Mining of Candidate Novel Alleles Using GWAS and Haplotype Identification for Rice Blast Resistance

Blast caused by Pyricularia oryzae (synonym Magnaporthe oryzae) is a major fungal disease affecting productivity and quality in rice-growing areas globally. A genome-wide association study (GWAS) was performed using the blast score(s) and whole-genome sequence data pertaining to a subset of 280 diverse accessions of the IRRI 3 K Rice Genome panel. Continuous variation was observed, with 8.9% of the total accessions resistant, 39.6% moderately resistant, 37.2% moderately susceptible and 14.2% susceptible, with average disease severity ratings of 0 to 3, > 3 to 5, > 5 to 7 and > 7 to 9, respectively, indicating the polygenic inheritance of the trait. We identified potential accessions in different subpopulations with a resistance disease reaction (IRGC 127151 [subtrop], 127738 [ind2], 132245 [aro] and 127130 [aus]), having the lowest average disease ratings of < 2. GWAS revealed the significant association of 22 quantitative trait nucleotides (QTNs)-20 main effect and two interaction effect-linked to blast resistance that led to the identification of 43 plant defence-related candidate genes. The haplo-pheno association analysis of the candidate genes (LOC_Os02g06470, LOC_Os02g06510, LOC_Os07g34370, LOC_Os08g29760, LOC_Os10g07470 and LOC_Os12g34290) associated with the superior haplotypes were identified and play a critical role in defence mechanisms. The identified resistant sources hold promise for stacking the superior haplotypes into an elite genetic background using a haplotype-based breeding approach for the development of cultivars with blast resistance to a wide range of pathotypes.