Metabolic reallocation in soybeans under shade stress alters phenylpropanoid profiles with implications for stress adaptation and seed composition.

Shade stress induces significant metabolic reallocation in soybeans, altering both nutritional composition and adaptation strategies to low-light environments. Using Partial Least Squares Discriminant Analysis (PLS-DA) of the shade-sensitive variety C103, we identified 19 differential metabolites (Variable Importance in Projection, VIP > 1; p < 0.05), including 9 upregulated metabolites-such as essential amino acids-that may enhance protein quality under shade. Conversely, 10 metabolites, primarily key flavonoids like daidzein and genistin, were downregulated, indicating potential compromises in antioxidant capacity and stress resilience. Shade stress markedly reshaped the phenylpropanoid pathway, particularly affecting the biosynthesis of isoflavones, anthocyanins, and lignin. Shade-tolerant varieties displayed elevated isoflavone and anthocyanin accumulation while moderating lignin synthesis, reflecting a strategic focus on metabolites with adaptive and health-promoting functions. In contrast, shade-sensitive varieties prioritized lignin production at the expense of isoflavones, potentially reducing their nutritional and functional value. Organ-specific responses were evident: in C103 seedlings, roots maintained sustained isoflavone accumulation under moderate shade (Red/Far-Red ratio, R/FR = 0.7), while leaves showed a decline with prolonged exposure. These results highlight a metabolic trade-off between defense investment and energy conservation in different tissues. Overall, this study underscores the pivotal role of metabolic reallocation-especially within the phenylpropanoid pathway-in mediating soybean shade adaptation and nutritional traits. By integrating metabolomic profiling with pathway analysis, our findings offer new insights for breeding and management strategies to enhance soybean performance and sustainability under low-light conditions.