Root architecture is a highly dynamic trait and contributes to plant adaptation to its environment. Many dicotyledonous plants such as Arabidopsis have a root system composed of a single primary root and numerous lateral roots. By contrast, cereals such as Oryza sativa (rice) develop a dense fibrous root system consisting primarily of numerous postembryonic adventitious roots that develop from the stem. Although the anatomy of the rice root apex has been intensively investigated, the molecular definition of its cell types is largely incomplete.

Scientists from CAS Center for Excellence in Molecular Plant Sciences (CEMPS)/Shanghai Institute of Plant Physiology and Ecology (SIPPE) now reported the rice root cell atlas based on single-cell RNA (scRNA) sequencing (scRNA-seq) and chromatin accessibility assays (ATAC-seq). The expression map of the rice root tip at single-cell resolution presented in this study provides a valuable resource for defining different cell types, and enables researchers to reconstruct continuous developmental trajectories of epidermal cells and ground tissues, and elucidate regulatory networks underlying cell fate determination in these cell lineages. The inter-species comparisons between rice and Arabidopsis root atlases further reveal evolutionally conserved genes involved in cell differentiation in the root tip, and identify species-specific genes that may reflect fundamental differences in monocot/dicot root biology.

The comprehensive definition of cell types by scRNA-seq lays the ground for understanding how root cell differentiation and root system architecture are shaped in response to environmental cues, such as drought, or flooding. Future work that generates roots scRNA-seq and ATAC-seq datasets of plants grown under different conditions or treatments should yield insights into how such environmental signals direct root growth.

This study was published on Nature Communications on 6^th April, 2021. Dr. Tian-Qi Zhang and Dr. Jia-Wei Wang at CEMPS are the co-corresponding authors of this paper. PhD student Yu Chen at CEMPS, Dr. Ye Liu at Nanjing Agricultural University and Professor Wen-Hui Lin at Shanghai Jiao Tong University jointly participated in this work. This study was supported by the National Natural Science Foundation of China, the Strategic Priority Research Program of the Chinese Academy of Sciences, Science and Technology Commission of Shanghai Municipality, Young Elite Scientists Sponsorship Program by CAST, and National Postdoctoral Program for Innovative Talents.

Article link: https://www.nature.com/articles/s41467-021-22352-4

Contact:
Dr. Jia-Wei Wang
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academic of Sciences
Tel: 86-21-54924263
Email: jwwang@cemps.ac.cn

Fig. 1. Generation of a rice radicle cell atlas.