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.本数据集包含野生型番茄品系（Alsa Craig、AC与M82）及5个番茄类胡萝卜素（carotenoid）突变体——杏黄（apricot, at）、黄肉（yellow flesh, r）、橘红（tangerine, t）、Beta（Beta, B）与Delta（Delta, Del）——在3个果实成熟阶段（MG：成熟绿（Mature Green）、Br：转色期（Breaker）、B10：转色后10天（Breaker+10 days））的番茄果实基因表达数据。类胡萝卜素是人体必需的天然营养化合物，在植物中既可作为光合色素，又可作为激素与脱辅基类胡萝卜素（apocarotenoids）的前体发挥关键作用。番茄是研究类胡萝卜素代谢的核心模式物种，其果实成熟过程中的遗传变异会显著影响类胡萝卜素的组成。本研究对上述5个番茄类胡萝卜素突变体在3个成熟阶段（成熟绿、转色期与红熟期）开展了全面的生化与分子特征分析。研究将基因表达谱分析（Affymetrix基因芯片（Affymetrix microarrays））与靶向类异戊二烯（isoprenoid）代谢组学（涵盖类胡萝卜素、叶绿素、生育酚类（tocochromanols）、醌类与脱落酸（ABA））及基于相关性的关联分析相结合。类异戊二烯谱图呈现出显著的阶段依赖性重塑，其变化范围远超预期的底物/产物改变范畴，同时伴随大量转录组变异，且这类变异通常与突变步骤在代谢通路中的位置无关。本次整合分析揭示了转录本与代谢物之间的调控关联，并指出番茄红素环化（lycopene cyclization）是果实成熟过程中类异戊二烯网络重布线的核心节点，从而加深了我们对调控番茄果实类异戊二烯积累机制的理解。