Unravelling candidate genes associated with blast disease resistance in an elite green super rice varietal panel using genome-wide association study

Saxena, Harshita, Varunseelan Murugaiyan, Bikash Ghimire, Christian John Robiso, Erik Jon De Asis, Mary Jeanie Yanoria, Paul L. Raymer, Bochra Amina Bahri, and Jauhar Ali (2025). Unravelling candidate genes associated with blast disease resistance in an elite green super rice varietal panel using genome-wide association study. Plant Pathology (2025): 1-17.

Rice blast disease, caused by the filamentous fungus jats:italicMagnaporthe oryzae</jats:italic>, significantly threatens global rice crops leading to yield losses worldwide. Given that existing resistance genes often fail to control rice blast due to the evolution of new virulent strains, identifying novel genes using modern breeding tools to enhance partial resistance is crucial for developing more durable and effective control measures. Here, we used a genome‐wide association study (GWAS) with 2698 high‐throughput single‐nucleotide polymorphism (SNP) markers to analyse 134 rice cultivars from the Green Super Rice breeding programme against two virulent rice blast isolates, M101‐1‐2‐9‐1 (M101) and M64‐1‐3‐9‐1 (M64). GWAS identified 12 potential quantitative trait loci (QTLs) for blast resistance: five against M101 on chromosomes 1, 2, 3, 4 and 7 and seven against M64 on chromosomes 1, 4, 5, 6 and 12, with no QTL in common against both. Notably, jats:italicqM101_2</jats:italic> is within the 500 kb linkage disequilibrium (LD) block containing the known resistance gene jats:italicPib</jats:italic> on chromosome 2, and jats:italicqM64_12</jats:italic>.jats:italic1</jats:italic> and jats:italicqM64_12</jats:italic>.jats:italic2</jats:italic> are within the jats:italicPi‐ta</jats:italic> and jats:italicPtr</jats:italic> gene cluster on chromosome 12. The remaining nine QTLs represented novel blast disease resistance sources. The identified candidate genes, including those encoding nucleotide‐binding site leucine‐rich repeats domains, protein kinases, resistance gene analogues and pathogenesis‐related proteins, may serve as a foundation for further studies to explore their potential role in enhancing disease resistance in rice.