Abstract：

Background: The 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 difcult to distinguish and isolate quiescent center cells for transcriptomic analysis.Results: To 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 diferentiation 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 specifc 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.Conclusions: This study provides a method for isolating rare cell types and generates long- and short-read transcriptomic atlases, ofering novel mechanistic insights into stem cell maintenance in monocot and eudicot roots. The fndings have implications for improving crop root systems.

Key Words:

Arabidopsis, Quiescent center, Rice, Single cell RNA-seq, Third-generation sequencing, Root development