Host-dependent variation in free amino acid profiles and physiological responses enhancing drought tolerance in Santalum album

Sandalwood (Santalum album L.), a highly valued hemi-parasitic tree, depends on host plants for nutrient acquisition, particularly under abiotic stress. However, the influence of host species on sandalwood’s free amino acid (FAA) profiles under water deficit stress remains poorly understood. This study investigated how 11 host species modulate FAA composition in sandalwood roots during water deficit stress, aiming to identify host-specific metabolic adaptations that enhance stress resilience. LC-MS/MS analysis revealed significant host-dependent variations in FAA profiles. Pongamia pinnata association led to the highest accumulation of aspartic acid (7.28 µg g^− 1 FW), glutamic acid (13.87 µg g^− 1 FW), and lysine (67.11 µg g^− 1 FW), while Sesbania grandiflora resulted in minimal arginine (0.55 µg g^− 1 FW). Acacia nilotica and Punica granatum enhanced physiological resilience, with higher chlorophyll content (5.57 µg mg^− 1 FW), relative water content (62.8%), and proline levels (18.38 µg g^− 1 FW). Principal component analysis (69.7% variance explained) highlighted arginine, lysine, and histidine as key contributors to metabolic shifts under stress. Hierarchical clustering further confirmed host-specific FAA patterns, with Pongamia pinnata and nitrogen-fixing hosts promoting stress-responsive amino acids. Host selection strongly influences sandalwood’s drought tolerance. Pongamia pinnata, Dalbergia sissoo, and Punica granatum enhance nitrogen metabolism, amino acid accumulation, and physiological traits under stress. These findings offer a practical, science-based strategy for improving sandalwood resilience in semi-arid regions through climate-smart host selection in agroforestry systems.