Single-cell RNA sequencing in roots of Arabidopsis thaliana exposed to boron toxicity at seedling stage

In this thesis, a single-cell RNA sequencing study was performed for the first time in the literature to reveal the molecular basis of boron (B) toxicity tolerance mechanism in Arabidopsis thaliana with high efficiency and at the single cell level. In this context, the roots of Arabidopsis thaliana were exposed to different concentrations of B toxicity at seedling stage. Protoplasts were isolated from stress-exposed roots and then single-cell RNA was sequenced. Total of 8 samples from control, 1 mM and 2 mM B groups were sequenced with Illumina NovaSeq 6000. Accordingly, a total population of 1554 cells were recovered across three replicates. Major tissues have been identified in this single-cell transcriptome, including the quiescent center, endodermis, root cap, columella, cortex, and trichoblast. Trichoblast and cortex had not been defined under B toxicity treatment. In addition, although similar pathways related to the genes and B tolerance mechanisms presented in the literature have been detected, many new cell-type specific genes were also identified. For example, the internal B toxicity tolerance mechanism, via the role of anthocyanins and GSTs may be in the columella cell cluster. Moreover, we found cell specific 13 TF families under B toxicity. Finally, the new pathways identified previously and new ones at cell cluster level will lead to new transgenic and breeding studies for B toxicity tolerance mechanism.