Physiological, transcriptomic and metabolomic dissection of GABA-mediated salt tolerance in Phaseolus vulgaris

Introduction Soil salinization is a critical abiotic stressor that severely compromises common bean ( Phaseolus vulgaris L .) growth and productivity by disrupting photosynthetic performance and inducing oxidative damage and ion imbalance. Gamma-aminobutyric acid (GABA), a non-protein amino acid, plays an important role in plant responses to salt stress; however, its regulatory mechanisms in common bean remain insufficiently understood. Methods Using the salt-sensitive common bean germplasm ‘Kaiman Brown’, we investigated the effects of exogenous GABA under salt stress by integrating physiological measurements, transcriptomic analysis, pan-targeted metabolomics, and weighted gene co-expression network analysis (WGCNA). Results Exogenous GABA alleviated salt-induced growth inhibition, enhanced the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), reduced malondialdehyde (MDA) accumulation and electrolyte leakage, and improved photosynthetic performance. Integrated omics analyses identified candidate pathways associated with GABA treatment, including the GABA shunt, 2-oxocarboxylic acid metabolism, abscisic acid (ABA)-associated signaling, flavonoid metabolism, and lignin biosynthesis. Candidate genes, including PLIP1, CHS, BCAT, PRODH, and GS, may be involved in the metabolic and stress-responsive processes associated with GABA treatment. Discussion These findings provide integrated physiological and molecular insights into the responses of common bean to salt stress following exogenous GABA application. The identified pathways and candidate genes provide a basis for further functional validation, although their direct causal roles and effects on metabolic fluxes remain to be established.