Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root

• Published in: Nature communications Vol. 12; no. 1; pp. 2053 - 12
• Main Authors: Zhang, Tian-Qi, Chen, Yu, Liu, Ye, Lin, Wen-Hui, Wang, Jia-Wei
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.04.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/39; 38/91; 631/449/1659; 631/449/2653/2656; Accessibility; Arabidopsis - cytology; Cell Aggregation; Cell differentiation; Cell Differentiation - genetics; Cell fate; Chromatin; Chromatin - metabolism; Epidermal Cells - cytology; Gene expression; Gene sequencing; Humanities and Social Sciences; Magnoliopsida; Meristems; multidisciplinary; Oryza - genetics; Plant Roots - cytology; Plant Roots - genetics; Plant Roots - growth & development; Ribonucleic acid; Rice; RNA; Root development; Science; Science (multidisciplinary); Single-Cell Analysis; Species Specificity; Transcription; Transcription, Genetic; Transcriptome - genetics; Transcriptomes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-22352-4

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 could aid understanding of the function of the root apical meristem in both dicots and monocots. Here, we present a single-cell RNA (scRNA) sequencing and chromatin accessibility survey of rice radicles. By temporal profiling of individual root tip cells we reconstruct continuous developmental trajectories of epidermal cells and ground tissues, and elucidate regulatory networks underlying cell fate determination in these cell lineages. We further identify characteristic processes, transcriptome profiles, and marker genes for these cell types and 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 modeling to identify a rice root meristematic mutant from a cell-specific gene cohort. Root meristems give rise to distinct cell types that differentiate across defined temporal and spatial gradients. Here, via single-cell RNA sequencing and surveying chromatin accessibility the authors profile gene expression of different cell types during rice root development.