Integrated transcriptomic and proteomic analysis reveals inhibitory effects of naringenin application on soybean roots mainly by interfering with auxin and ROS concentrations

Background Flavonoids play a crucial role as secondary metabolites in plant growth and development. Naringenin is a central intermediate in flavonoid biosynthesis. It is also a pivotal branching point that gives rise to metabolites such as flavonols, anthocyanins, and isoflavonoids. However, the mechanisms underlying plant root development regulated by flavonoids remain fragmentary, especially in crops. Results In this study, we observed a significant inhibition of soybean (Glycine max) root growth after exposure to 75 μM naringenin. The treated roots showed reduced auxin content and increased reactive oxygen species (ROS) levels in root tips. Through RNA-sequencing and nanoElute high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analyses, we further investigated molecular responses of soybean roots to naringenin treatment. A total of 6,390 differentially expressed genes (DEGs) were identified. Among them, 3,910 genes were up-regulated and 2,480 were down-regulated. These DEGs notably included genes related to ROS metabolism and the auxin signaling pathway. We also detected 806 differential accumulation proteins (DAPs), including 481 up-regulated and 325 down-regulated proteins. The integration of transcriptomic and proteomic data showed a close association between DEGs and DAPs in roots, especially in pathways related to glutathione metabolism. Conclusion Taken together, this comprehensive analysis highlights the intricate and specific responses of soybean roots to naringenin exposure, mainly affecting the levels of auxin and ROS. It provides valuable insights and candidate genes for further investigating root growth regulated by flavonoids.