Abstract
Rice sheath blight (ShB) disease, caused by Rhizoctonia solani, is a significant threat to global rice production, causing substantial yield losses. Earlier, we identified a land race, Phougak possessing resistance against R. solani and developed recombinant inbred line (RIL) population by crossing it with an elite cultivar, Improved Samba Mahsuri (ISM) susceptible to sheath blight. A dual approach combining whole population QTL linkage analysis and QTL-seq of the phenotypic extremes was employed. Significant variation among the RILs was observed for the phenotypic data on ShB disease response and yield traits across two seasons. Histograms displayed a normal distribution of the traits, suggesting their inheritance governed by minor effect loci. Correlation analysis demonstrated the effect of disease severity on grain yield. The QTL linkage analysis detected nine minor QTLs for ShB disease reaction, highlighting its complex inheritance. Additionally, a major QTL, qSBR3.1 explaining a variance of 15.58% was detected on chromosome 3 and it overlapped with QTLs for other important agronomic traits like grain yield and quality, chlorophyll content and abiotic stress tolerance highlighting the diverse functional contributions of this region in improving both productivity and stress resilience. Further analysis revealed candidate genes, encoding NB-LRR receptor family proteins and Phenylalanine ammonia-lyase, known for their role in pathogen recognition and plant defence responses, suggesting that these genes contribute to the ShB resistance. This finding suggests that while ShB resistance is governed by multiple minor QTLs, qSBR3.1 may play a crucial role in the genetic control of sheath blight tolerance. Of the 10 QTLs detected through linkage analysis, seven (qSBR1.1, qSBR1.2, qSBR3.1, qSBR3.2, qSBR5.1, qSBR5.4, qSBR6.1) were common regions identified through QTL-seq. Additionally, QTL-seq revealed four novel genomic regions associated with ShB tolerance, one each on chromosome 4 and 8 and two on chromosome 5. The region 30.73 to 32.47 Mb on chromosome 5 harbours multiple chitinase genes that are directly linked to ShB resistance in rice. The study highlights the intricate genetic control of ShB disease response governed by both minor and major QTLs which are notably independent of the QTLs associated with plant height. Further insights from multi-location testing of the RILs across different seasons and disease hotspots could help decipher on QTL X Environment interactions. This would aid in identifying stable and consistent ShB-resistant QTLs for use in marker-assisted breeding programs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04574-1.