Combined transcriptomic and metabolomic analysis reveals molecular mechanisms governing the effect of foliage-sprayed calcium chloride on tomato fruit quality.

Calcium fertilizers are widely used to enhance tomato fruit quality, however, the molecular mechanisms underlying these effects remain not fully elucidated. In this study, 'Micro-Tom' tomato plants were subjected to foliar sprays of calcium chloride at different concentrations, and 0.05mol·L⁻¹ was identified as the optimal concentration. Transcriptomic profiling, untargeted metabolomics, and RT-qPCR validation were integrated to characterize the molecular responses to calcium supplementation. Foliar application of 0.05mol·L⁻¹ calcium chloride significantly increased fruit firmness, vitamin C content, lycopene content, and the sugar-acid ratio. Untargeted metabolomics identified 429 differentially accumulated metabolites, including 281 upregulated and 148 downregulated metabolites, with lipids and phenylpropanoids representing the most enriched classes. Transcriptomic analysis identified 2514 differentially expressed genes, which were predominantly enriched in the phenylpropanoid biosynthesis pathway. Several key genes in this pathway, including SlCCoA-OMT, SlPER42, SlPER43, and Sl1-CysPrx, were significantly upregulated following calcium treatment. The increased accumulation of two lignin precursors, ferulic acid and sinapic acid, together with the enhanced expression of their pathway genes, was associated with greater fruit firmness, suggesting that increased precursor availability may promote cell wall reinforcement. These results identify candidate genes and metabolic pathways associated with calcium-mediated improvements in tomato fruit quality and provide preliminary molecular insights into calcium fertilization and the breeding of high-quality tomato cultivars.