Chromatin Accessibility Survey of Rice Radicles

Root development relies on the establishment of meristematic tissues that give rise to distinct cell types that differentiate across defined temporal and spatial gradients. Dissection of the developmental trajectories and the transcriptional networks that underlie them is therefore crucial for better understanding of the function of the root apical meristem in both dicots and monocots. Here we performed a single-cell RNA (scRNA) sequencing and chromatin accessibility survey of rice radicles. The temporal profiling of individual root tip cells enabled the reconstruction of continuous developmental trajectories of epidermal cells and ground tissues, and elucidation of the regulatory networks underlying cell fate determination of these cell lineages. We further identified characteristic processes, transcriptome profiles, and marker genes for these cell types and used them to reveal conserved and divergent root developmental pathways between dicots and monocots. Finally, we demonstrate the potential of the platform for functional genetic studies by using spatiotemporal modelling to identify a novel rice root meristematic mutant from a cell-specific gene cohort.