resistance evaluation methods. Here, we applied a newly established neck injection method and performed a genome‐wide association study (GWAS) on 335 diverse accessions from the 3K Rice Genomes Project to identify loci associated with NB resistance. We detected a significant association on chromosome 12 ( qNB1 ) explaining 15%–18% of the phenotypic variations caused by a highly virulent blast isolate (M64‐1‐3‐9‐1). Linkage disequilibrium analysis refined this region to a 42.3‐kb interval containing Ptr , a known gene for leaf blast resistance. We found that two Ptr allelic variants, Ptr _a and Ptr _c , both harboring the variant A/G (Lys879) in the last exon (Chr12:10,833,400), are associated with NB resistance. IR64 and the CO39 near‐isogenic line (NIL) (IRBLta2‐Pi[CO]), both harboring Ptr _a , were resistant, whereas CRISPR‐Cas9 knockout of Ptr _a in IR64 caused susceptibility to M64‐1‐3‐9‐1 and IK81‐25 isolates. Furthermore, the CO39 near‐isogenic line (IRBLta2‐Pi[CO]) and Lijiangxintuanheigu monogenic line (IRBLta2‐Pi) harboring the Ptr _a allele exhibited resistance to 75% (six of eight isolates) and 85% (17 of 20 isolates) of Philippine differential blast isolates, respectively. Haplotype analysis revealed a superior haplotype containing two major single‐nucleotide polymorphism (SNPs; A/G and A/C at Chr12:10,833,400 and Chr12:10,845,095, respectively) and occurring in 83% of International Rice Research Institute (IRRI) elite indica breeding lines. These SNPs can be used to select NB‐resistant genotypes with an accuracy of 86%. Our findings identify Ptr _a as a major contributor to NB resistance and provide a valuable genetic resource for developing blast‐resistant rice.