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

TL;DR

Researchers identified a new gene linked to rice resistance against brown spot disease, which could help develop more disease-resistant rice varieties.

Contribution

A new major QTL and candidate gene OsRBSq3 for brown spot resistance in rice are identified through QTL analysis and gene expression profiling.

Findings

A new major locus on chromosome 3 is associated with brown spot resistance in rice.

The gene OsRBSq3, encoding a ribosome-inactivating protein, shows differential expression between resistant and susceptible rice varieties.

32 candidate genes were identified within the QTL interval using qRT-PCR-based expression profiling.

Abstract

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.

The online version contains supplementary material available at 10.1038/s41598-025-33890-y.

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