A single cell view of the transcriptome during lateral root initiation

Plant root architecture is a major determinant of fitness, and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can also alter the position, spacing, density, and length of secondary or lateral roots. Lateral root development is among the best-studied developmental processes in Arabidopsis thaliana, yet the earliest steps of organogenesis remain elusive. Among the challenges faced in capturing these early molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. The advent of single-cell sequencing affords the opportunity to isolate cells undergoing this fate transition and examine their transcriptomes independently. Using this approach, we successfully captured the transcriptomes of lateral root primordia and discovered many previously unreported upregulated genes. To further study this process, we developed a method to selectively repress genes in the xylem pole pericycle cells where lateral roots originate. We found that expression of several of the upregulated genes was required for normal root development. In addition, we discovered a subpopulation of cells in the endodermal cell file that respond to lateral root initiation, further highlighting the benefits of the single cell approach. Overall design: Using the 10X single cell transcriptomics platform, we isolated cells from Arabidopsis roots to study lateral root formation. To stimulate lateral root formation, Arabidopsis seedlings were rotated 90 degrees and cells from the root bend were captured 08 hours, and 20 hours after the stimulus. Cells from a no bend control, 00 hours, were collected as well. The RDS files (included on Jan 25, 2021) are the processed Monocle 3 cell data structures, which can be loaded directly into R, to help those trying to reproduce analysis results or those who want to use the UMAPs for further analysis.