Multi-omics profiling of soybean leaves under Fe deficiency with different phosphorus supply

Iron (Fe) and phosphorus (P) are essential nutrients whose interactions profoundly shape plant growth, yet how P modulates Fe-deficiency responses remains poorly understood. Soybean seedlings were exposed to Fe-sufficient (CK) and Fe-deficient conditions with three P levels (0, 150, and 300 µM P) and analyzed via phenotyping, transcriptomics, and metabolomics. Under Fe deficiency, shoot dry weight increased with P supply but remained below CK; leaf Fe concentration was maintained under moderate P (150 P) yet declined under high P (300 P), while leaf P plateaued at 300 P. Transcriptomic comparisons revealed striking P-dependent reprogramming: only a single differentially expressed gene was shared among the three Fe-deficient versus CK comparisons, indicating that most Fe-deficiency-responsive genes are controlled by P availability. Metabolomics identified 360 shared differentially accumulated metabolites. Integrative analysis pinpointed four critical pathways—ABC transporters, hormone signal transduction, the pentose phosphate pathway, and ubiquinone/terpenoid-quinone biosynthesis—forming a hierarchical regulatory chain. Five hub genes ( ABCB1, ERS1, PRS1, G6PD, VTE4 ) bridged gene expression, metabolite profiles, and phenotypes. Based on these observations, we propose a working model of a "sensing–integration–execution–buffering" chain, providing a conceptual framework and candidate targets for future functional studies on soybean nutrient use efficiency.