Time-Resolved Transcriptome and Network Remodeling in Panax ginseng Under Pre-Symptomatic Ambient Waterlogging

Korean ginseng (Panax ginseng C. A. Meyer) is a perennial medicinal crop highly sensitive to waterlogging stress. Although excess soil moisture is known to induce oxygen limitation in the rhizosphere, the resulting metabolic constraints may precede visible shoot symptoms such as wilting, chlorosis, or necrosis. To examine the molecular responses under sustained high soil moisture before overt shoot necrosis, one-year-old ‘Yunpoong’ plants were exposed to ambient waterlogging at 45–55% volumetric soil water content (VSWC), while control plants were maintained at 25% VSWC. Phenotypic observations and hyperspectral imaging were conducted immediately after treatment initiation (week 0) and at weeks 1, 2, and 3, whereas whole-plant samples for RNA-seq were collected at weeks 1–3. Hyperspectral imaging and normalized difference vegetation index (NDVI) analysis indicated limited temporal changes in canopy-level spectral traits during the treatment period. In contrast, transcriptomic analyses revealed time-dependent changes in whole-plant gene expression. A total of 6448 unique differentially expressed genes (DEGs) were identified, of which 4369 were specific to week 3. Gene Ontology (GO) enrichment analysis suggested a stepwise adaptive pattern consisting of early priming, transient stabilization, and long-term remodeling. Hypoxia-, jasmonic acid-, and lignin-related processes were enriched at week 1, water deprivation and protein quality control responses were adjusted at week 2, and glycolysis, phosphate starvation, and repression of growth-related processes became prominent at week 3. Weighted gene co-expression network analysis (WGCNA) and STRING-based protein–protein interaction (PPI) analysis further identified functional modules associated with RNA processing, photosystem regulation, proteostasis, and central carbon, energy, and phosphate metabolism. Integrated transcriptome and network analyses prioritized six candidate genes, GAPC2, MDH, PGI1, PPC1, Lhb1B1, and RD21A, for further functional validation in relation to prolonged ambient waterlogging responses.