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Wang Q, Guo Q, Shi Q, Yang H, Liu M, Niu Y, Quan S, Xu D, Chen X, Li L, Xu W, Kong F, Zhang H, Li P, Li B, Li G. Histological and single-nucleus transcriptome analyses reveal the specialized functions of ligular sclerenchyma cells and key regulators of leaf angle in maize. MOLECULAR PLANT 2024; 17:920-934. [PMID: 38720461 DOI: 10.1016/j.molp.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/17/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024]
Abstract
Leaf angle (LA) is a crucial factor that affects planting density and yield in maize. However, the regulatory mechanisms underlying LA formation remain largely unknown. In this study, we performed a comparative histological analysis of the ligular region across various maize inbred lines and revealed that LA is significantly influenced by a two-step regulatory process involving initial cell elongation followed by subsequent lignification in the ligular adaxial sclerenchyma cells (SCs). Subsequently, we performed both bulk and single-nucleus RNA sequencing, generated a comprehensive transcriptomic atlas of the ligular region, and identified numerous genes enriched in the hypodermal cells that may influence their specialization into SCs. Furthermore, we functionally characterized two genes encoding atypical basic-helix-loop-helix (bHLH) transcription factors, bHLH30 and its homolog bHLH155, which are highly expressed in the elongated adaxial cells. Genetic analyses revealed that bHLH30 and bHLH155 positively regulate LA expansion, and molecular experiments demonstrated their ability to activate the transcription of genes involved in cell elongation and lignification of SCs. These findings highlight the specialized functions of ligular adaxial SCs in LA regulation by restricting further extension of ligular cells and enhancing mechanical strength. The transcriptomic atlas of the ligular region at single-nucleus resolution not only deepens our understanding of LA regulation but also enables identification of numerous potential targets for optimizing plant architecture in modern maize breeding.
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Affiliation(s)
- Qibin Wang
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; State Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Qiuyue Guo
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China
| | - Qingbiao Shi
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; State Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hengjia Yang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China
| | - Meiling Liu
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yani Niu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China
| | - Shuxuan Quan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China
| | - Di Xu
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; State Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Xiaofeng Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China
| | - Laiyi Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China
| | - Wenchang Xu
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Fanying Kong
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Haisen Zhang
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Pinghua Li
- State Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China.
| | - Gang Li
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
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Guerrero-Méndez C, Abraham-Juárez MJ. Factors specifying sex determination in maize. PLANT REPRODUCTION 2024; 37:171-178. [PMID: 37966579 DOI: 10.1007/s00497-023-00485-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/21/2023] [Indexed: 11/16/2023]
Abstract
Plant architecture is an important feature for agronomic performance in crops. In maize, which is a monoecious plant, separation of floral organs to produce specific gametes has been studied from different perspectives including genetic, biochemical and physiological. Maize mutants affected in floral organ development have been key to identifying genes, hormones and other factors like miRNAs important for sex determination. In this review, we describe floral organ formation in maize, representative mutants and genes identified with a function in establishing sexual identity either classified as feminizing or masculinizing, and its relationship with hormones associated with sexual organ identity as jasmonic acid, brassinosteroid and gibberellin. Finally, we discuss the challenges and scopes of future research in maize sex determination.
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Affiliation(s)
- Cristina Guerrero-Méndez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 36821, Irapuato, Mexico
| | - María Jazmín Abraham-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 36821, Irapuato, Mexico.
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3
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He J, Wang J, Zhang Z. Toward unveiling transcriptome dynamics and regulatory modules at the maternal/filial interface of developing maize kernel. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2124-2140. [PMID: 38551088 DOI: 10.1111/tpj.16733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 06/14/2024]
Abstract
The basal region of maize (Zea mays) kernels, which includes the pedicel, placenta-chalazal, and basal endosperm transfer layers, serves as the maternal/filial interface for nutrient transfer from the mother plant to the developing seed. However, transcriptome dynamics of this maternal/filial interface remain largely unexplored. To address this gap, we conducted high-temporal-resolution RNA sequencing of the basal and upper kernel regions between 4 and 32 days after pollination and deeply analyzed transcriptome dynamics of the maternal/filial interface. Utilizing 790 specifically and highly expressed genes in the basal region, we performed the gene ontology (GO) term and weighted gene co-expression network analyses. In the early-stage basal region, we identified five MADS-box transcription factors (TFs) as hubs. Their homologs have been demonstrated as pivotal regulators at the maternal/filial interface of rice or Arabidopsis, suggesting their potential roles in maize kernel development. In the filling-stage basal region, numerous GO terms associated with transcriptional regulation and transporters are significantly enriched. Furthermore, we investigated the molecular function of three hub TFs. Through genome-wide DNA affinity purification sequencing combined with promoter transactivation assays, we suggested that these three TFs act as regulators of 10 basal-specific transporter genes involved in the transfer of sugars, amino acids, and ions. This study provides insights into transcriptomic dynamic and regulatory modules of the maternal/filial interface. In the future, genetic investigation of these hub regulators must advance our understanding of maternal/filial interface development and function.
