Integrated metabolomic and transcriptomic analyses revealed the overlapping response mechanisms of banana to cold and drought stress

Banana (Musa spp.), a vital tropical fruit and food crop, faces significant challenges from cold and drought stress, which threaten its productivity. Uncovering the overlapping mechanisms of crop responses to abiotic stresses is essential for the development of multi-resistant crop varieties. This study investigates the overlapping response mechanisms of banana to cold and drought stress through integrated metabolomic and transcriptomic analyses. We conducted physiological assessments alongside these analyses to elucidate shared mechanisms. Our results showed that both cold and drought stress disrupted cell membrane stability and reduced relative water content and chlorophyll content in banana leaves. Metabolomic analysis identified 1800 annotated metabolites, with 636 and 405 differentially accumulated metabolites (DAMs) under cold and drought stress, respectively, and flavonoids represented the most abundant metabolite class. Transcriptomic analysis revealed that 5687 differentially expressed genes (DEGs) were induced under both stress conditions, with significant enrichment in pathways related to ascorbic acid, arginine, and proline metabolism. Integrating metabolomic and transcriptomic data highlighted carbohydrate, amino acid, and flavonoid metabolism as the central pathways shared in response to cold and drought stresses. Notably, while these pathways were common, specific structural genes and accumulated metabolites varied between stress types. Additionally, our results suggest that GDP-mannose is the primary ascorbate synthesis route under cold stress, whereas myo-inositol and galacturonic acid pathways dominate under drought stress. These findings enhance our understanding of banana's adaptive responses and provide a foundation for breeding multi-stress-resistant crop varieties in an era of climate change.