Root system architecture modulates nitrogen uptake and use efficiency, influencing grain yield in rice

Nitrogen (N) is essential for rice productivity, yet excessive fertilization increases costs and environmental risks, making improvement of nitrogen use efficiency (NUE) a key breeding target. We evaluated 99 rice genotypes to investigate relationships between root system architecture (RSA) and NUE using three complementary experiments. In hydroponics under full (N100) and half N (N50), ImageJ-SmartRoot analysis revealed substantial variation in RSA. Principal component analysis identified 12 contrasting genotypes with vigorous and weak RSA, which were further evaluated under pot and field conditions. Under pot conditions, DJ123 and KSK-133 maintained the highest grain yields under reduced nitrogen, whereas IR30 and TKM6 showed the lowest yields. Thousand grain weight (TGW) under the same treatment was also highest in KSK-133 (15.8 g) and DJ123 (15.3 g), compared with IR30 (6.6 g) and TKM6 (7.6 g). Field results confirmed this trend, with TGW ranging from 23.9 g in KSK-133 to only 11.4 g in TKM6 under N50. Ammonium nutrition improved SPAD, biomass, and yield by up to 7.65%, 25.3%, and 27.2%, respectively, compared with nitrate. Efficient genotypes maintained superior performance under reduced N, with DJ123 and KSK-133 showing up to 10.3% and 43.2% increases in nitrate reductase activity. Overall, these genotypes represent promising donor parents and can serve as valuable genetic resources for breeding rice with enhanced NUE and stable yield under low-N conditions.