The Center for Excellence in Molecular Plants of the Chinese Academy of Sciences reveals a panoramic view of the heterogeneity and differentiation of rice root single cells
By: Date: 2021-04-11 Categories: foodtechnology Tags: ,
   On April 6, Nature Communications published online the research paper Single-Cell Transcriptome Atlas and Chromatin Accessibility Landscape Reveal Differentiation Trajectories in the Rice Root by Wang Jiawei, a researcher at the Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences. . This research system reveals the heterogeneity of rice root single cells, depicts the differentiation trajectory of rice root epidermal cells and ground tissue cells, and clarifies the relationship between gene expression and root tip stem cell differentiation. The relevance of gene chromatin accessibility, and clarified the evolutionary conservation of the monocotyledonous plant rice and the dicotyledonous plant Arabidopsis in root tip cell types.
  Rice is one of the important food crops. Roots are important tissues and organs of rice, responsible for fixing and supporting plants, absorbing water and mineral elements from the soil to supply plants for growth and development, and participating in the interaction between plants and biological or non-biological signals. Different from the dicotyledonous model plant Arabidopsis thaliana, rice is a fibrous root plant with different growth and development patterns. In addition, in order to better adapt to the aquatic environment, rice has also evolved specialized structures such as exodermis, thick-walled tissue (sclerenchyma), ventilated tissue, and multi-cell layered cortical cells (cortical cells). Genetic mutant screening is a powerful method for traditional developmental biology and functional genomics to obtain important regulatory genes, but it is often limited by unfavorable factors such as long research cycles, black box testing, quantitative traits, and heavy workload. In recent years, with the invention and application of single-cell RNA sequencing technology, researchers can systematically understand the heterogeneity of living cells at the single-cell level, depict the differentiation and development trajectory of various types of cells, and accelerate the development of important regulatory factors in the development process. Mining process.
Preliminary research work in the    laboratory described the root single-cell map of the dicot model plant Arabidopsis (Zhang et al., Molecular Plant, 2019). In order to further explore the development pattern of monocot plant roots and reveal the evolution of monocotyledonous plant roots, researchers have applied scRNA-seq and ATAC-seq technologies to the study of rice roots. The scRNA-seq experiment captured 27469 high-quality single-cell transcriptome data. Through cluster analysis, these cells were annotated into 21 different cell groups (clusters), corresponding to rice root epidermis, outer cortex, thick-walled tissue, cortex, endothelial layer, pericyll, meristem, vascular tissue, etc. Cell groups. Through in situ hybridization and construction of reporter genes, a series of brand-new cell type marker genes were discovered and verified. Further through the rearrangement of transition state cells and pseudo-time analysis, the development process of epidermal meristem cells dividing and differentiation into trichoblasts or non-trichoblasts (atrichoblasts) was described, and the basic meristem progenitor cells were clarified. (Ground tissue initial) differentiation to form the differentiation track of the cortex, thick-walled tissue and outer cortex. The integration analysis of scRNA-seq and ATAC-seq shows that the chromatin open state of some important regulatory factors is temporally and spatially related to their gene expression patterns. Combining reverse genetics experiments, it is found that the transcription factor OsGATA6, which is specifically expressed in rice root meristems, is involved in the development of rice root basic tissues and vascular bundle tissues, suggesting that single-cell sequencing technology can effectively enhance the success of crop reverse genetics. ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? effectiveness.
  The research through the integration analysis with the Arabidopsis root single-cell transcriptome data set found that the two cell types are less conservative in evolution. Only in root hair, xylem, phloem and other cell types, there are high similarities. Further in-depth comparison and analysis of these conserved cell types, mining some potential core cell type regulatory genes. These research results helped us draw a single-cell map of rice roots, and laid a good foundation for analyzing the fine process and molecular mechanism of rice root development, artificially customizing the root system, and improving nutrient absorption capacity in the future.
  Zhang Tianqi, a postdoctoral fellow at the Center for Molecular Plant Excellence and Innovation, is the first author of the paper, and Zhang Tianqi and Wang Jiawei are the co-corresponding authors of the paper. Doctoral student Chen Yu from the Center for Excellence in Molecular Plant Innovation, Liu Ye, a lecturer at Nanjing Agricultural University, and Lin Wenhui, a professor at Shanghai Jiaotong University, participated in the research. The research work was funded by the National Natural Science Foundation of China’s Basic Science Center Project, the Chinese Academy of Sciences Strategic Leading Science and Technology Project, the Chinese Association for Science and Technology Young Talents Support Project, and the China Postdoctoral Innovative Talent Support Program.