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Affiliation(s)
- Juan He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jincang Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
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4
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Guo C, Huang Z, Chen J, Yu G, Wang Y, Wang X. Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model. PLANTS (BASEL, SWITZERLAND) 2024; 13:1276. [PMID: 38732491 PMCID: PMC11085074 DOI: 10.3390/plants13091276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Deep learning has emerged as a powerful tool for investigating intricate biological processes in plants by harnessing the potential of large-scale data. Gene regulation is a complex process that transcription factors (TFs), cooperating with their target genes, participate in through various aspects of biological processes. Despite its significance, the study of gene regulation has primarily focused on a limited number of notable instances, leaving numerous aspects and interactions yet to be explored comprehensively. Here, we developed DEGRN (Deep learning on Expression for Gene Regulatory Network), an innovative deep learning model designed to decipher gene interactions by leveraging high-dimensional expression data obtained from bulk RNA-Seq and scRNA-Seq data in the model plant Arabidopsis. DEGRN exhibited a compared level of predictive power when applied to various datasets. Through the utilization of DEGRN, we successfully identified an extensive set of 3,053,363 high-quality interactions, encompassing 1430 TFs and 13,739 non-TF genes. Notably, DEGRN's predictive capabilities allowed us to uncover novel regulators involved in a range of complex biological processes, including development, metabolism, and stress responses. Using leaf senescence as an example, we revealed a complex network underpinning this process composed of diverse TF families, including bHLH, ERF, and MYB. We also identified a novel TF, named MAF5, whose expression showed a strong linear regression relation during the progression of senescence. The mutant maf5 showed early leaf decay compared to the wild type, indicating a potential role in the regulation of leaf senescence. This hypothesis was further supported by the expression patterns observed across four stages of leaf development, as well as transcriptomics analysis. Overall, the comprehensive coverage provided by DEGRN expands our understanding of gene regulatory networks and paves the way for further investigations into their functional implications.
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Affiliation(s)
| | | | | | | | | | - Xu Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (C.G.); (Z.H.); (J.C.); (G.Y.); (Y.W.)
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5
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Sahab S, Tibbits J, Spangenberg G, Mason J, Hayden M. Fluorescence-activated protoplast sorting for crop improvement. TRENDS IN PLANT SCIENCE 2024; 29:605-606. [PMID: 38199831 DOI: 10.1016/j.tplants.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Sareena Sahab
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia.
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
| | - German Spangenberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia; Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - John Mason
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
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6
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Ramírez Gonzales LY, Cannarozzi G, Jäggi L, Assefa K, Chanyalew S, Dell'Acqua M, Tadele Z. The role of omics in improving the orphan crop tef. Trends Genet 2024; 40:449-461. [PMID: 38599921 DOI: 10.1016/j.tig.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
Tef or teff [Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research.
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Affiliation(s)
| | - Gina Cannarozzi
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland
| | - Lea Jäggi
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland
| | - Kebebew Assefa
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, PO Box 32, Debre Zeit, Ethiopia
| | - Solomon Chanyalew
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, PO Box 32, Debre Zeit, Ethiopia
| | | | - Zerihun Tadele
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland.
