Transcriptional and Physiological Analysis Reveal New Insights into the Regulation of Fertilization (N, P, K) on the Growth and Synthesis of Medicinal Components of Dendrobium denneanum

Dendrobium denneanum is an important medicinal and ornamental plant. Its ornamental and medicinal values are affected by its vegetative growth conditions and chemical composition accumulation. This study adopted an orthogonal experimental design to treat D. denneanum with nine different levels of nitrogen (N), potassium (K), and phosphorus (P). The morphological indicators of the plant were positively correlated with the nitrogen concentration. The polysaccharide content was the highest at 1500 mg·L(−1) nitrogen and 3000 mg·L(−1) phosphorous and was 26.84% greater than the control. The flavonoid content increased by 36.2% at 500 mg·L(−1) nitrogen, 2000 mg·L(−1) phosphorous, and 300 mg·L(−1) potassium. Principal component score analysis showed that nitrogen had the most significant impact on the various indicators of D. denneanum, followed by phosphorus and potassium. The comprehensive score showed that the T9 treatment (N: 1500 mg·L(−1), P: 3000 mg·L(−1), K: 500 mg·L(−1)) had the strongest effect on D. denneanum. Transcriptional analysis showed that compared with the control, the T9 treatment led to 2277 differentially expressed genes (1230 upregulated and 1047 downregulated). This includes fifteen genes enriched in the MAPK signaling pathway, five genes in phenylpropanoid biosynthesis, and two genes in flavonoid biosynthesis. These genes may be involved in regulating plant growth and the biosynthesis of polysaccharides and flavonoids. This study provides guidance for the optimal use of N, P, and K in the cultivation of D. denneanum.