Genotyping by sequencing of wild interspecific mapping population detected novel genetic locus harbouring OsPT11for rice yield under nutrient stress conditions

Nutrient deficiency is a major constraint to crop production, severely impairing crop establishment and yield. The development of high-yielding cultivars with enhanced tolerance to limited nutrient availability is therefore essential for sustainable crop production. Wild introgression lines, which have evolved to grow and reproduce under adverse environmental conditions, represent valuable genetic resources and potential donors of traits and genes that confer adaptation to nutrient-limited environments. In this study, wild introgression lines derived from Oryza rufipogon were evaluated across six environments, comprising four environments under the recommended dose of phosphorus (RDP) and two environments under low-phosphorus (low P) conditions. Genotyping-by-sequencing (GBS) enabled the identification of 113 quantitative trait loci (QTLs) associated with key agronomic traits. Of these, 41 major QTLs were detected under RDP, while 21 major QTLs were identified under low P stress, explaining up to 28.06% and 30.23% of the phenotypic variance, respectively. Notably, two major QTLs governing grain yield were consistently detected under low-phosphorus conditions, with favourable alleles enhancing yield derived from O. rufipogon. QTLs for days to 50% flowering, number of tillers per plant, and number of productive tillers per plant were consistently identified across both environments. Furthermore, a QTL hotspot region was detected on chromosome 1, harbouring eight QTLs associated with biomass, total tiller number, productive tiller number, total dry matter, and thousand-grain weight. Candidate gene analysis within this hotspot region identified the Pi t ransporter gene OsPT11 , which is involved in phosphorus acquisition and translocation and plays a key role in activating mycorrhizal symbiosis. These findings suggest that this QTL region represents a promising target for improving grain yield under low-nutrient conditions and may enhance root–microbiome interactions, facilitating more efficient nutrient uptake under stress. Declaration of generative AI and AI-assisted technologies in the preparation of graphical abstract AI-based tools were used to assist in the conceptual design of the graphical abstract. All content was critically reviewed, edited, and finalized by the authors. • An interspecific population derived from Oryza sativa / Oryza rufipogon cross was evaluated for yield performance under optimum and low RDP • GBS-based QTL mapping revealed novel genomic regions for nutrient stress tolerance • QTL hotspot region detected on chromosome 1, harboured the candidate gene OsPT11 for Pi acquisition, translocation and activation of mycorrhizal symbiosis at phosphorus starvation