Integrated Morphological, Physiological, and Transcriptomic Analyses Reveal a Biphasic Growth–Defense Trade-Off Strategy in Allium mongolicum Under Drought Stress

Drought severely constrains grassland stability and forage productivity. Allium mongolicum Regel, a dominant species in desert steppes, exhibits high drought tolerance, yet its multi-level adaptive responses remain incompletely understood. Here, drought stress of different intensities (15%, 30%, 45%, and 60% PEG-6000) was simulated, and root phenotypes, physiological traits, and time-series transcriptomic profiles were integrated to characterize its drought-responsive patterns. The results revealed a biphasic phenotypic response: mild to moderate drought (15–30% PEG) promoted root elongation and surface expansion, consistent with a growth-prioritized response pattern, whereas severe drought (60% PEG) suppressed elongation and induced compensatory thickening, suggesting a shift toward a more structural defense-oriented response. Physiological analyses showed progressive MDA accumulation accompanied by increased SOD and POD activities and proline content, indicating enhanced antioxidant and osmotic regulation under stress. Time-series transcriptomics suggested a three-phase transcriptional adjustment pattern, including early alarm, intermediate acclimation, and late compensation. Early-stage DEGs were mainly enriched in photosystem regulation and ROS-related pathways, while intermediate stages were associated with translational control and protein folding. At the late stage, genes involved in mitochondrial metabolism and amino acid catabolism were prominently represented, implying increased respiratory activity under prolonged drought. WGCNA further identified two key modules associated with these shifts: the steelblue module, negatively correlated with root growth traits, and the darkturquoise module, positively correlated with growth-related traits and antioxidant activities. Collectively, these results outline a multi-level adaptive framework for drought responses in A. mongolicum and provide insights into how desert plants may balance growth and defense under water-limited conditions.