Synergistic Activation of Proline/Arginine and Energy Metabolism Confers Alkali Tolerance in Wild Soybean Cotyledons

Soil alkalization poses a significant threat to global food security, affecting approximately 10% of the world's arable land. Wild soybean (Glycine soja) is considered an important genetic resource for alkali stress tolerance. However, the adaptive mechanisms of its cotyledons at the vegetative emergence (VE) stage remain poorly understood. In this study, wild and cultivated soybean (Glycine max) were exposed to simulated alkali stress at the VE stage. To elucidate the cotyledon responses, an integrated approach combining physiological, ultrastructural, photosynthetic, transcriptomic, and metabolomic analyses was employed. Following alkali stress, the wild soybean cotyledons maintained a stable morphological structure, whereas those of cultivated soybean showed severe wilting. Furthermore, chloroplast integrity and photosynthetic performance were maintained in wild soybean. A metabolite-gene network analysis revealed the specific activation of proline and arginine metabolic modules in wild soybean, which exhibited synergistic interactions with the TCA cycle module. Overall, wild soybean mitigated alkali stress at the VE stage by stabilizing chloroplast structure, optimizing stomatal conductance, coordinating activation of a nitrogen-buffering mechanism mediated by proline and arginine metabolism, and enhancing the energy supply driven by the TCA cycle. Key genetic targets, including P5CS, SAMDC, and SDH, were identified for their influence in improving crop alkali tolerance, thereby providing valuable insights for breeding alkali-resistant varieties.