Comparative RNA-Seq and Phytochemical Profiling Reveal Year-Dependent Bioactive Variations and Delineate Key Metabolic Pathways in Polygonatum sibiricum Red. Rhizome Nodes

Polygonatum sibiricum Red. is a medicinal and edible homologous plant whose rhizome quality determines its clinical efficacy and commercial value. However, conventional evaluations typically treat the entire rhizome as homogeneous, overlooking the intrinsic heterogeneity along age nodes, and the regulatory mechanisms governing such age-dependent quality variation remain largely unclear. In this study, four-year-old rhizomes were precisely segmented into four age nodes (HJ1–HJ4), and the contents of polysaccharides, flavonoids, and saponins were systematically determined alongside comparative transcriptome sequencing to dissect the age-dependent bioactive variation and underlying molecular mechanisms. The three bioactive components exhibited markedly asynchronous accumulation patterns, with polysaccharides peaking at HJ3, flavonoids at HJ4, and saponins at HJ1. Transcriptomic analysis identified 19,638 differentially expressed genes (DEGs), with KEGG enrichment pointing to starch and sucrose metabolism, flavonoid biosynthesis, and steroid biosynthesis as the pivotal pathways. A coordinated transcriptional reprogramming emerged across development, characterized by early upregulation of backbone-construction genes and progressive activation of modification-and-decoration genes—yet it manifested through pathway-specific regulatory logics, with Mantel tests further confirming that key genes, including β-amylase3, CYP75B11, and squalene epoxidase (SQLE), were significantly correlated with the accumulation of polysaccharides, flavonoids, and saponins, respectively. These findings challenge the conventional assumption that older nodes are universally superior and establish that age-node differentiation reflects fundamental metabolic reprogramming, supporting a node-targeted utilization strategy encompassing HJ3 for polysaccharide-based products, HJ4 for antioxidant applications, HJ1 for saponin extraction, and HJ2 for bulk materials, while providing both mechanistic insights and practical guidance for precision harvesting and quality-oriented management of P. sibiricum.