Review Article | Open Access
Volume 2024 |Article ID 0029 |

Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

Md Torikul Islam,1,2,8 Yang Liu,1,8 Md Mahmudul Hassan,3 Paul E. Abraham,1,2 Jean Merlet,2,4 Alice Townsend,2,4 Daniel Jacobson,1,2 C. Robin Buell,5,6,7 Gerald A. Tuskan ,1,2 Xiaohan Yang 1,2

1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
2The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
3Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
4Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN 37996, USA
5Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
6Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
7Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, USA
8These authors contributed equally to this work

14 Sep 2023
28 Jan 2024
29 Feb 2024


Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings of complex plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity. Furthermore, scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology, which aims to modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational design for increasing crop yield and quality, promoting the bioeconomy and enhancing environmental sustainability. In particular, data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build–Design–Test–Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects. To date, scRNA-seq has been demonstrated in a limited number of plant species, including model plants (e.g., Arabidopsis thaliana), agricultural crops (e.g., Oryza sativa), and bioenergy crops (e.g., Populus spp.). It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants. In this review, we summarize current technical advancements in plant scRNA-seq, including sample preparation, sequencing, and data analysis, to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples. We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research. Finally, we discuss the challenges and opportunities for the application of scRNA-seq in plants.

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