Navea, I. P.; Monsur, M. A.; Telebanco-Yanoria, M. J.; De La Rosa, D. G.; Hechanova, S. L.; Tuano, A. P.; Cumagun, C. J.; Choi, I.-R.; Kadaru, S.; Kim, S.-R.; Zhou, B.; Schepler-Luu, V.

Neck blast (NB), caused by Magnaporthe oryzae, damages rice panicles 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 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, explaining 15-18% of the symptom variations caused by a highly virulent Philippine blast isolate (M64-1-3-9-1). Linkage disequilibrium analysis refined this region to a 42.3-kb interval containing Pita2, a known leaf blast resistance gene. We found that two Pita2 allelic variants, Pita2a and Pita2c, both harboring the variant A/G (Lys879) in the last exon (Chr12:10,833,400), are associated with NB resistance. IR64 and a CO39 near-isogenic line (NIL) IRBLta2-Pi[CO] harboring Pita2a were resistant, whereas CRISPR-Cas9 knock-out of Pita2a in IR64 caused susceptibility to M64-1-3-9-1 and IK81-25. These results indicate that Pita2a is required for NB resistance. Furthermore, the CO39 NIL, IRBLta2-Pi[CO], and Lijiangxintuanheigu monogenic line (IRBLta2-Pi) harboring the Pita2a allele exhibited broad-spectrum resistance to 75% and 80% of Philippine differential blast isolates, respectively. The superior haplotype of Pita2 contains two major SNPs (A/G and A/C at Chr12:10,833,400 and Chr12:10,845,095) occurs in 83% of IRRI elite breeding lines and can be used to select NB-resistant genotypes with an accuracy of 86%. Our findings identify Pita2a as a major gene for NB resistance and provide a valuable genetic resource for developing blast-resistant rice.