Affymetrix array data of tomato fruit mutants in carotenoid biosynthesis

Expression data from tomato fruit at three ripening stages (MG Mature Green, Br Breaker, B10 Breaker+10 days) in wild type lines (Alsa Craig, AC, and M82) and five tomato carotenoid mutants: apricot (at), yellow flesh (r), tangerine (t), Beta (B), and Delta (Del). Carotenoids are essential natural compounds for human nutrition and play key roles in plants as photosynthetic pigments and as precursors of hormones and apocarotenoids. Tomato is a major model for carotenoid metabolism, where genetic variation strongly influences carotenoid composition during fruit ripening. Here we present an extensive biochemical and molecular characterization of five tomato carotenoid mutants—apricot (at), yellow flesh (r), tangerine (t), Delta (Del) and Beta (B)—across three ripening stages (mature green, breaker and red ripe). Gene-expression profiling (Affymetrix microarrays) was integrated with targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones and ABA) and correlation-based analyses. Isoprenoid profiles showed strong, stage-dependent remodeling that extended beyond expected substrate/product changes and was accompanied by substantial transcriptional variation, often independent of the position of the mutated step in the pathway. The integrated analysis highlighted regulatory links between transcripts and metabolites and pointed to lycopene cyclization as a central node in isoprenoid network rewiring during ripening, improving our understanding of mechanisms controlling isoprenoid accumulation in tomato fruit.