Integrated Transcriptomic, Proteomic, and Metabolomic Analysis of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Governing Fatty Acids and Storage Proteins in Soybean Seeds

Background/Objectives: The significant negative correlation between protein and oil content in soybean seeds is a long-standing bottleneck for conventional breeding. Its root cause lies in insufficient understanding of related molecular regulatory processes. Methods: We selected the CSSL_R19, a chromosome segment substitution line, to thoroughly investigate the intrinsic effects of the substituted segment on the high seed storage protein (SSP) and low fatty acid (FA) phenotype. Transcriptomic, proteomic, and metabolomic analyses were performed on the recurrent parent and R19. Results: A total of 1821 differentially expressed genes (DEGs), 12 differentially expressed proteins (DEPs), and 10 differentially accumulated metabolites (DEMs) were detected. Subsequently, an integrative examination of the data demonstrated that 28 DEGs, 5 DEPs, and 4 DEMs participated in biological processes such as carbohydrate metabolism, lipid degradation, as well as protein synthesis and transport. Mechanistically, down-regulation of PGM reduces the carbon source supply for FA synthesis; up-regulation of LOX, LACS, ACX, and KAT promotes FA degradation. SRP, SAR1, and HSP70 are involved in the synthesis and transport of SSP. Crucially, qRT-PCR validation performed on all 28 core DEGs showed that their expression trends were highly consistent with the transcriptome data, confirming the reliability of the findings. Conclusions: In conclusion, we propose a potential regulatory network that enhances SSP accumulation and reduces FA content. Altogether, these findings advance our understanding of storage compound accumulation in soybeans and guide future breeding strategies.