High‐density single nucleotide polymorphism‐based linkage mapping reveals novel quantitative trait loci for rice (Oryza sativa) sheath blight resistance from wild rice (Oryza rufipogon)‐derived introgression line

Rice sheath blight is one of the most important fungal disease‐causing yield losses up to 50%. An Oryza rufipogon ‐derived introgression line (Pusa 1908‐13‐12‐5) identified to be highly resistant to sheath blight was used for developing a RIL population by crossing with a highly susceptible rice cultivar, Pusa Basmati 1 (PB 1). The RIL population was genotyped with 80K Rice Pangenome (RPAN) single nucleotide polymorphism (SNP) array and phenotyped for disease response under artificial inoculation for 2 consecutive years. Inclusive composite interval mapping could identify six quantitative trait loci (QTLs) for two traits, namely, relative lesion height and relative yield loss per plant. Among these QTLs, four were major QTLs and three are novel QTLs. Three major QTLs were co‐localised within 1.4 Mb region on chromosome 1. In silico analysis revealed the presence of 12 candidate genes with potential role in disease resistance. Kompetitive Allele Specific PCR (KASP™) assay was developed for the linked SNPs and used for validation in an independent BC 1 F 2:3 population (PB 1121/Pusa 1908‐13‐12‐5). One SNP (AX‐182186537) on chromosome 1 was validated, which offers scope for its utilisation in marker‐assisted breeding.