Transcriptomic Analysis of Early Fruit Development in Micro-Tom Tomato Reveals Conserved and Cultivar-Specific Mechanisms

Early fruit development in tomato is driven by complex gene expression patterns and metabolic reprogramming, a crucial phase that shapes the fruit’s final size and structure. Previous studies using the Micro-Tom model have largely focused on later stages of development, especially ripening, leaving early developmental processes relatively unexplored. To address this knowledge gap, we performed RNA-seq analyses on Micro-Tom fruits harvested at three key developmental stages: 3, 5, and 8 days post-anthesis (DPA). Pairwise differential gene expression analyses revealed that the most extensive transcriptional reprogramming occurs during the transition from 5 to 8 DPA, while comparatively fewer changes were observed between 3 and 5 DPA. K-means clustering of 11,035 stably expressed genes revealed nine distinct expression profiles associated with specific developmental phases, including cell proliferation, transition, and cell expansion. Integrating transcriptomic and metabolomic datasets uncovered coordinated shifts in gene expression and metabolite accumulation, highlighting both conserved regulatory mechanisms and cultivar-specific pathways governing early fruit development. These findings advance our understanding of the molecular regulation of early fruit development in Micro-Tom tomatoes and provide a basis for future efforts to improve fruit quality and yield.