Lipidomic profiles reveal the membrane lipid phase transition pattern in chilling-shocked cotton seedlings

Cotton ( Gossypium spp ), originating from tropical and subtropical regions, is an important natural fiber crop and is currently cultivated across a wide range of latitudes. With the intensification of global climate change, cotton seedlings frequently suffer extreme low-temperature events in spring, often accompanied by delayed cold damage phenotypes. When exposed to chilling stress, membrane lipid phase transition is the fundamental causes of plant chilling damage. Through time-series relative electrolyte leakage (REL), subcellular ultrastructure, and lipidomic analysis, we find that at 6-hour time point under 4°C treatment, the membrane permeability of cotton leaves already undergoes significant changes, with key cell membrane components sphingolipids and phospholipids exhibiting opposite alteration patterns. Lipidomic analysis of chilling-tolerant seedlings generated by GIGANTEA ( GI ) silencing revealed dynamic changes in lipid profiles, particularly in medium- to long-chain free fatty acids (FFAs) and triacylglycerols (TGs). Notably, Arachidonic Acid (FFA, 20:4) exhibited a distinctive accumulation in chilling-shocked GI -silenced plants, suggesting its potential functional role in enhancing chilling tolerance. Understanding membrane lipid phase transitions and related lipid dynamics facilitates the selection of chilling-tolerant cotton varieties, which is beneficial for improving chilling tolerance and yield stability during the cotton seedling stage. • Cotton membrane lipid phase transition occurs within 6-h of chilling shock. • Sphingolipids and phospholipids decrease while lysophospholipids increase in chilling-stressed cotton Seedling leaves. • Silencing GIGANTEA enhances chilling tolerance by elevating arachidonic acid. • Triacylglycerols and long-chain free fatty acids are key lipid markers for chilling tolerance.