Transcriptomics and metabolomics analyses reveal the differential molecular mechanisms of cold tolerance between Cavendish and Dajiao banana cells

Low temperature is a major environmental factor that limits the growth, yield, and geographical distribution of bananas. Given the complex nature of cold tolerance traits in bananas, the molecular mechanisms and associated gene networks responsible for cold tolerance are poorly understood. The aim of this study is to identify cold stress response genes, metabolites, and metabolic pathways through integrated transcriptomics and metabolomics analyses, with the goal of comprehensively understanding the mechanism underlying the differential cold tolerance between cold-sensitive Cavendish and cold-tolerant Dajiao bananas. Our findings show that cold-tolerant Dajiao accumulates more lipids than cold-sensitive Cavendish under cold stress. Moreover, we identified 4626 and 5516 differentially expressed genes under cold stress in Cavendish and Dajiao, respectively. By integrating the transcriptomic and metabolomic datasets, we discovered that the lipid metabolism pathway and the ABA-independent MAPK cascade-ICE1 signal transduction pathway play crucial roles in cold tolerance of Dajiao. Our study provides new insight into the molecular basis of cold response and the mechanism of cold tolerance in bananas, with potential applications for genetic improvement of cold tolerance in bananas.