Integrated morphological, physiological, and transcriptomic profiling unveils a root-centric defense network mediating aluminum tolerance in Trifolium repens L

Aluminium (Al) toxicity in acid soils severely limits forage productivity, and dissecting Al-tolerance mechanisms is crucial for securing forage supply in acid-soil regions. White clover (Trifolium repens L.), an excellent acid-soil-adapted forage with pronounced Al tolerance, serves as an ideal model for studying legume Al-tolerance mechanisms. We exposed white clover seedlings to gradient Al^³⁺ concentrations (0, 2, 4, 6, 10 mmol·L^⁻¹) to characterize the core physiological and molecular responses underlying its Al adaptation. Al^³⁺ stress inhibited growth in a concentration-dependent manner, suppressing both root and shoot development. Roots adopted a prioritised defence strategy, with enhanced antioxidant enzyme activity and soluble sugar accumulation mitigating oxidative damage. Transcriptome analysis revealed coordinated regulation of key pathways: flavonoid biosynthesis showed a core inhibition-branch-specific activation pattern, photosystem-related genes were upregulated to reinforce photosynthetic function, and hormone signalling networks were extensively rewired with divergent responses among auxin, gibberellin, cytokinin, ABA and JA pathways. White clover copes with Al^³⁺ stress via an integrated mechanism featuring root-prioritised defence, photosynthetic maintenance and hormone network remodelling. These findings provide new insights into legume Al tolerance and a framework for breeding Al-tolerant forages. Future studies will quantify Al content in shoots and roots, and perform functional validation of upregulated hormone-related genes to clarify their roles in the Al-tolerance regulatory network.