Integrated Analysis of Physiological Responses and Transcriptome of Cotton Seedlings Under Drought Stress

Investigating the physiological responses and resistance mechanisms in plants under drought stress provides critical insights for optimizing irrigation water utilization efficiency and promoting the development of irrigation science. In this study, cotton seedlings were cultivated in a light incubator. Three drought stress levels were applied: mild (M1, 50–55% field moisture), moderate (M2, 45–50%), and severe (M3, 40–45%). Transcriptome analysis was performed under mild and severe stress. The results revealed that differentially expressed genes (DEGs) related to proline degradation were down-regulated and proline content increased in cotton. Under different stress treatments, cotton exhibited a stress-intensity-dependent regulation of carbohydrate metabolism and soluble sugar content decreased and then increased. And the malondialdehyde content analysis revealed a dose-dependent relationship between stress intensity and membrane lipid peroxidation. Stress activated the antioxidant system, leading to the down-regulation of DEGs for reactive oxygen species production in the mitogen-activated protein kinase (MAPK) signaling pathway. Concurrently, superoxide dismutase activity and peroxidase content increased to mitigate oxidative damage. Meanwhile, the photosynthetic performance of cotton seedlings was inhibited. Chlorophyll content, stomatal conductance, the net photosynthetic rate, the transpiration rate and water use efficiency were significantly reduced; intercellular carbon dioxide concentration and leaf stomatal limitation value increased. But photosynthesis genes (e.g., PSBO (oxygen-evolving enhancer protein 1), RBCS (ribulose bisphosphate carboxylase small chain), and FBA2 (fructose-bisphosphate aldolase 1)) in cotton were up-regulated to coordinate the photosynthetic process. Furthermore, cotton seedlings differentially regulated key biosynthesis and signaling components of phytohormonal pathways including abscisic acid, indoleacetic acid and gibberellin. This study elucidates the significant gene expression of drought-responsive transcriptional networks and relevant physiological response in cotton seedlings and offers a theoretical basis for developing water-saving irrigation strategies.