The homeostasis of ions and reactive oxygen species in root and shoot play crucial roles in the tolerance of alfalfa to salt alkali stress.

High pH saline-alkali stress, mainly NaHCO, limited the development of animal husbandry in Songnen Plain. Ion imbalance and reactive oxygen species (ROS) metabolism disorder caused by saline-alkali stress inhibited plant growth. In this study, we compared the differences in ion absorption, transport and ROS metabolism between saline-tolerant alfalfa (ZD) and saline-sensitive alfalfa (ZM) under NaHCO stress using physiology and transcripomics techniques. WGCNA analysis identified key genes associated with NaHCO stress-induced changes. NaHCO stress inhibited the absorption of K and Mg, but activated Ca signal. Furthermore, ZD maintained higher K, Mg and Ca contents and the K/Na ratio than ZM, this is mainly related to the higher expression of proteins or channel-encoding genes involved in ion absorption and transport in ZD. Antioxidant enzyme systems can be activated in response to NaHCO stress. Peroxidase (EC 1.11.1.6), catalase (EC 1.11.1.7) and glutathione transferase (EC 2.5.1.18) activities were higher in ZD than ZM, and most genes encoding the relevant enzymes also demonstrated a stronger up-regulation trend in ZD. Although NaHCO stress inhibited Trx-Prx pathway, ZD related enzymes and their genes were also inhibited less than ZM. WGCNA results identified many genes involved in ion absorption, transport and antioxidant systems that play an important role in NaHCO stress adaptation. Collectively, ZD has the stronger ion homeostasis regulation and ROS scavenging ability, so it's more resistant to NaHCO. The results provide theoretical guidance for further understanding of the molecular mechanism of NaHCO resistance and provide potential genes for research to improve saline-alkali tolerance in alfalfa.