Molecular mapping of sheath blight resistance QTLs from the wild rice Oryza rufipogon accession CR100438

Background Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani Kühn (AG1 IA), is one of the most destructive diseases of rice ( Oryza sativa L.). Breeding resistant cultivars is constrained by the absence of complete resistance in cultivated germplasm and the quantitative nature of resistance. Therefore, exploiting wild rice germplasm is essential for developing ShB-resistant cultivars. Results The BC ₂ F ₅ and BC ₂ F ₆ populations derived from PR114/ O . rufipogon accession CR100438 were evaluated against sheath blight. Seven disease-associated traits, namely plant height, lesion height, relative lesion height, disease score, number of tillers, number of infected tillers, and heading date, exhibited continuous variation, confirming the quantitative nature of ShB resistance. A subset of 118 progenies with consistent performance across seasons was selected for genotyping-by-sequencing. A total of 3,531 high-quality SNP markers were used for QTL mapping. Composite interval mapping identified 26 QTLs distributed across chromosomes 2, 3, 5, 6, 7, 8, 9, 10, 11, and 12. Six major QTLs ( qLH6 , qLH11 , qLH12 , qRLH6 , qRLH7 , and qRLH12 ) explained 9.10-14.26% of the phenotypic variance. A QTL hotspot containing qLH6, qRLH6 , and qDS6 was identified on chromosome 6. Pre-breeding lines with relative lesion height less than 25 percent and desirable agronomic traits such as days to flowering, plant height etc. have been identified for further use in breeding program. Conclusions This study identified promising QTLs with superior pre-breeding lines derived from O . rufipogon CR100438. These findings provide valuable genetic resources for fine mapping, marker-assisted breeding, and development of sheath blight-resistant rice cultivars.