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

Cell-specific transcriptional responses to environmental stimuli are yet to be fully characterized in plants. In this study, we apply single-cell RNA sequencing to Arabidopsis thaliana roots exposed to boron (B) toxicity to characterize the transcription map at cellular resolution and thus, to understand how B toxicity can alter gene expression and development at single cell resolution. Single-cell transcriptomes from protoplasts of more than 2750 Arabidopsis thaliana root cells were obtained. Plotting the single-cell transcriptomes via t-SNE projections yielded six major cell clusters including quiescent cells (QC), endodermis, cortex, columella, trichoblast (root-hair), and root cap. The maximum number of most significantly upregulated genes were determined in columella under 1 mM B and in endodermis under 2 mM B condition. Additionally, the maximum number of most significantly upregulated genes under 3 mM B and 5 mM B conditions was determined in the root cap, implying a critical role against severe B toxicity conditions. We also showed that these upregulated genes are highly correlated with "glutathione metabolism" in columella and "carbon metabolism" in root cap. 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.