Abstract
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.
Highlights
Root development relies on the establishment of meristematic tissues that give rise to distinct cell types that differentiate across defined temporal and spatial gradients
The inference of rice root cell types based on the expression of orthologous Arabidopsis genes is difficult because of variation in the number and nature of the cell types in monocots and dicots
The multilayered cortex of the rice root can differentiate into aerenchyma, an anatomical adaptation to water submergence, at late developmental stages, a capacity that is absent in Arabidopsis[53]
Summary
Root development relies on the establishment of meristematic tissues that give rise to distinct cell types that differentiate across defined temporal and spatial gradients. 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 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 (Supplementary Note 1)[1,2]. The transcriptome analysis of the individual cells at different developmental stages reveals a continuous differentiation trajectory of root development following their spatial distribution and temporal order[19,20,21,22,23,24,25]
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