Single-Cell RNA Sequencing of Plant Roots

Single-cell RNA sequencing (scRNA-seq) has been used extensively to study gene expression in individual animal cells, but it has not been widely applied to plants.  As part of our PGRP project, we have aimed to develop scRNA-seq for plant roots.  Using a commercially available platform (10x Genomics Chromium System), we have demonstrated the feasibility and utility of scRNA-seq on Arabidopsis root protoplasts.  Shown below are some examples of the results we obtain.  To learn more, read our recent publication (doi: 10.1104/pp.18.01482 [PMID: 30718350]) ) and our protocol for generating root protoplasts for scRNA-seq.  Also, if you wish to analyze the expression of your favorite gene(s) using these data, check out the Single-cell eFP Browser at BAR.

Distribution of single-cell transcriptomes from wild-type Arabidopsis root protoplasts. Each dot represents the transcriptome from one cell (~5000 expressed genes detected/cell); the relative position of a dot indicates its transcriptome’s relationship to the other transcriptomes. Left, distribution of transcriptomes from 3 biological replicates of wild type (Columbia) roots. Right, nine major clusters of single-cell transcriptomes.

Differentiation status of individual root cells. The ratio of meristematic zone vs. differentiation zone gene expression was determined for each cell transcriptome and indicated by color (red = cell predominantly expressing meristematic genes; purple = cell predominantly expressing differentiation genes). Note that the youngest (meristematic) cells are located at the center.

Distribution of single-cell transcriptomes among five scRNA-seq samples from Arabidopsis roots. These include 3 wild-type replicates, a gl2 (glabra2) mutant sample, and an rhd6 mutant sample.  Note that the mutants lack cells in specific clusters, consistent with their phenotypes (gl2 lacks non-hair cells; rhd6 lacks hair cells).