Physiological and molecular mechanisms underlying waterlogging tolerance in Salvia miltiorrhiza: Implications for breeding stress-resilient crops

Waterlogging (WG) severely constrains the productivity and pharmacological quality of medicinal crops. However, the molecular and physiological mechanisms underlying the responses of Salvia miltiorrhiza to WG stress remain poorly understood. In this study, we compared a WG-tolerant variety (WTV) to a WG-sensitive variety (WSV) using integrated morphological, physiological, and transcriptomic analyses. The WTV exhibited significantly less root damage and developed adaptive features, such as thickened stomatal walls and elongated epidermal hairs, under WG conditions. Scanning electron microscopy further revealed a higher reduction in stomatal aperture and thicker guard cell walls in the WTV, indicating enhanced ability to limit water loss and maintain hydraulic stability. Physiologically, the WTV displayed stronger antioxidant capacity, with a greater increase in peroxidase activity and lower malondialdehyde accumulation than the WSV ( p < 0.01), indicating a more efficient reactive oxygen species (ROS) scavenging system. Transcriptomic profiling revealed extensive transcriptional reprogramming under WG conditions, with global repression of photosynthesis-, carbohydrate-, and secondary metabolism-related pathways. Although both phenylpropanoid and terpenoid biosynthetic pathways were downregulated, the WTV attenuated the suppression of key metabolic genes ( PAL , 4CL , DXS , and HDS ), reflecting greater metabolic stability. Concurrent enrichment of plant–pathogen interactions and defense-related signaling genes in the WTV suggested enhanced stress perception and energy reallocation under hypoxia. Collectively, these findings revealed that the WTV achieves superior WG tolerance through coordinated antioxidant regulation, energy-saving photosynthetic suppression, and structural adaptation. This study provides valuable insights into the molecular breeding of waterlogging-tolerant S. miltiorrhiza and offers a framework for enhancing the resilience of medicinal crops to increasingly frequent flooding.