A Single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis.

The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and the genetic improvement of crops. This developmental process incorporates a series of cell fate transitions and reprogramming. However, our knowledge of cell heterogeneity and of the mechanisms of cell fate transition during callus induction remains quite limited. Here, we performed a time series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0 days, 1 day, and 4 days, and we constructed a detailed single-cell transcriptional atlas of the callus induction process. We identified the cell types responsible for initiating the early callus: lateral root primordia-initiating (LRPI)-like cells and quiescent center (QC)-like cells. LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia. We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells. QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration. We further inferred the transcription factors that regulating QC-like cells and the gene expression signatures that are related to cell fate decisions. Overall, our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transition during callus formation, and significantly improves understanding of callus formation.