Glutathione metabolism is a central pathway in tomato (Solanum lycopersicum L.) roots responding to salt, alkali, and combined saline-alkaline stresses

To explore the physiological and molecular mechanisms underlying tomato root responses to salt stress, alkali stress, and combined saline-alkaline stress. Here, the tomato cultivar ‘M82’ was cultivated with the following four treatments: (1) 1x Hoagland nutrient solution (control; CK); (2) 1x Hoagland nutrient solution + 100 mmol/L NaCl (NC); (3) 1x Hoagland nutrient solution + 100 mmol/L NaHCO 3 (NH); and (4) 1x Hoagland nutrient solution + 50 mmol/LNaCl+50 mmol/L NaHCO 3 (NB). The root morphological traits, physiological parameters, transcriptomic profiles, and metabolomic signatures of the plants under these treatments were analyzed. In this experiment, the three stresses significantly inhibited root growth through distinct mechanisms: NC reduced branch number and total length, NH diminished surface area and diameter, while NB synergistically suppressed root volume. In addition, these stresses activated antioxidant enzymes and elevated oxidative markers, indicating stress-specific defense strategies. Furthermore, a combined analysis of the transcriptome and metabolome of roots revealed that 39 metabolic pathways were enriched which included biosynthesis of secondary metabolites and plant hormone signal transduction were enriched under salt stress. Notably, alkali stress resulted in extensive pathway enrichment [7527 differentially expressed genes (DEGs)], sharing the three most significantly enriched pathways with salt stress treatment. The combination of saline and alkali stress specifically activated the glutathione metabolic pathway, with 56.6 % of DEGs encoding glutathione S-transferases (GSTs), pivotal for detoxification and redox homeostasis. Besides, the study found that a coordinated network involving the upregulation of SlGRAS1/2/4 transcription factors (161.97 % induction under NH) and GSH biosynthetic genes (GSH1, GR) underpinned pH adaptation. Meanwhile, non-additive effects were observed in NB, with a lower suppression of SlGRAS10 (−25.12 %) than under NH (−66.25 %), suggesting a cross-talk that buffers oxidative damage. These findings provide novel insights for breeding saline-alkaline-resilient crops and designing stress management strategies targeting glutathione metabolism.