CHARACTERIZING THE GENETIC RESISTANCE MECHANISMS IN RICE AGAINST RICE BLAST DISEASE: EXPLORING NEW AVENUES FOR DISEASE CONTROL

Abstract

Rice blast (Magnaporthe oryzae) poses a major threat to global rice production, yet durable, broad‐spectrum resistance remains elusive. Here, we combined high‐throughput phenotyping of 300 diverse indica, japonica, and aus accessions with whole‐genome resequencing (>10× coverage) and pangenome assembly to perform mixed‐model GWAS and identify 45 SNPs (p < 1×10⁻⁵) across all 12 chromosomes. Meta-QTL integration with >400 published loci refined 23 candidate intervals and highlighted six robust regions enriched for NLR and receptor-like kinase genes. We prioritized 100 candidates by domain architecture and differential expression upon infection. Functional validation via CRISPR/Cas9 (knockout and allele-swap) in the susceptible Kitaake cultivar generated eight lines with on-target editing efficiencies of 71–99 %, no detectable off-target mutations, and lesion score reductions up to 80 %. The positive correlation between editing efficiency and resistance enhancement underscores the feasibility of precision allele pyramiding. Pangenome presence–absence analysis revealed 20 % novel resistance alleles absent from the Nipponbare reference, expanding the genetic toolkit for breeding. Growth‐curve assays confirmed that genome editing did not impair early vegetative development. Our integrative pipeline—spanning germplasm screening, GWAS, meta-QTL mapping, pangenomics, and targeted editing—provides a scalable model for rapid deployment of resistance genes against evolving pathogen races. These findings pave the way for multi-locus editing strategies and field validation toward sustainable, resilient rice cultivars, ultimately contributing to food security in blast‐endemic regions.