Shade partially alleviates drought stress in soybean through genotype-dependent phenylpropanoid regulation and interorgan aglycone redistribution

Soybean grown in dense planting and intercropping systems frequently experiences drought together with canopy shade, yet the mechanisms by which shade modifies drought responses remain poorly understood. Here, we compared the responses of the shade-tolerant genotype ND12 and the shade-sensitive genotype C103 under combinations of normal light or shade and well-watered, moderate-drought, or severe-drought conditions. Morphological, root, gas-exchange, phytohormone, exploratory metabolomic, targeted metabolic, gene-expression, and ¹³ C-isotope tracing analyses were integrated to characterize genotype-specific acclimation strategies. Moderate shade partially alleviated drought-induced inhibition of biomass accumulation, root development, photosynthetic performance, and water-use efficiency, with a stronger beneficial effect in ND12. Exploratory metabolomic profiling repeatedly highlighted phenylpropanoid-related pathways under combined stress. Targeted analyses further showed that ND12 preferentially accumulated isoflavones, including bioactive aglycones, in leaves, whereas C103 exhibited reduced leaf isoflavone accumulation together with enhanced lignification. These contrasting metabolic patterns were accompanied by genotype- and organ-specific expression of phenylpropanoid and isoflavone biosynthetic genes. In ND12, root-fed [ring- ¹³ C₆]-L-phenylalanine remained confined to roots, whereas newly synthesized ¹³ C-labelled aglycones were detected in hypocotyls under both light regimes and in leaves only under shade. These results support a model in which shade promotes interorgan redistribution of downstream aglycones rather than long-distance transport of their biosynthetic precursor. Collectively, our findings indicate that soybean adaptation to simultaneous shade and drought depends on coordinated physiological maintenance, tissue-specific phenylpropanoid regulation, and interorgan metabolite redistribution. This study provides a mechanistic framework for understanding genotype-dependent acclimation to concurrent light and water limitation and offers a basis for improving soybean performance in intercropping and other low-light, water-limited production systems.