Reducing nitrogen application at the panicle stage improves eating quality of high-quality late indica rice by optimizing starch structure, functionality and sucrose metabolism

Reduced panicle nitrogen fertilizer (PNF) impacts indica rice grain quality by altering starch and protein composition, but the underlying mechanisms remain unclear. Field and pot experiments involving four PNF treatments (NE: full basal shift; LN: zero panicle nitrogen; DN: 50% reduction in panicle nitrogen; NN: normal panicle nitrogen) showed that, compared to the NN treatment, the NE, LN, and DN significantly increased amylose content while decreasing processing and appearance qualities, and protein content. Meanwhile, the LN and DN treatments decreased the proportion of amylopectin extremely short chains (DP 0-12) and short chains (DP 13-36), large granule starch, and starch gelatinization enthalpy, while increased the amylose extremely long chain, resulted in increasing peak viscosity and breakdown, and decreasing setback, ultimately improving rice eating quality. Furthermore, compared to the NN treatment, both the NE and LN treatments significantly downregulated genes governing nucleic acid processing (endonucleases, phosphodiester hydrolysis), RNA modification, and chloroplast function; and the anabolic substances related to protein, including sphingolipids, amino acids, and purines, thereby impairing grain filling and diminishing the processing, appearance, and nutritional qualities. In contrast, the LN and DN treatments upregulated genes involved in trehalose synthesis, driving the conversion of trehalose to glucose-1-phosphate and thereby facilitating ADP-glucose formation. These metabolic approaches decreased short-chain amylopectin synthesis while increasing long-chain amylose, contributing to the improvement of rice eating quality, especially for high-quality indica rice. Overall, the DN treatment achieves the optimal improvement effect on eating quality while ensuring good agronomic traits of the rice.