Comparative Transcriptome Analysis Reveals Novel Insights into Regulatory Mechanisms of Seed Protein and Oil Accumulation in Soybeans

Soybean seed quality is defined by an inverse relationship between oil and protein content. Understanding the spatiotemporal regulation of this trade-off is crucial for breeding. This study aims to dissect the transcriptomic networks governing carbon and nitrogen partitioning during seed development. Here, transcriptomic and co-expression network analyses were performed on cotyledon and seedcoat tissues of high-protein (HP) and low-protein (LP) soybean cultivars across three seed developmental stages. We identified 4910 HP/LP-specific differentially expressed genes (DEGs), with striking transcriptional alterations in the early developmental stage. Notably, some important DEGs were enriched in carbon/lipid metabolism, protein folding, and hormone/circadian signaling pathways, among which key gene families (e.g., OLEs, SWEETs, HSPs), core regulators (e.g., LACS, L1L, ABF1), and QTL-localized candidate genes (e.g., FA9) were characterized. Mechanistically, C/VIF1-mediated post-translational inhibition of CWINV1 may restrict carbon flux to oil synthesis in HP seeds; upstream circadian/hormone signaling and L1L-sHSPs jointly promote protein deposition, uncoupling the oil–protein trade-off and enabling HP trait formation. In contrast, LP cultivars upregulated SWEETs, OLEs, and LTPs to facilitate high carbon flux into lipid biosynthesis and storage. These findings provide valuable genetic targets for precision breeding programs aimed at optimizing resource allocation.