Single-cell transcriptional profiling in Arabidopsis root exposed to boron toxicity at seedling stages.

Cell-specific transcriptional responses to environmental stimuli are yet to be fully characterized. Single-cell sequencing technology allows us to analyze different cell types under different conditions. Here, high-throughput single-cell RNA sequencing (scRNA-seq) was performed in Arabidopsis thaliana roots exposed to different B toxicity conditions by using a commercially available droplet-based microfluidics platform (10xGenomics) to understand how B toxicity altered gene expression and development at single-cell resolution. Accordingly, we found that 2755 cells could be annotated using cell-specific marker genes into 10 cell-type clusters including lateral root cap + epidermis + quiescent cells (QC) + columella, stele, cortex, cortex + endodermis, metaxylem, columella, trichoblast, pericycle initial cells + protoxylem, metapholem and phloem. Upregulated genes were highly associated with glutathione and sulfur metabolism in the columella, endodermis, and QC under B toxicity. Further analysis revealed that upregulated genes were highly correlated with the ribosome pathway in lateral root cap + epidermis + quiescent cells + columella, stele, and cortex clusters. Moreover, we identified the transcription factors at the cortex, lateral root cap + epidermis + quiescent cells + columella, cortex + endodermis, and trichoblast cell clusters in Arabidopsis root under severe B toxicity conditions. Taken together, for the first time in the literature, our study provides a gene expression map at single-cell resolution and describes the extent of heterogeneity at the molecular level among populations of different cell types in Arabidopsis root under B toxicity conditions and will significantly promote the investigation of the molecular mechanisms underlying the B toxicity.