Comprehensive Metabolomic and Transcriptomic Analyses Reveal SlSnRK2.6/SlCHPP-SlbHLH95-SlPDS Module Regulating Tomato Fruit Carotene Biosynthesis

Carotenoid content is crucial for fruit appearance and nutritional quality. This study utilized “xh49♂-cr-1”, a tomato mutant with SlSnRK2.6 and SlCHPP knockout, which showed significantly higher lycopene content than the wild type. Integrated metabolome and transcriptome analyses revealed that phytoene and lycopene were specifically upregulated during late ripening in the mutant. Transcriptomics linked differentially expressed genes to carotene biosynthesis, with correlation analysis identifying transcription factor SlbHLH95 as a key positive regulator. Molecular validation demonstrated that SlSnRK2.6, SlCHPP, and SlbHLH95 form a protein complex with the biosynthetic enzyme SlPDS. Concurrently, SlbHLH95 acts as a central hub, binding to the promoters of SlPDS, SlSnRK2.6, and SlCHPP and activating their transcription to establish a feedback and feed-forward loop. Our findings reveal that the SlSnRK2.6/SlCHPP-SlbHLH95-SlPDS module regulates carotenoid biosynthesis in tomato, providing a theoretical basis for fruit quality improvement.