Genome-Wide DNA Methylation Analysis of the Toxicological Responses to Foliar Cerium Application in Soybean

The increasing agricultural and industrial use of rare earth elements (REEs) has raised growing concerns about their environmental accumulation and ecotoxicity, yet the molecular and epigenetic basis underlying their dose-dependent effects on crops remains poorly understood. In this study, soybean plants were foliar treated with Cerium (Ce) at 0, 5, 10, and 50 mg·L−1. Growth, elemental uptake, genome wide DNA methylation, and gene expression were analyzed using ICP-MS, WGBS, and qRT-PCR. Low dose Ce (5 mg·L−1) showed a hormetic effect, promoting growth and grain quality, whereas high dose Ce (50 mg·L−1) markedly inhibited growth. Foliar absorbed Ce was poorly translocated to roots and seeds, thus reducing food chain contamination risk. Ce significantly altered methylation levels of CG, CHG, and CHH contexts in soybean leaves. Low Ce increased CG methylation, while high Ce decreased CHH methylation. Differentially methylated genes (Low-dose Ce induced 52 hypermethylated DMGs and 23 hypomethylated DMGs, while high-dose Ce induced 76 hypomethylated DMGs and 17 hypermethylated DMGs) were enriched in oxidation–reduction, DNA repair, and cell cycle pathways. qRT-PCR confirmed that Ce mediated toxic responses and growth by regulating methylation related enzymes, oxidative detoxification, and DNA repair genes. This study provides novel genome-wide bisulfite sequencing evidence linking foliar Ce exposure to context-specific DNA methylation reprogramming in a major legume crop. These results demonstrate that the dose-dependent phytotoxicity of Ce in soybean is associated with context-specific changes in genome-wide DNA methylation, supporting the safety evaluation and rational agricultural application of rare earth elements.