Effects of nitrogen management on grain yield, quality, and transcriptomic responses in rice

While nitrogen (N) fertilizer is critical for rice productivity, its effects on grain yield and quality and the associated transcriptional responses under field conditions remain incompletely characterized. In this study, we investigated the effects of different N management strategies, including varying N application rates and ratios, on rice yield, grain quality, and the transcriptional profiles of leaves at heading stage, using the high-quality japonica rice cultivar Liaojing 419. In 2023, a field experiment with four N application rates (0, 135, 225, and 315 kg ha −1 ) showed that increasing N levels significantly enhanced grain yield by increasing panicle number and grain number per panicle, while the highest N rate (315 kg ha −1 ) further improved milling quality but was accompanied by greater chalkiness and lower eating quality. These grain-quality changes coincided with increased protein content. Comparative transcriptomic analysis revealed that differential N application was associated with changes in the expression of genes related to amino acid metabolism and photosynthesis. In 2024, we further examined three N allocation ratios—basal:tiller:panicle ratios of 6:3:1 (S1), 5:3:2 (S2), and 4:3:3 (S3)-under a fixed total N rate of 225 kg ha −1 . N allocation ratios had relatively limited effects on agronomic and processing-quality traits. S3 increased chalkiness and total protein, particularly albumin, but did not significantly alter taste value, amylose content, or the levels of any of the 17 measured free amino acids. Transcriptomic analysis showed that S1 was associated with changes in photosynthesis-related genes, whereas S3 was associated with GO terms related to response to stimulus, without sufficient evidence to establish these responses as direct physiological stress effects. Moreover, N rates and, to a lesser extent, N allocation ratios altered the activities of several enzymes involved in starch and nitrogen metabolism during early grain filling. Overall, this study provides agronomic evidence and transcriptomic insights into how N management is associated with changes in rice grain yield and quality.