Interactive Effects of Nitrogen Application Rate and Fertilization Method on Yield, Quality, and Grain-Filling Characteristics of High-Quality japonica Rice Koshihikari

To elucidate the synergistic effects of nitrogen application rate and fertilization method on the yield and quality of high-quality japonica rice, a two-year field experiment (2024 and 2025) was conducted using Koshihikari with three fertilization methods—farmers’ practice (FP), light and simplified fertilization (LSF), and precise quantitative side-deep fertilization (PQSF)—and five nitrogen rates (0, 45, 90, 135, and 180 kg ha−1). In 2024, comprehensive traits were evaluated, including grain-filling dynamics, protein fractions, panicle traits, milling quality, multidimensional quality, and yield. In 2025, only core yield and quality traits were measured for validation. Superior grains had higher filling rates and earlier initiation, whereas inferior grains showed delayed initiation and later peak timing; however, high nitrogen shortened effective filling duration and exacerbated delayed filling in inferior grains. Protein accumulation was closely associated with grain-filling parameters, with glutelin and prolamin showing more persistent associations than albumin and globulin. Milling quality was optimal at 90 kg ha−1 (N90), whereas appearance and eating quality deteriorated with increasing nitrogen; springiness and adhesion force peaked at N45. Under high nitrogen, PQSF sustained inferior grain filling and mitigated the negative effects of excessive storage protein accumulation on eating quality. LSF achieved the highest yield (approximately 8900 kg ha−1) within 135–153 kg ha−1, whereas PQSF combined with 135 kg ha−1 provided a quality-oriented strategy, increasing taste value by 3.00 and 2.33 points and reducing chalkiness percentage by 1.70 and 0.25 percentage points relative to FP and LSF, respectively, while maintaining lower hardness. PCA and hierarchical clustering analyses revealed that nitrogen rate established the fundamental framework for yield and quality, while fertilization method provided secondary regulation. The core yield and quality findings were consistent across both years, confirming the robustness of the conclusions and providing a basis for precise nitrogen management of high-quality japonica rice in the Liaodong coastal rice region; however, the mechanistic insights were mainly derived from 2024 and require further multi-year validation.