Integrative WGCNA Analysis Uncovers the Molecular Framework of Melatonin-Mediated Drought Stress Mitigation in Potato

Drought is one of the major abiotic stress factors limiting the growth, development, and yield of potato ( Solanum tuberosum L.). Melatonin, a novel plant hormone, has recently shown significant potential in enhancing plant stress resistance. However, its regulatory mechanisms in response to drought stress in potato remain unclear. In this study, potato seedlings were treated with different concentrations of exogenous melatonin (50, 100, and 150 µmol/L) under controlled drought conditions to systematically evaluate their physiological and molecular responses. The results demonstrated that appropriate melatonin application—especially at 100 µmol/L—effectively alleviated drought-induced growth inhibition, oxidative stress, and photosynthetic impairment. This was evidenced by increased plant height, enhanced photosynthetic efficiency, reduced reactive oxygen species (ROS) accumulation, decreased cell death and lipid peroxidation, as well as elevated antioxidant enzyme activities (SOD, CAT, POD) and levels of osmoprotectants (proline and soluble sugars). Transcriptome analysis revealed that melatonin modulates numerous drought-responsive differentially expressed genes (DEGs), including multiple transcription factor families (e.g., MYB, NAC, ERF), and pathways related to photosynthesis, antioxidative metabolism, hormone signaling, and carbon metabolism. Furthermore, weighted gene co-expression network analysis (WGCNA) and Mfuzz clustering identified key gene modules and central hub genes strongly associated with photosynthetic performance and antioxidant indicators. This study provides a theoretical foundation for applying melatonin in potato drought stress mitigation and lays a molecular basis for developing hormone-based drought-resistant agricultural strategies.