Single-Cell Transcriptome Analysis in Plants:Advances and Challenges

The rapid and enthusiastic adoption of single-cell RNA sequencing(scRNA-seq)has demonstrated that this technology is far more than just another way to perform transcriptome analysis.It is not an exaggeration to say that the advent of scRNA-seq is revolutionizing the details of whole-transcriptome snapshots from a tissue to a cell.With this disruptive technology,it is now possible to mine heterogeneity between tissue types and within cells like never before.This enables more rapid identification of rare and novel cell types,simultaneous characterization of multiple different cell types and states,more accurate and integrated understanding of their roles in life processes,and more.However,we are only at the beginning of unlocking the full potential of scRNA-seq applications.This is particularly true for plant sciences,where single-cell transcriptome profiling is in its early stage and has many exciting challenges to overcome.In this review,we compare and evaluate recent pioneering studies using the A rabidopsis root model,which has established new paradigms for scRNA-seq studies in plants.We also explore several new and promising single-cell analysis tools that are available to those wishing to study plant development and physiology at unprecedented resolution and scale.In addition,we propose some future directions on the use of scRNA-seq technology to tackle some of the critical challenges in plant research and breeding.

Symplastic communication in the root cap directs auxin distribution to modulate root development

Root cap not only protects root meristem,but also detects and transduces the signals of environmental changes to affect root development.The symplastic communication is an important way for plants to transduce signals to coordinate the development and physiology in response to the changing enviroments.However,it is unclear how the symplastic communication between root cap cells affects root growth.Here we exploit an inducible system to specifically block the symplastic communication in the root cap.Transient blockage of plasmodesmata(PD)in differentiated collumella cells severely impairs the root development in Arabidopsis,in particular in the stem cell niche and the proximal meristem.The neighboring stem cell niche is the region that is most sensitive to the disrupted symplastic communication and responds rapidly via the alteration of auxin distribution.In the later stage,the cell division in proximal meristem is inhibited,presumably due to the reduced auxin level in the root cap.Our results reveal the essential role of the differentiated collumella cells in the root cap mediated signaling system that directs root development.

An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis

Light perception at dawn plays a key role in coordinating multiple molecular processes and in entraining the plant circadian clock.The Arabidopsis mutant lacking the main photoreceptors,however,still shows clock entrainment,indicating that the integration of light into the morning transcriptome is not well understood.In this study,we performed a high-resolution RNA-sequencing time-series experiment,sampling every 2 min beginning at dawn.In parallel experiments,we perturbed temperature,the circadian clock,photoreceptor signaling,and chloroplast-derived light signaling.We used these data to infer a gene network that describes the gene expression dynamics after light stimulus in the morning,and then validated key edges.By sampling time points at high density,we are able to identify three light-and temperature-sensitive bursts of transcription factor activity,one of which lasts for only about 8 min.Phytochrome and cryptochrome mutants cause a delay in the transcriptional bursts at dawn,and completely remove a burst of expression in key photomorphogenesis genes(HY5 and BBX family).Our complete network is available online(http://www-users.york.ac.uk/∼de656/dawnBurst/dawnBurst.html).Taken together,our results show that phytochrome and cryptochrome signaling is required for fine-tuning the dawn transcriptional response to light,but separate pathways can robustly activate much of the program in their absence.

Nodulation:a SHORTROOT-SCARECROW perspective

Nitrogen is a limiting element for all living organisms,including plants grown in the wild and in agriculture.A group of plants,largely legumes,have developed strategies to"grab"free atmospheric nitrogen by symbiotically housing nitrogen-fixing bacteria,collectively referred to as rhizobia,in highly specialized organs called root nodules.