Nitrogen fertilizer application rate and storage duration are critical agronomic and environmental factors affecting rice quality stability. The milling appearance, eating and nutritional quality, physicochemical properties, microstructure, and volatile metabolic profiles during long-term storage were investigated using three indica-japonica hybrid cultivars at four nitrogen fertilizer application levels. High nitrogen fertilizer application (300 kg hm⁻²) promoted an over-filled protein matrix and induced structural defects such as micropores in starch granules, which acted as “trigger points” for accelerated aging. Specifically, storage duration was the dominant factor reshaping volatile profiles and lipid degradation, but high nitrogen amplified these effects by promoting lipid oxidation and the accumulation of off-flavor compounds. Correlation analysis revealed that gel consistency (GC) is a core determinant of eating quality, exhibiting significant negative correlations with amylose content, setback, hardness and fatty acid values, while showing positive correlations with peak viscosity, breakdown value, and adhesiveness. All correlation patterns collectively contributed to the deterioration of rice eating quality after storage, indicating GC might be served as an indirect indicator for evaluating rice deterioration and applied in the breeding of rice varieties with improved storage tolerance. Microstructural analysis via SEM high nitrogen induced distinct cultivar-specific deterioration characteristics after 12 months storage.

Chalkiness is a complex quantitative trait regulated by both genetic and environmental factors. Reducing chalkiness has long been a research focus in rice genetics and breeding. A total of 108 markers on/closely linked to starch biosynthesizing genes, grain shape and chalkiness QTLs were used to detect interactions affecting chalkiness. A total of 30 and 39 marker pairs with significant bigenic epistasis were identified for percentage of grain with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), respectively, of which 16 were commonly found in both traits. Using markers associated with chalkiness and marker pairs with significant epistatic effects as candidate predictors increased the coefficient of determination (R²) of the best multiple regression models for predicting both traits. GBSSI, SSIIa and the interaction between GBSSI and GBSSII were consistently identified in optimal models, indicating their critical roles in regulating rice chalkiness. R² for DEC and PGWC ranged from 36.5% to 42.7% and from 52.9% to 73.8% in two environments, respectively. PGWC decreased significantly from 38.9% to 15.10% after three cycles using marker-assisted recurrent selection (MARS). This study suggests that epistasis contributes substantially to the regulation of chalkiness, and demonstrates that MARS can effectively improve chalkiness without imposing obvious negative impacts on eating quality.