Time-Series Transcriptome Reveals Differential Regulation of Flavonoid Biosynthesis in Dendrobium huoshanense Under Musical–Acoustic Stimuli: Insights for Green Horticultural Production

Background: Sound vibration is an emerging physical signal that influences plant growth and secondary metabolism; however, the genome-wide transcriptional responses of valuable medicinal orchids to complex acoustic stimuli remain largely uncharacterized. Methods: Here, we performed time-series RNA-seq on acclimatized plantlets of Dendrobium huoshanense exposed to two musically structured acoustic stimuli with contrasting acoustic characteristics (Forest Fantasy and Erquan Yingyue) plus a no-music control; leaf samples were collected at 1, 6, 12, and 24 h, and quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the transcriptome data. Results: The two acoustic treatments triggered distinct transcriptional reprogramming of flavonoid biosynthesis. Early biosynthetic genes chalcone synthase (CHS) and naringenin 7-O-methyltransferase (NOMT) were rapidly up-regulated under Forest Fantasy, whereas late-step modification genes (naringenin 3-dioxygenase (F3H), flavonoid 3′-monooxygenase (F3′H), hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT), caffeoyl-CoA O-methyltransferase (CCoAOMT)) were persistently suppressed by Erquan Yingyue. Differentially expressed gene (DEG)-derived hub structural genes (cinnamate 4-hydroxylase (C4H), F3′H, CCoAOMT) and co-expressed transcription factor candidates (MYB, WRKY, NAC) were identified via Pearson correlation-based network analysis. Conclusions: These results indicate that D. huoshanense can differentiate complex musical signals at the transcript level, suggesting short-term natural-style acoustic stimulation as a promising potential horticultural strategy for quality improvement of this precious medicinal orchid.