Single-cell transcriptomic analysis of plant quiescent center by third-generation sequencing reveals developmental trajectories.

backgroundThe quiescent center of plant roots plays a critical role in maintaining stemness and proliferative activity of surrounding meristem cells that drive root growth. However, it remains difficult to distinguish and isolate quiescent center cells for transcriptomic analysis.

resultsTo overcome the challenges, we develop a protocol for isolating intact quiescent center cells from Arabidopsis root tips and perform single-cell long-read RNA sequencing of quiescent center cells across two developmental stages. The analysis reveals a transition from hormone signaling and proliferation toward differentiation between 5 and 10 days after germination. We capture 6,713 previously unannotated transcripts, including several isoform types. We validate ROOT MERISTEM GROWTH FACTOR 10 (RGF10) as a quiescent center specific marker gene. We also detect enrichment in transcripts associated with cell growth, auxin response, and cell division at 5 days, but lost at 10 days, after germination. Functional analysis suggests that the quiescent center marker, TERMINAL EAR1-like (TEL1), is involved in maintaining stem cell identity via regulation of WUSCHEL-RELATED HOMEOBOX 5 (WOX5). Comparative analysis of rice quiescent center transcriptomes reveals distinct auxin biosynthesis and signaling pathways compared to that in Arabidopsis.

conclusionsThis study provides a method for isolating rare cell types and generates long- and short-read transcriptomic atlases, offering novel mechanistic insights into stem cell maintenance in monocot and eudicot roots. The findings have implications for improving crop root systems.