QTL-Seq and pyramiding of yield-related loci from wild rice (Oryza rufipogon Griff.) introgression lines under nutrient-deficient conditions

). Selected F₃ pyramiding lines (PyL) developed through marker-assisted selection showed a 16-40% increase in panicle weight under no nitrogen (-N) conditions. Under nutrient-deficient (-NPK) conditions, the selected pyramiding line PyL14 showed a tendency towards higher brown rice yield (approximately 12%) compared with the best introgression line parent (KRIL8). Although the difference was not statistically significant, the trend shows a positive interaction between the pyramided QTLs. Candidate genes harboring nonsynonymous SNPs with high SNP indices were identified, and cultivar-specific expression patterns were observed for these genes under low ammonium conditions, including genes associated with yield-related traits and nutrient transport. These results identify PyL14 as a promising genetic resource with the potential to improve rice yield under nutrient-deficient conditions. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-026-01651-y.