Abstract

Soil salinisation has become one of the major abiotic stresses limiting crop growth in the world. To enhance soybean productivity on saline lands, understanding its salt-stress response and underlying mechanisms is necessary. In this study, the salt-tolerant soybean Kefeng 1 and the salt-sensitive soybean Qihuang 1 were used to elucidate the synergistic regulatory networks underlying soybean salt tolerance. After 12 days of 150 mM NaCl treatment, both varieties were subjected to phenotypic evaluation, physiological measurements, and integrated transcriptomic and metabolomic analysis. The results showed that the salt tolerance in Kefeng 1 primarily originated from its root. Under salt stress, Kefeng 1 maintained Na+/K+ion homeostasis by up-regulatingCation/H+Exchanger 15(CHX15) andCation Exchanger 3(CAX3), and down-regulatingCyclic Nucleotide-Gated Channel 13(CNGC13). Furthermore, Kefeng 1 stabilised auxin (IAA) homeostasis by inhibiting IAA biosynthesis and regulating concentrations through PIN-FORMED 3 (PIN3)-mediated efflux. It also scavenged reactive oxygen species (ROS) by employing enhanced enzymatic antioxidant systems, specifically aldo-keto reductase 1 (AKR1), glutathione S-transferase (GST), and catalase (CAT), alongside non-enzymatic antioxidants like the isoflavone genistein. Gene–metabolite correlation network analysis identifiedGlyma.09G117900(PIN3) andGlyma.19G244200(AKR1) as two hub genes. These two genes were specifically up-regulated in Kefeng 1 root under NaCl stress, and the proteins they encoded played important roles in salt tolerance in Kefeng 1 root as described above. Accordingly, these two genes were identified as candidate genes for salt tolerance in Kefeng 1. This study offered a theoretical framework and genetic resources for developing salt-tolerant soybean cultivars.