Integrated physiological and transcriptomic analysis reveals key genes and modules in Taraxacum mongolicum...

Waterlogging stress severely impairs plant growth and productivity. Taraxacum mongolicum Hand.-Mazz (T. mongolicum) exhibits notable resilience to this stress, yet its systemic adaptation mechanisms remain unexplored. This study integrated physiological and transcriptomic analyses to investigate dandelion's response to waterlogging. Physiologically, waterlogging induced oxidative stress, evidenced by increased H₂O₂ and MDA, while activating antioxidant enzymes (SOD, POD, CAT, APX), non-enzymatic antioxidants (GSH, GSSG) and accumulating osmolytes (proline, soluble sugars). Growth was significantly inhibited but partially recovered under moderate stress. Transcriptome profiling of roots and leaves revealed dynamic, tissue-specific responses. Early signaling and secondary metabolism were highlighted in leaves, whereas roots prioritized metabolic reprogramming (e.g., starch/sucrose metabolism) and transport. Weighted gene co-expression network analysis identified four key modules (MEgreen, MEpink, MEorange, MEcoral) strongly correlated with waterlogging traits. Hub genes within these modules function in circadian regulation (LUX, RVE8), secondary metabolism (HST-2), signaling (APRR1/5), and protein homeostasis (HSP70/90), forming a coordinated molecular network. Heatmap analysis further uncovering tissue- and time-specific expression patterns. Co-expression network analysis demonstrates that circadian clock-related core genes primarily coordinate downstream stress responses-such as ROS homeostasis and osmotic balance-indirectly through signal transduction cascades, forming a hierarchical "core regulation-signal transduction-effector execution" framework that parallels the circadian control of antioxidant defense in animals. Our findings elucidate the integrated mechanisms underlying dandelion's waterlogging tolerance and provide valuable genetic resources for crop improvement.