Qing Huan
Ke Li
Wenfeng Qian
a. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China
Funds: We thank Dr. Xiao Chu, Dr. Ying Chen, Yan-Ming Chen, Yuliang Zhang, Min Dai, and Dr. Xiaofeng Gu for supports in data analyses, Ting Li and Yanbo Tian for supports in flow cytometry and fluorescence microscopy, Dr. Caihuan Tian for supports in protoplast isolation, and Dr. Taolan Zhao and Dr. Yuling Jiao for reading the manuscript. This work was supported by grants from the National Natural Science Foundation of China (31900229 to Q.H. and 31922014 to W.Q.).
Received Date: 2021-06-08
Accepted Date:2021-06-09
Publish Date:2021-06-18
Abstract
Abstract
As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses to environmental stimuli. In this study, we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses and characterize transcriptomes for a total of 237,431 individual cells. We identify 15 and 9 cell types in the leaf and root, respectively, and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer, except for endodermis or epidermis. Abiotic stress stimuli alter gene expression largely in a cell type-specific manner, but for a given cell type, different stresses often trigger transcriptional regulation of roughly the same set of genes. Besides, we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology.Keywords: Single-cell RNA-seq,
Rice seedling,
Cell-to-cell heterogeneity,
Plant tissue layer,
Developmental trajectory,
Abiotic stress
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