Abstract
Tomato (Solanum lycopersicum L.) is rich in the antioxidant lycopene, which often degrades postharvest. Pulsed light shows promise in preserving lycopene, yet its molecular mechanisms remain unclear. This study integrates transcriptomics, proteomics, and metabolomics to elucidate how pulsed light affects lycopene synthesis in tomatoes. The results showed that lycopene content increased significantly in pulsed light-treated tomatoes. Transcriptomic analysis identified 1092 significantly differentially expressed genes (DEGs), proteomic analysis identified 1046 significantly differentially accumulated proteins (DAPs), and metabolomic analysis identified 272 significantly differentially accumulated metabolites (DEMs). These were significantly enriched in pathways such as terpenoid backbone biosynthesis, carotenoid biosynthesis, the tricarboxylic acid cycle (TCA), and photosynthesis. The upregulation of eight key genes central to lycopene biosynthesis was validated by qRT-PCR, confirming their involvement in the observed accumulation. Integrated multi-omics analysis revealed coordinated regulation of photosynthesis, carbohydrate metabolism, and terpenoid synthesis, highlighting the reprogramming of energy metabolism and secondary metabolite synthesis in lycopene accumulation. This study provides a comprehensive understanding of the molecular mechanisms by which pulsed light enhances lycopene content in tomatoes. The findings suggest that pulsed light treatment activates key metabolic pathways, leading to increased lycopene synthesis. This research offers a theoretical basis for optimizing pulsed light technology and developing new preservation strategies to maintain and enhance the nutritional quality of tomatoes during postharvest storage.