Rice blast, caused by Magnaporthe oryzae, is one of the most destructive rice diseases, leading to 20–30% annual yield losses, equivalent to feeding 70 million people. Over 100 leaf blast resistance genes have been identified, with 23 cloned and characterized. At IRRI, we focus on identifying optimal gene combinations and integrating them into elite rice varieties. Notably, combinations of Pi9, Pi35, Pik-h, Pi54, Pi2-A15, and pi21 have been incorporated into multiple elite lines. To support breeding and surveillance, we developed PathoTracer (http://3.0.204.70/pathotracer2/) a high-throughput system for tracking pathogen populations and avirulence genes.
Neck blast, or panicle blast, affects the panicle and neck, causing sterility and significant yield reductions. Developing reliable inoculation methods has been a challenge. To improve resistance screening, we established a robust injection-based inoculation system and evaluated 342 global rice accessions against two M. oryzae isolates from the Philippines. A genome-wide association study (GWAS) using 3,253,465 SNP markers identified 35 significant SNPs associated with disease incidence, severity index, and lesion length. The strongest SNP signal mapped to the Pita2 locus, a known broad-spectrum blast resistance gene. Eight accessions displayed strong resistance to 10 neck blast isolates, with seven carrying Pita2. Additionally, four monogenic lines with Pita2 exhibited high resistance. CRISPR/Cas9-mediated knockout of Pita2 in IR64 is used to confirm its role. Furthermore, 22 candidate genes were identified near the most significant SNP, with five superior alleles linked to reduced lesion size. Our findings provide valuable insights for marker-assisted selection and breeding of blast-resistant rice varieties.