Flower development in Brassica rapa: Linking anatomy, physiology, transcriptomics, and metabolomics

Flowering is essential to most plants, and is regulated by environmental and internal signals. This study investigates the molecular mechanisms regulating flower development in Brassica rapa L. by performing, anatomical studies, RNA sequencing, analysis of photosynthetic parameters and metabolomics at different developmental stages. We conducted RNA sequencing and analysed 47,135 genes across three pairwise comparisons: Vegetative vs. Pre-Bolting, Pre-Bolting vs. Bolting, and Bolting vs. Post-Bolting. The greatest differential gene expression was observed between the vegetative and pre-bolting stages, with significant changes in 3618 genes. Functional enrichment analysis revealed that photosynthesis, circadian rhythm regulation, response to environmental stimuli, and glucosinolate biosynthesis were the most enriched biological processes during floral transition. Photosynthetic parameters showed a significant increase from the vegetative to bolting stages, peaking from pre-bolting to bolting, and decreasing post-bolting. Metabolomic analysis identified 23 metabolites with significant changes during development. Key metabolites such as campesterol and gamma sitosterol increased during bolting, indicating a role in promoting floral meristem formation. Our study identified several key regulatory genes involved in the photoperiod, circadian clock, and gibberellin pathways, such as GIGANTEA (GI), SOC1, and ELF3. Upregulation of these genes from pre-bolting to bolting stages correlated with enhanced photosynthetic activity and gene expression related to light signaling, carbohydrate metabolism, carbon metabolism, and glucosinolate biosynthesis. These findings provide a comprehensive view of the transcriptional changes and regulatory networks governing the transition from vegetative growth to flowering in B. rapa L., highlighting the integration of environmental and internal cues in this complex process.