Subcellular Distribution of Brominated Flame Retardants in Rice Governs Root-to-Shoot Translocation via a DNA Methylation-Mediated Multilayered Regulatory Network

Brominated flame retardants (BFRs) in soil can be absorbed by crops and enter the food chain, posing risks to food safety and human health. Understanding how plants manage BFR uptake and translocation is key to risk control. This study compared two rice japonica cultivars with contrasting BFR accumulation: a tolerant cultivar (TOL) and a sensitive cultivar (SENS). Subcellular localization revealed that TOL sequestered more BFRs in root cell walls and cytoplasm, limiting upward translocation, whereas SENS accumulated more in cell organelles. Spatial colocalization analysis of reactive oxygen species (ROS) and nuclei showed that ROS signals were highly concentrated around nuclei in SENS, suggesting oxidative challenge, while spatially decoupled in TOL. Integrated multiomics revealed a molecular cascade: TOL reduced genome-wide DNA methylation, activating cell wall and lipid homeostasis genes (e.g., CL4, CCR). This boosted phenylpropanoid pathway products (e.g., flavonoids; fold change = 2.04-19.4), thickening cell walls and enhancing BFR sequestration. In contrast, SENS showed hypermethylation of lignin- and gibberellin-related genes, weakening physical defense and disrupting the growth-defense balance. These findings highlight that epigenetic regulatory network stability is crucial for stress adaptation. Precision epigenetic editing could help develop high-yielding, pollution-resilient crops, offering a strategy for sustainable agriculture in contaminated areas.