Integrating multi-omics with regular analyses to elucidate the effects of ZnO nanomaterials on improving soybean quality.

With rising global demand for high-quality food crops, soybean production is constrained by an inherent yield-quality trade-off that conventional practices cannot easily overcome. Zinc oxide nanomaterials (ZnO NMs) show great potential for crop improvement, but their molecular mechanism underlying soybean quality regulation remains unclear. This study investigated the effects of ZnO quantum dots (ZnO QDs, 5.56 nm) and ZnO nanoparticles (ZnO NPs, 29.68 nm) on soybean growth and quality via root and foliar application with different concentrations (0, 5, 10, 20, 50 and 100 mg/kg). Among these experimental groups, root application of 50 mg/kg ZnO QDs (R-QD-50) was selected as the optimal combination based on regular analyses and used for integrated transcriptomic, proteomic and metabolomic analyses. The results showed that ZnO NMs significantly promoted soybean growth, yield and quality in ZnO NMs type, application mode and concentration-dependent manner. Multi-omics integration identified three common pathways: taurine and hypotaurine metabolism, butanoate metabolism, and phenylpropanoid biosynthesis. Among them, only phenylpropanoid biosynthesis formed a complete transcriptome-proteome-metabolome regulatory chain. Key genes phenylalanine ammonia lyase (PAL) and cinnamic acid-4-hydroxylase (C4H) were significantly upregulated, the related synthases increased by   35% at the protein level, and downstream metabolites including isoflavones, lignin and phenolic acids were increased by   52%. Overall, this study clarified the potential molecular mechanism of ZnO NMs in improving soybean quality and provided theoretical reference for the application of ZnO NMs in soybean quality improvement under controlled pot conditions.