Proteomic and transcriptomic analyses reveal a novel synergistic mechanism between lipid synthesis and protein accumulation in developing seeds of Xanthoceras sorbifolium

Yellowhorn ( Xanthoceras sorbifolium Bunge) is an economically important tree species in China. Its seeds are distinguished by exceptionally high levels of both oil and protein, making it an attractive model for studying the coordination of storage reserve accumulation. To elucidate the molecular mechanisms underlying these two traits, we conducted the first comprehensive multi-omics study, integrating proteomic and transcriptomic analyses during kernel development. Untargeted proteomic analysis identified 4861 proteins, of which 820 exhibited differential expression across different kernel developmental stages. Transcriptome analysis identified 18,935 differentially expressed genes (DEGs) across developmental stages, and functional annotation further identified 66 DEGs associated with lipid biosynthesis and 39 DEGs related to storage protein synthesis. Interestingly, the integrated analysis revealed 22 transcription factors (TFs) from the bZIP, NF-Y, MYB, and C3H families, potentially playing pleiotropic regulatory roles in lipid and protein metabolism. LEC1 and bZIP38 exhibited peak expression at the S2 stage, temporally synchronized with the critical phase of seed oil/protein biosynthesis. Our multi-omics data demonstrate that the synergy between oil and protein biosynthesis in Yellowhorn is likely orchestrated by a shared transcriptional network, rather than resulting from resource competition as commonly observed in other oil crops. This study reveals conserved transcriptional networks coordinating lipid-protein co-allocation in seeds, providing molecular insights for engineering high-oil/protein cultivars through precision breeding.