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

Developing rice cultivars adapted to low-nutrient conditions is essential for sustainable production, and wild rice offers valuable genetic resources for improving stress resilience in cultivated varieties. In this study, we demonstrate that pyramiding yield-related quantitative trait loci (QTLs) derived from wild rice enhances panicle yield under nutrient-limited conditions. Two wild rice introgression lines, KRIL8 and KRIL37, each carrying a small Oryza rufipogon genomic segment in the O. sativa L. cv. Koshihikari background, exhibited significantly higher panicle weight than the recurrent parent (KH) under limiting nitrogen and/or NPK (nitrogen, phosphorus, potassium) conditions. Using next-generation sequencing-based QTL-seq analysis, QTLs associated with panicle weight were identified in KRIL8 ( qPW1 ) and KRIL37 ( qPW6 ). 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.