Identification of key pathways and genes underlying melatonin-enhanced drought tolerance in cotton

Drought stress is a significant environmental constraint that adversely affects the growth of upland cotton ( Gossypium hirsutum ) by inducing complex physiological disruptions. Emerging research evidence indicates that melatonin (MT), as a plant growth regulator, is extensively involved in the process of plant stress resistance regulation. This study explored the role of exogenous MT in enhancing drought tolerance in cotton, employing both physiological parameter analysis and transcriptomic profiling to unravel the underlying mechanisms of its stress mitigation effects. The results demonstrated that MT treatment significantly enhanced drought resistance in cotton plants by upregulating leaf superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities, elevating proline (PRO) content, and decreasing malondialdehyde (MDA) accumulation, thus confirming its physiological role in alleviating drought stress. Transcriptome analysis revealed that MT specifically modulates the “plant circadian rhythm”, “thiamine metabolism”, and “taurine and hypotaurine metabolism” pathways under drought stress conditions, thereby playing a pivotal role in drought adaptation. Further analysis of the 276 differentially expressed genes (DEGs) specifically modulated by MT under drought stress, combined with co-expression network analysis, identified two MT-specific induced Basic Helix-Loop-Helix (bHLH) family transcription factors ( GhPIF8 and GhMYC5 , gene IDs: Ghi_A11G05431 and Ghi_D03G05926) as key regulatory candidates in MT-mediated drought tolerance. This study establishes a theoretical framework for understanding the physiological and molecular mechanisms underlying MT-mediated drought tolerance in cotton, while also informing practical applications of MT in cotton agriculture.