Integrated multi-omics analysis reveals that salt-tolerant pepper enhances salinity adaptation through coordinated glutathione and galactose metabolism

Soil salinization severely limits pepper production. This study compared the salt-tolerant variety ‘Xiangla 762′ (XL762) and salt-sensitive ‘Xiangyan 1142’ (XY1142) under 150 mM NaCl to elucidate pepper ( Capsicum annuum L.) salt tolerance mechanisms. XL762 showed superior growth, with higher shoot and root dry weight under stress. Its roots had lower malondialdehyde (MDA) content but higher activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), indicating enhanced reactive oxygen species (ROS) scavenging and membrane stability. Integrated transcriptomic and metabolomic analyses identified the glutathione and galactose metabolism pathways as key differentiators. In XL762, the expression of related genes (e.g., CaGST-13, CaGLB1–3 ) was significantly higher, accompanied by specific accumulation of raffinose family oligosaccharides and glutathione-pathway metabolites. qRT-PCR validation confirmed that these key genes maintained high or induced expression in XL762 but were downregulated or weakly induced in XY1142 under salt stress. In summary, XL762 enhances salt adaptation by synergistically employing a pre-established antioxidant baseline and stress-induced osmolyte accumulation, coordinating redox and osmotic homeostasis. This study provides crucial candidate genes and metabolic markers for breeding salt-tolerant pepper.