Transcriptional landscape of rice roots at the single-cell resolution

Liu, Qing; Liang, Zhe; Feng, Dan; Jiang, Sanjie; Wang, Yifan; Du, Zhuoying; Li, Ruoxi; Hu, Guihua; Zhang, Pingxian; Ma, Yuju; Lohmann, Jan U.; Gu, Xiaofeng

doi:10.1016/j.molp.2020.12.014

Cited by 154 publications

(146 citation statements)

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“…indica variety 93-11 and Oryza sativa ssp. japonica variety Nipponbare from a previously published paper (GSE146035) (Liu et al, 2020), which included more than 20,000 single cells from 250 tips of crown roots, were used in this study. Cells with fewer than 1000 detected genes and genes detected in fewer than 10 cells were removed from further analysis.…”

Section: Methodsmentioning

confidence: 99%

“…The first 50 principal components (PCs) with a resolution parameter of 1.0 were used for clustering, and UMAP (Becht et al, 2018) was used to visualize clusters. We used the gene markers of eight previously reported cell types (Liu et al, 2020) to identify cell types in indica or japonica rice varieties. Then, we combined the cells from indica or japonica rice varieties with the removal of batch effects.…”

Section: Methodsmentioning

confidence: 99%

“…Commonly, there are a variety of cell types in multicellular plants, including cultivated rice, and these cells work as an interactive network to maintain the survival and reproduction of individual plants (Liu et al, 2020;Wang et al, 2020) in addition to responding to stresses and adapting to various environments. Different organs and even different cell types have their own roles in the regulation of organisms-for example, the cortex is related to water and fluid transport, and the epidermis near root hairs is related to extracellular and external stimuli in rice roots (Liu et al, 2020). Therefore, understanding the differences in gene expression among different organs and different cell types is important for understanding the development and physiology of plants (Denyer et al, 2019;Ryu et al, 2019;Shulse et al, 2019;Liu et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Different organs and even different cell types have their own roles in the regulation of organisms-for example, the cortex is related to water and fluid transport, and the epidermis near root hairs is related to extracellular and external stimuli in rice roots (Liu et al, 2020). Therefore, understanding the differences in gene expression among different organs and different cell types is important for understanding the development and physiology of plants (Denyer et al, 2019;Ryu et al, 2019;Shulse et al, 2019;Liu et al, 2020). However, analyses involving traditional bulk RNA sequencing cannot identify cell type-specific heterogeneity due to the mixture of cell types in the test samples (Dai et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…However, analyses involving traditional bulk RNA sequencing cannot identify cell type-specific heterogeneity due to the mixture of cell types in the test samples (Dai et al, 2019). In the last decade, the development of single-cell RNA sequencing has provided a new opportunity to study the heterogeneity of cell types in plants (Denyer et al, 2019;Ryu et al, 2019;Shulse et al, 2019;Liu et al, 2020). In addition, quiescent center (QC) cells are an important group of cells in plant root tips that play a key role in the control of tip growth and the regulation of stem cells in roots (Ryu et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

et al. 2021

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Background: As Oryza sativa ssp. indica and Oryza sativa ssp. japonica are the two major subspecies of Asian cultivated rice, the adaptative evolution of these varieties in divergent environments is an important topic in both theoretical and practical studies. However, the cell type-specific differentiation between indica and japonica rice varieties in response to divergent habitat environments, which facilitates an understanding of the genetic basis underlying differentiation and environmental adaptation between rice subspecies at the cellular level, is little known.Methods: We analyzed a published single-cell RNA sequencing dataset to explore the differentially expressed genes between indica and japonica rice varieties in each cell type. To estimate the relationship between cell type-specific differentiation and environmental adaptation, we focused on genes in the WRKY, NAC, and BZIP transcription factor families, which are closely related to abiotic stress responses. In addition, we integrated five bulk RNA sequencing datasets obtained under conditions of abiotic stress, including cold, drought and salinity, in this study. Furthermore, we analyzed quiescent center cells in rice root tips based on orthologous markers in Arabidopsis.Results: We found differentially expressed genes between indica and japonica rice varieties with cell type-specific patterns, which were enriched in the pathways related to root development and stress reposes. Some of these genes were members of the WRKY, NAC, and BZIP transcription factor families and were differentially expressed under cold, drought or salinity stress. In addition, LOC_Os01g16810, LOC_Os01g18670, LOC_Os04g52960, and LOC_Os08g09350 may be potential markers of quiescent center cells in rice root tips.Conclusion: These results identified cell type-specific differentially expressed genes between indica-japonica rice varieties that were related to various environmental stresses and provided putative markers of quiescent center cells. This study provides new clues for understanding the development and physiology of plants during the process of adaptative divergence, in addition to identifying potential target genes for the improvement of stress tolerance in rice breeding applications.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

