Transcriptome and Metabolome-Based Analysis of Carbon–Nitrogen Co-Application Effects on Fe/Zn Contents in Dendrobium officinale and Its Metabolic Molecular Mechanisms

To explore the impact of combined carbon–nitrogen fertilization on the concentrations of Fe (ferrum) and Zn (zinc) in Dendrobium officinale (D. officinale), and to elucidate the underlying metabolic regulatory mechanisms, two-year-old seedlings of D. officinale were selected as the experimental subjects. Three treatment groups were established: a control group (CK), an α-ketoglutaric acid (AKG) treatment group (C treatment, CT), a urea treatment group (N treatment, NT), and an AKG and urea combined treatment group (CT_NT). Samples were collected at 0, 8, 16, 24, and 32 days post-treatment. Physiological and biochemical analyses measured stem contents of iron, zinc, copper, nitrate nitrogen, soluble proteins, and citric acid. Transcriptomic and metabolomic technologies were employed to elucidate molecular mechanisms. Physiological studies have shown that combined carbon–nitrogen application exerts time-dependent regulation on Fe, Zn, and their key metabolites in the stems of D. officinale, presenting a trend of first increasing and then decreasing. Metabolomic analysis revealed that flavonoids, phenolic compounds, and organic acids are involved in Fe chelation, while quercetin, dopamine, and other substances promote Zn absorption. Transcriptomic analysis indicated that combined carbon–nitrogen application activates the accumulation of Fe and Zn contents by upregulating the expression of related genes. Integrated analysis demonstrated that carbon–nitrogen metabolism affects the metabolic network of D. officinale by regulating primary and secondary metabolic pathways. This study elucidated the physiological and molecular mechanisms underlying the regulation of Fe and Zn contents in D. officinale by combined carbon–nitrogen application, providing theoretical support and a scientific basis for the high-efficiency cultivation and quality improvement of D. officinale.