Metabolome and transcriptome profiling reveals distinct regulatory networks underlying high-protein and high-oil traits in soybean cultivars Wandou 28 and Zhongdou 63

Soybean is a vital global source of protein and oil. Breeding is constrained by a persistent trade-off between seed protein content, oil content, and yield. To dissect the molecular basis of this trade-off, we conducted an integrated transcriptomic and metabolomic analysis of two elite soybean cultivars with contrasting traits: high-protein Wandou 28 and high-oil, high-yield Zhongdou 63. The cultivars exhibited distinct systemic resource-allocation strategies. Wandou 28 demonstrated a “defense-oriented” strategy, with sustained investment in specialized metabolism and stress responses across leaves, stems, and pods, particularly through the 9S-lipoxygenase-mediated oxylipin pathway, diverting linoleic acid from seed oil synthesis. In leaves at flowering, Wandou 28 accumulated high levels of asparagine and expressed elevated asparagine synthetase, indicating nitrogen retention in source tissues. Conversely, Zhongdou 63 employed a “yield-construction” strategy, characterized by coordinated up-regulation of biosynthetic and transport pathways, characterized by coordinated up-regulation of biosynthetic and transport pathways, efficient nitrogen assimilation and rapid export from leaves, and suppression of costly specialized metabolism such as phenylpropanoid biosynthesis. In stems during pod-filling, Zhongdou 63 activated auxin signaling and oxidative phosphorylation pathways. Gene co-expression analysis identified a greenyellow module in stems strongly correlated with oil content and yield, and a tan module capturing the protein-oil trade-off across tissues. Key regulatory differences were pinpointed: in Wandou 28, nitrogen retention and active 9S-lipoxygenase pathway activity limit precursor flux to seeds; in Zhongdou 63, streamlined metabolism and auxin-dominated hormone signaling maximize resource partitioning to reproductive sinks. This systems-level analysis demonstrates that the high-protein and high-oil/high-yield phenotypes are governed by fundamentally different whole-plant strategies involving specific metabolic pathways and co-expression networks. The identification of the greenyellow and tan modules, along with the divergent regulation of nitrogen partitioning (asparagine synthetase) and linoleic acid metabolism (9S-lipoxygenase), provides testable hypotheses and candidate targets for future functional studies aimed at overcoming the classical protein-yield trade-off in soybean breeding.