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

• DOI: 10.1111/ppa.14059
• Publication Date: 2025-02-03T05:20:36Z
• Authors: Williams Mohanavel; Ajay Prasanth Ram...; Bharathi Ayyenar; Veera Ranjani Raj...; Vignesh Mohanavel; Samuthirapandi Su...; Sudha Manickam; Raghu Rajasekaran; Gopalakrishnan Ch...; Manonmani Swamina...; Ramasamy Perumal; Raveendran Muthur...; P. V. Vara Prasad

ABSTRACTBlast 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.