Functional analysis of tomato SlPP2C-A gene subfamily, highlighting SlPP2C7’s role in regulating saline-alkali stress tolerance

The type A protein phosphatase 2C (PP2C-A) gene family is vital for regulating the ABA signaling pathway and plant stress responses. In this research, 14 SlPP2C-A genes were identified in the tomato genome, distributed across six chromosomes. Most SlPP2C-A genes contain cis-acting elements associated with growth, development, light, hormones, and stress responses. Collinearity analysis revealed high homology between the tomato and Arabidopsis PP2C-A gene families. Tissue-specific expression analysis indicated that SlPP2C7 is highly expressed in flowers, leaves, and mature fruits, and is significantly induced by saline-alkali stress. Gene-edited SlPP2C7 knockout mutants subjected to saline-alkali stress confirmed that SlPP2C7 negatively regulates saline-alkali tolerance in tomato. Combined transcriptomic and metabolomic analyses showed that under saline-alkali stress, metabolic pathways such as flavonoid biosynthesis, isoflavonoid biosynthesis, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and phenylalanine metabolism were significantly enriched. These outcomes imply that SlPP2C7 may enhance tolerance to saline-alkali stress through modulating flavonoid biosynthesis pathways. This research reveals comprehension of the physiological and molecular mechanism responsible for saline-alkali stress tolerance mediated by SlPP2C7 in tomato.