Unveiling key genetic loci and candidate genes for brown spot disease resistance in rice based on QTL analysis.

Rice brown spot, a widespread disease caused by the fungus Bipolaris oryzae (teleomorph: Cochliobolus miyabeanus), significantly diminishes both grain yield and quality. Developing resistant rice cultivars remains the most sustainable and effective strategy for managing this disease. In this study, we conducted quantitative trait locus (QTL) analysis to identify genetic loci and candidate genes associated with brown spot resistance. A mapping population was generated from a cross between the resistant variety ‘Cheongcheong’ and the susceptible variety ‘Nagdong’. Disease evaluations were performed following inoculation with a mixture of six Cochliobolus miyabeanus isolates collected in 2023 to represent current field diversity, and disease severity was assessed seven days post-inoculation using a 0–9 scale. The QTL analysis revealed a new major locus on chromosome 3 linked to brown spot resistance, between markers RM15749 and RM15689. Within this genomic interval, 32 candidate genes were identified using qRT-PCR-based expression profiling. Among them, a gene designated OsRBSq3 (Os03g0687400), encoding a ribosome-inactivating protein family member that plays a role in defense mechanisms against necrotrophic pathogens, exhibited notable differential expression between Cheongcheong and Nagdong. These results provide new insights into the genetic architecture underlying brown spot resistance in rice and highlight OsRBSq3 as a potential target for marker-assisted selection and functional studies.