Integrated Metabolomic and Transcriptomic Analysis Reveals Mechanisms Underlying Increased Nitrogen and Protein Concentrations by Phosphorus Deficiency in Soybean Seeds

Phosphorus (P) deficiency reduces the crop yield, yet its impact on legume seed quality remains unclear. Herein, we found that phosphate (Pi) starvation led to a significant decrease in soybean (<i>Glycine max</i>) yield. However, seed nitrogen, protein, and amino acid concentrations were significantly increased by Pi starvation. Combined with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and RNA sequencing analyses of developing seeds, a total of 522 differentially accumulated metabolites (DAMs) were identified, particularly increased accumulations of amino acids, such as l-arginine and l-glutamine. Meanwhile, a total of 3793 differentially expressed genes (DEGs) were detected, with 1764 upregulated and 2029 downregulated by Pi starvation. Notably, the integration of metabolomic and transcriptomic analyses revealed a tight connection between DEGs and DAMs in developing seeds, especially for nitrogen translocation and assimilation. Collectively, this study highlights the complex and distinct responses of young soybean seeds to P deficiency, which provides candidate genes for improving the soybean seed protein concentration.