Integrated transcriptomics, proteomics, and metabolomics offer novel insights into salt resistance in soybean

Soybean productivity and planting area are severely limited by salt stress, and growing salt-tolerant cultivars is an effective countermeasure. However, the molecular mechanisms underlying soybean adaptation to salt stress remain unclear. Here, we investigated adaptive mechanisms of the salt-sensitive “Dongnong50 (D)” together with salt-tolerant variety “Qihuang34 (Q)” under salt-induced stress through phenotypic, physiological, proteomic, transcriptomic, and metabolomic analyses. Salt-tolerant cultivars can sustain improved growth metrics, upsurged antioxidant enzyme functions, and reduced malondialdehyde when exposed to salt stress. Under salt stress, the variety Q displayed 3278 differentially expressed genes (DEGs), 637 differentially expressed proteins (DEPs), and 403 differentially abundant metabolites (DAMs). In contrast, the variety D exhibited 11,875 DEGs, 643 DEPs, and 408 DAMs. Activating flavonoid biosynthesis, glutathione metabolism, and ABC transporter synthesis pathways is crucial for soybean adaptation to salt stress. The Q variety showed that increased transcription levels and protein abundance of CYP75B1 (Glyma.05G022100) and glutathione S-transferase (GST) (Glyma.08G174900 and Glyma.10G192900), as well as enhanced stability and content of certain metabolites (e.g., luteolin), result in reactive oxygen species clearance. Meanwhile, seven organic acids also exhibit high accumulation. Consequently, these candidate genes and metabolites may mediate salt stress adaptation. Also, higher protein abundance of ABCB1 and ABCC10 may help the Q variety maintain ion homeostasis and hormone transport, thereby aiding adaptation to salt stress. The presented results provide substantial insight into the molecular underpinnings of soybean responses to salt stress, thereby facilitating the generation of improved salt-tolerant soybean cultivars. • Multi-omics and physiological indicators analyze the differences in soybean salt response. • Flavonoids, GSH and ABC transporter are the key for soybean to adapt to salt stress. • Luteolin and γ-GC are the key metabolites for salt stress adaptability. • CYP75B1 and GST may affect the differences in salt stress adaptability. • ABCB1 and ABCC10 contribute to the ionic balance of salt-tolerant variety.