Integrated transcriptome and metabolome analyses reveal that SlEIL4 represses SlALDH2B4 to regulate GABA accumulation in tomato fruit

• Tropane piperidine and pyridine alkaloid biosynthesis influences fruit quality. • Arginine and proline metabolism influences fruit quality. • SlEIL4 transcription factor represses SlALDH2B4 to enhance GABA synthesis. • Variations in SlEIL4 regulation across tomato varieties affect GABA levels. Extended harvest periods in tomato cultivation cause significant quality variation among fruits from different spikes, but the underlying regulatory mechanisms remain unclear. In this study, transcriptomic and metabolomic analyses were used to investigate the differential metabolic profiles. Based on the combined analysis, a regulatory network for arginine and proline metabolism, as well as tropane piperidine and pyridine alkaloid biosynthesis, was constructed. Further regulatory analysis showed that SlEIL4 directly binds to the SlTR1 promoter and represses its transcription and also inhibits SlALDH2B4 expression to promote GABA content. To summarize, these findings provide insights into tomato quality formation and establish a foundation for intensive cultivation of tomatoes and breeding cultivars with stable-quality fruits during long harvest stages.