et al. 2021

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The Promise of eQTL Studies in Dissecting Crop Genetic Basis and Evolution

Leng

Wang

et al. 2022

Annual Plant Reviews Online

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Most traits important for crop production are affected by polymorphisms in the genome. The application of genome‐wide association studies (GWASs) has analysed numerous genetic loci controlling complex traits, highlighting the significant roles of non‐coding regulatory variants and networks. During the past decade, there have been continuous advancements in high‐throughput RNA sequencing technology applied to crop genomes, along with expression quantitative trait locus (eQTL) mapping based on GWASs with diverse lines. These developments have facilitated considerably superior resolution to uncover the detailed genetic basis of whole transcriptomic variation, which can connect DNA polymorphism to individual genes and provide an effective approach to elucidate the regulatory networks underlying phenotypes. In this article, we comprehensively summarise the technical and computational considerations of eQTL mapping, especially using RNA sequencing of association populations. Through integration with trans hotspots, response or dynamic eQTLs, and network analyses, eQTL studies on crops aid in understanding the regulatory networks and connections among genes in metabolic pathways, development, or response to stimuli. We outline the approaches to integrate eQTL results with GWASs, which can greatly improve the possibility of identifying causal genes and regulatory networks responsible for complex traits. Regulation information from eQTL mapping can also be used to elucidate the divergence and stabilisation of gene expression during crop evolution. Although facing several technical challenges and presently limited to a few sample points in crops, eQTL studies hold great potential for advancing our knowledge of the genomic base and evolution of complex traits, and supports molecular breeding of crops.

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A Single‐Nucleus Resolution Atlas of Transcriptome and Chromatin Accessibility for Peanut (Arachis Hypogaea L.) Leaves

Liu,

Guo,

Gangurde

et al. 2023

Advanced Biology

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The peanut is an important worldwide cash‐crop for edible oil and protein. However, the kinetic mechanisms that determine gene expression and chromatin accessibility during leaf development in peanut represented allotetraploid leguminous crops are poorly understood at single‐cell resolution. Here, a single‐nucleus atlas of peanut leaves is developed by simultaneously profiling the transcriptome and chromatin accessibility in the same individual‐cell using fluorescence‐activated sorted single‐nuclei. In total, 5930 cells with 50 890 expressed genes are classified into 18 cell‐clusters, and 5315 chromatin fragments are enriched with 26 083 target genes in the chromatin accessible landscape. The developmental trajectory analysis reveals the involvement of the ethylene‐AP2 module in leaf cell differentiation, and cell‐cycle analysis demonstrated that genome replication featured in distinct cell‐types with circadian rhythms transcription factors (TFs). Furthermore, dual‐omics illustrates that the fatty acid pathway modulates epidermal‐guard cells differentiation and providescritical TFs interaction networks for understanding mesophyll development, and the cytokinin module (LHY/LOG) that regulates vascular growth. Additionally, an AT‐hook protein AhAHL11 is identified that promotes leaf area expansion by modulating the auxin content increase. In summary, the simultaneous profiling of transcription and chromatin accessibility landscapes using snRNA/ATAC‐seq provides novel biological insights into the dynamic processes of peanut leaf cell development at the cellular level.

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Transcriptional landscape of rice roots at the single-cell resolution

Cited by 154 publications

References 41 publications

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

The Promise of eQTL Studies in Dissecting Crop Genetic Basis and Evolution

A Single‐Nucleus Resolution Atlas of Transcriptome and Chromatin Accessibility for Peanut (Arachis Hypogaea L.) Leaves

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