Transcriptomics and Non-Targeted Metabolomics Reveal the Mechanisms of Leaf Color Changes in Red-Leaf Cotton Under Drought Stress and Rewatering

This study investigates the dynamic leaf color changes (red-green-red) in red-leaf cotton under drought stress and rewatering, and reveals the molecular and biochemical mechanisms through integrated transcriptomics and metabolomics analysis. Under mild drought stress, red-leaf cotton enhances anthocyanin accumulation to improve its antioxidant capacity, exhibiting strong photoprotection. Under severe drought stress, anthocyanin levels decrease, leading to significant reductions in water retention capacity and photosynthesis, and the plant shifts to survival strategies. After rewatering, red-leaf cotton reactivates the flavonoid biosynthesis pathway and gradually restores anthocyanin synthesis, showing clear phenotypic recovery. Transcriptomic analysis shows reprogramming of gene expression related to flavonoid biosynthesis and drought tolerance pathways, and WGCNA analysis further identifies gene modules closely associated with anthocyanin synthesis and water retention capacity. Metabolomic analysis indicates dynamic metabolic regulation in red-leaf cotton during drought, with metabolites such as phenylalanine and 2-hydroxyquinoline providing precursors for anthocyanin synthesis. After rewatering, the recovery of metabolites lays the foundation for phenotypic restoration, revealing the strong metabolic repair and stress memory abilities of red-leaf cotton. These mechanisms provide theoretical support for the breeding of drought-resistant cotton varieties.