Soybean is an important oilseed crop, providing abundant protein and fat for human consumption. However, in practical production, there exists a significant negative correlation between soybean oil and protein content, making it difficult to obtain soybean varieties with both high protein and high oil content. There is limited research on the regulatory network governing soybean oil and protein content. We selected four soybean varieties, Sui Xiao Li (SXL), Ji Da 5 (JD5), Ji Da 33 (JD33), and Ji Yu 202 (JY202), and determined their protein and oil content. We found that SXL and JD33 are high-protein, low-oil varieties, while JD5 and JY202 are high-oil, low-protein varieties. Subsequently, transcriptomic and proteomic analyses were conducted on these four soybean varieties. The results revealed a total of 7182 differentially expressed genes (DEGs) and 1037 differentially expressed proteins (DAPs) among the four soybean varieties SXL, JD5, JD33, and JY202. Through KEGG analysis, we identified 96 and 319 DEGs involved in fatty acid metabolism and protein metabolism, respectively, as well as 23 and 28 DAPs involved in fatty acid metabolism and protein metabolism, respectively. Additionally, based on WGCNA and PPI interaction networks, several central genes were identified, which potentially play a role in the accumulation of protein content and oil content. These potential genes mainly participate in processes such as glycolysis and carbon metabolism. Joint analysis of transcriptomic and proteomic data revealed generally poor correlation between gene expression at the transcriptional and protein levels, with 240 co-regulated genes identified. Combining metabolic pathways, we identified 12 and 5 genes that are involved in lipid metabolism and protein synthesis at both transcriptional and translational levels, respectively. Finally, based on predictions of correlation and interaction, we identified 22 genes that may simultaneously regulate protein and oil content negatively at the transcriptional and translational levels. This study provides important scientific guidance for the genetic improvement of soybean quality components.
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