Multi-omics analyses reveal the mechanisms of developmental toxicity of a covalent organic framework to the roots of rice (Oryza sativa) seedlings

Abstract

Covalent organic frameworks (COFs) are increasingly explored for applications in chemistry, medicine, and biology, yet their ecotoxicological profiles remain poorly defined. In this study, we assessed the developmental toxicity of ethidium bromide-based covalent organic frameworks (EB-COFs) in rice (Oryza sativa) seedlings in hydroponic culture. Seedlings were exposed to EB-COFs at concentrations ranging from 0.1 to 1000 mg L⁻¹ for 14 days. Shoot length, fresh weight, total chlorophyll content, and photosynthetic rate were unaffected at 100 to 1000 mg L⁻¹; however, root length was significantly inhibited, particularly at 1000 mg L⁻¹, where oxidative damage was observed in roots. To elucidate underlying mechanisms, we performed transcriptomic and metabolomic profiling on roots exposed to 1000 mg L⁻¹ EB-COFs. Differentially expressed genes (DEGs) involved in development and stress responses, for example, WRKY24, were found to be upregulated. Metabolomic profiling identified 1190 differentially accumulated metabolites (DAMs), including key compounds involved in oxidative stress response and root development such as ferulic acid and p-coumaric acid. Pathway enrichment analysis revealed that EB-COFs primarily affected phenylpropanoid biosynthesis, glutathione metabolism, and tryptophan metabolism, which are critical for root growth and stress defense. Our study provides the first comprehensive demonstration that EB-COFs selectively impair rice root growth by inducing oxidative stress and perturbing key metabolic and signaling pathways. These results suggest that future environmental safety assessments of COF materials should include their potential impact on plant health, particularly focusing on oxidative stress and root development.