Time-Course Transcriptome Analysis Reveals Dynamic Nitrogen Response Mechanisms and Key Regulatory Networks in Sugarcane

Nitrogen is an essential mineral nutrient for plant growth and development. However, the molecular response mechanisms of sugarcane under varying nitrogen regimes remain unclear. This study investigated the dynamic responses of sugarcane (GT42) leaves to nitrogen treatment using hydroponic systems. Leaf samples were collected under low nitrogen (LN, 0.2 mM NH4NO3) and normal nitrogen (NN, 2 mM NH4NO3) treatments at 1, 3, 6, 12, 24, 48, and 72 h, as well as under high nitrogen (HN, 6 mM NH4NO3) treatment at 3, 6, and 24 h. RNA-Seq analysis identified differentially expressed genes (DEGs) between LN/NN and HN/NN treatments at corresponding time points. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs from both LN/NN and HN/NN comparisons revealed significant enrichment in nitrogen metabolism and zeatin biosynthesis pathways. These findings aligned with our Weighted Gene Co-Expression Network Analysis (WGCNA) results from LN-treated samples. Through detailed reconstruction of the nitrogen metabolic pathway and zeatin biosynthesis co-expression networks, we established their pivotal regulatory roles in sugarcane’s adaptation to varying nitrogen availability. Our results demonstrate a dynamic, concentration-dependent regulatory network in sugarcane leaves under nitrogen treatment. These findings provide potential targets for improving nitrogen use efficiency (NUE) in sugarcane breeding programs. The study offers new insights into the molecular mechanisms underlying sugarcane’s response to nitrogen fluctuations, with implications for developing nitrogen-efficient cultivars.