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
• Keywords: Identification; Genome-wide Association Study

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