Multi-Omics Analysis Reveals Molecular and Biochemical Mechanisms Underlying Alkaline Stress Adaptation in Solanum lycopersicum L.

Alkaline stress significantly disrupts plant metabolism by affecting osmotic and ionic balance, impairing ion uptake, destabilising cellular ion homeostasis, and inhibiting growth and productivity. This study investigates the adaptive responses of Solanum lycopersicum L. to alkaline stress through an integrative omics approach, encompassing transcriptomics, biochemical changes, and leaf ion concentration. Two tomato lines, A10 (tolerant) and M56 (sensitive), were selected based on their contrasting responses to alkaline stress. Hydroponically grown plants were subjected to Hoagland solution adjusted to two pH levels, 8.2 or 9.2, using NaOH concentrations of 1 mM or 1.5 mM. Transcriptomic analysis revealed minimal gene expression changes in M56 under alkaline stress, while A10 showed marked modulation of MAPK and ethylene signalling pathways. The upregulation of SlGAD1 and SlGAD2 at pH 8.2 resulted in maximum GABA accumulation in the A10 genotype. Additionally, elevated glutamate levels were observed at pH 9.2. In M56, both proline and polyphenol contents declined under alkaline stress. Proline decreased by 26.56% at pH 8.2 and 37.67% at pH 9.2, while polyphenol levels dropped slightly by 1.85% at pH 8.2 and more significantly by 33.06% at pH 9.2. In contrast, A10 showed increased proline levels of 17.4% at pH 8.2 and 36.92% at pH 9.2, alongside a marked rise in polyphenol content, with increases of 58.81% at pH 8.2 and 96.42% at pH 9.2. Ionomic analysis revealed a substantial increase in sodium uptake in M56 (6.5- and 9-fold at pH 8.2 and 9.2, respectively), compared to controls, while A10 exhibited a relatively moderated sodium uptake (5- and 4-fold, respectively). The A10 line unveiled multifaceted mechanisms of tolerance to alkaline stress, comprising the modulation of oxidative stress response genes, enhanced proline and polyphenol biosynthesis, and restricted sodium uptake. These findings provide insights into the molecular and physiological responses to alkaline stress in tomatoes, suggesting potential targets for breeding stress-tolerant cultivars.