Transcriptomics and non-targeted metabolomics reveal the mechanisms of leaf color changes in red-leaf cotton under drought stress and rewatering.

This study aims to investigate the pattern of dynamic leaf color changes (red-green-red) in red-leaf cotton under drought stress and rewatering, and to reveal the underlying molecular and biochemical mechanisms. Integrated transcriptomics and metabolomics analyses, combined with weighted gene co-expression network analysis (WGCNA), were employed to systematically study the physiological, gene expression, and metabolite changes in red-leaf cotton under mild drought, severe drought, and after rewatering. Under mild drought stress, red-leaf cotton accumulated higher levels of anthocyanins while maintaining relatively good photosynthetic performance, demonstrating an effective photoprotective response. In contrast, severe drought stress led to a significant decrease in anthocyanin content, accompanied by sharply reduced water retention and photosynthetic capacity, indicating a shift in physiological strategy towards survival priority. After rewatering, red-leaf cotton reactivated the flavonoid biosynthesis pathway, gradually restored anthocyanin synthesis, and showed clear phenotypic recovery. Transcriptomic analysis revealed the reprogramming of gene expression related to anthocyanin synthesis and drought tolerance pathways. Metabolomic analysis identified metabolites such as phenylalanine and 2-hydroxyquinoline, which provide precursors for anthocyanin synthesis.The research indicates that red-leaf cotton responds to drought and rewatering by dynamically regulating the flavonoid synthesis and metabolic network, demonstrating robust metabolic repair and stress memory capabilities. These mechanisms provide important theoretical support for breeding drought-resistant cotton varieties.