Identification and fine mapping of qTGW11, a QTL conferring high nitrogen use efficiency in Dongxiang wild rice (Oryza rufipogon Griff.)

The extensive utilization of synthetic nitrogen fertilizers has substantially increased crop yields while severely disrupting the ecological balance. Consequently, enhancing nitrogen use efficiency in crops has become imperative for sustainable agricultural development. Dongxiang wild rice (DXWR), demonstrating remarkable tolerance to low-nitrogen stress, represents a precious germplasm resource for breeding nitrogen-efficient rice cultivars. In this study, we conducted quantitative trait loci (QTL) mapping for plant height, effective panicle number, grain number per panicle, grain yield per plant, and thousand-grain weight under low-nitrogen and normal-nitrogen conditions using 150 backcross recombinant inbred lines (BILs) derived from a cross between the indica maintainer line GanxiangB and DXWR, with a genetic linkage map comprising 153 SSR markers. Of 23 QTLs identified across 11 chromosomes, 9 were consistently detected under both nitrogen conditions. A stable QTL qTGW11 was identified under both nitrogen conditions; explaining 8.37–9.57 % of the phenotypic variation. Through map-based cloning, qTGW11 was precisely localized to a 117-kb genomic region harboring 16 candidate genes, among which LOC_Os11g40100 was identified as the most likely causal gene through quantitative reverse transcription PCR (qRT-PCR) validation.