Tropine alkaloid-driven panomic (transcriptome–metabolome) reprogramming delivers insights into cold stress tolerance in rapeseed (Brassica napus L.)

Secondary metabolites, particularly alkaloids, are crucial for plant adaptation to abiotic stresses, including cold stress, which significantly hampers rapeseed (Brassica napus L.) productivity. Our previous research demonstrated that elevated alkaloid levels confer cold tolerance in Arabidopsis, but the precise molecular mechanisms underlying this function remain poorly understood. In this study, we investigated the role of scopolamine (SCOP; a "tropine alkaloid" and close to "neurotransmitters") in mediating cold tolerance in rapeseed. Exogenous application of TAs, using SCOP as an example, significantly mitigated cold-induced damage and improved seedling survival rate. To elucidate the underlying mechanisms, we performed an integrated transcriptomic and metabolomic analysis of SCOP-treated (150 nmol/plant) seedlings under cold stress. This analysis identified over 8000 differentially expressed genes (DEGs) and over 3000 primary differentially accumulated metabolites (DAMs). A combined analysis discovered a strong correlation between 11 DEGs and 12 DAMs, indicating that SCOP orchestrates a comprehensive response to cold stress at both transcriptional and metabolic levels. Further pathway enrichment analysis demonstrated that these key genes and metabolites are predominantly involved in amino acid and carbohydrate metabolism, as well as in phenylpropanoid and secondary metabolic pathways. Collectively, our results provide a deeper understanding of the TA-mediated cold response independent of the traditional CBF pathway, highlighting its role in carbon reallocation, cell wall reinforcement, and reactive oxygen species scavenging. In short, this study offers significant insights into the molecular mechanisms by which SCOP regulates cold tolerance in rapeseed, and identifies new targets for future engineering applications to fast-track stress-smart breeding for crop improvement.