Network-Based Transcriptomic Analysis of Waterlogging Stress Responses in Panax ginseng

다국어 초록 (Multilingual Abstract)

Panax ginseng is a perennial crop cultivated in the same field for several years, leading to a gradual shortage of suitable new land for production. Consequently, cultivation has expanded into paddy fields, where waterlogging has emerged as a major constraint. Even when soil remains chronically wet without visible symptoms, root yield and quality can decline. However, the time-dependent transcriptomic adaptations that enable ginseng roots to cope with such conditions remain poorly understood. This study investigated transcriptomic adaptation in roots of one-year-old 'Yunpoong' plants exposed to sustained waterlogging at 45–55% volumetric soil water content (VSWC). Root samples were collected at 0, 1, 2, and 3 weeks post-treatment for RNA-Seq analysis (three biological replicates, 24 libraries total). Hyperspectral imaging (400–1000 nm) and NDVI analysis revealed no significant differences in shoot morphology or spectral characteristics between treatments, confirming establishment of a non-necrotic ambient waterlogging model. Differential expression analysis using DESeq2 (FDR < 0.05, |log₂FC| ≥ 1) identified 6,448 unique differentially expressed genes (DEGs) across the treatment period. Approximately 68% of these DEGs were specific to week 3, indicating large-scale transcriptome reprogramming under prolonged waterlogging. Gene Ontology enrichment analysis revealed three distinct adaptation phases: week 1 featured early defense responses involving hypoxia, jasmonic acid signaling, and lignin related processes; week 2 reflected an adaptive stabilization phase characterized by water-deprivation responses and attenuation of endoplasmic reticulum stress; and week 3 exhibited long-term metabolic reconfiguration with glycolysis activation, phosphate-starvation responses, and suppression of photosynthesis related processes. Weighted gene co-expression network analysis (WGCNA) identified four modules strongly correlated with treatment duration and waterlogging conditions. Protein–protein interaction (PPI) analysis of 1,100 genes from these modules yielded six high-confidence subnetworks. By integrating week3 DEGs, enriched GO terms, and PPI network nodes, six key waterlogging responsive genes (glyceraldehyde-3-phosphate dehydrogenase C2, malate dehydrogenase, phosphoglucose isomerase 1, phosphoenolpyruvate carboxylase 1, light-harvesting chlorophyll-protein complex II subunit B1, Granulin repeat cysteine protease family protein) were identified. These genes integrate carbon, energy, and phosphate metabolism, modulate the photosystem II antenna complex, and regulate circadian linked proteolysis. This study provides a systems-level view of three phase transcriptomic adaptation in ginseng roots under non-necrotic ambient waterlogging. The identified genes and regulatory modules provide targets for functional validation and foundation for developing molecular markers for early stress detection in Panax ginseng.

목차 (Table of Contents)

• Ⅰ. INTRODUCTION 1
• Ⅱ. RESEARCH HISTORY 4
• 2.1 Panax ginseng: cultivation and waterlogging sensitivity 4
• 2.2 Crop responses to waterlogging and submergence stress 6
• 2.3 Hyperspectral imaging and RNA-Seq network analysis 9
• Ⅲ. MATERIALS AND METHODS 13
• 3.1 Plant materials, growth conditions, and RNA-Seq data production 13
• 3.2 Hyperspectral image acquisition and analysis 14
• 3.3 RNA-Seq preprocessing, differential expression, and GO analysis 15
• 3.3.1 Read preprocessing and quality control 15
• 3.3.2 Transcript quantification and gene level summarization 16
• 3.3.3 Differential expression analysis 17
• 3.3.4 GO enrichment analysis 17
• 3.4 WGCNA, PPI analysis, and candidate gene selection 18
• 3.4.1 Weighted gene co-expression network analysis (WGCNA) 18
• 3.4.2 Protein-protein interaction network analysis 19
• 3.4.3 Selection of key ambient waterlogging responsive genes 20
• Ⅳ. RESULTS 22
• 4.1 Ambient waterlogging model and hyperspectral validation 22
• 4.2 Global RNA-Seq patterns and DEG overview 26
• 4.3 GO based temporal reprogramming under ambient waterlogging 36
• 4.4 WGCNA modules associated with time and condition 46
• 4.5 PPI subnetworks and key ambient waterlogging responsive genes 50
• V. DISCUSSION 67
• 5.1 Establishment of an ambient waterlogging model in ginseng 67
• 5.2 Phase specific transcriptional reprogramming 70
• 5.2.1 DEG based three phase response framework 70
• 5.2.2 Transcriptional axes of the early phase (Week 1) 71
• 5.2.3 Functional characteristics of the adaptation phase (Week 2) 76
• 5.2.4 Long term reprogramming phase (Week 3) 81
• 5.2.5 Integrated view of phase specific reprogramming 87
• 5.3 PPI modules underlying ambient waterlogging responses 88
• 5.3.1 Selection of WGCNA derived seed genes and construction of the PPI network 88
• 5.3.2 Functional interpretation of condition and time associated PPI subnetworks 89
• 5.4 Network modules and key genes in ambient waterlogging adaptation 99
• REFERENCE 103
• 국문초록 114