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7
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Wang Y, Luo Y, Guo X, Li Y, Yan J, Shao W, Wei W, Wei X, Yang T, Chen J, Chen L, Ding Q, Bai M, Zhuo L, Li L, Jackson D, Zhang Z, Xu X, Yan J, Liu H, Liu L, Yang N. A spatial transcriptome map of the developing maize ear. NATURE PLANTS 2024; 10:815-827. [PMID: 38745100 DOI: 10.1038/s41477-024-01683-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 04/03/2024] [Indexed: 05/16/2024]
Abstract
A comprehensive understanding of inflorescence development is crucial for crop genetic improvement, as inflorescence meristems give rise to reproductive organs and determine grain yield. However, dissecting inflorescence development at the cellular level has been challenging owing to a lack of specific marker genes to distinguish among cell types, particularly in different types of meristems that are vital for organ formation. In this study, we used spatial enhanced resolution omics-sequencing (Stereo-seq) to construct a precise spatial transcriptome map of the developing maize ear primordium, identifying 12 cell types, including 4 newly defined cell types found mainly in the inflorescence meristem. By extracting the meristem components for detailed clustering, we identified three subtypes of meristem and validated two MADS-box genes that were specifically expressed at the apex of determinate meristems and involved in stem cell determinacy. Furthermore, by integrating single-cell RNA transcriptomes, we identified a series of spatially specific networks and hub genes that may provide new insights into the formation of different tissues. In summary, this study provides a valuable resource for research on cereal inflorescence development, offering new clues for yield improvement.
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Affiliation(s)
- Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Yunfu Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiali Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenwen Shao
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjie Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaofeng Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- China National GeneBank, Shenzhen, China
| | - Tao Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- China National GeneBank, Shenzhen, China
| | - Jing Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- China National GeneBank, Shenzhen, China
| | - Lihua Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Qian Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Minji Bai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Li Li
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China.
- Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Shenzhen, China.
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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8
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Adema K, Schon MA, Nodine MD, Kohlen W. Lost in space: what single-cell RNA sequencing cannot tell you. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00066-9. [PMID: 38570278 DOI: 10.1016/j.tplants.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their workflows. Maximizing the potential of scRNA-seq requires a proper understanding of the spatiotemporal context of cells. However, positional information is inherently lost during scRNA-seq, limiting its potential to characterize complex biological systems. In this review we highlight how current single-cell analysis pipelines cannot completely recover spatial information, which confounds biological interpretation. Various strategies exist to identify the location of RNA, from classical RNA in situ hybridization to spatial transcriptomics. Herein we discuss the possibility of utilizing this spatial information to supervise single-cell analyses. An integrative approach will maximize the potential of each technology, and lead to insights which go beyond the capability of each individual technology.
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Affiliation(s)
- Kelvin Adema
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael A Schon
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands; Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael D Nodine
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands; Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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9
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Grones C, Eekhout T, Shi D, Neumann M, Berg LS, Ke Y, Shahan R, Cox KL, Gomez-Cano F, Nelissen H, Lohmann JU, Giacomello S, Martin OC, Cole B, Wang JW, Kaufmann K, Raissig MT, Palfalvi G, Greb T, Libault M, De Rybel B. Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. THE PLANT CELL 2024; 36:812-828. [PMID: 38231860 PMCID: PMC10980355 DOI: 10.1093/plcell/koae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 01/19/2024]
Abstract
Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.
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Affiliation(s)
- Carolin Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
- VIB Single Cell Core Facility, Ghent 9052, Belgium
| | - Dongbo Shi
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Manuel Neumann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Lea S Berg
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Yuji Ke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Kevin L Cox
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Fabio Gomez-Cano
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Jan U Lohmann
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefania Giacomello
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Olivier C Martin
- Universities of Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette 91192, France
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Michael T Raissig
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Gergo Palfalvi
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Thomas Greb
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marc Libault
- Division of Plant Science and Technology, Interdisciplinary Plant Group, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65201, USA
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
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10
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Yuan Y, Du Y, Delaplace P. Unraveling the molecular mechanisms governing axillary meristem initiation in plants. PLANTA 2024; 259:101. [PMID: 38536474 DOI: 10.1007/s00425-024-04370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/22/2024] [Indexed: 04/24/2024]
Abstract
MAIN CONCLUSION Axillary meristems (AMs) located in the leaf axils determine the number of shoots or tillers eventually formed, thus contributing significantly to the plant architecture and crop yields. The study of AM initiation is unavoidable and beneficial for crop productivity. Shoot branching is an undoubted determinant of plant architecture and thus greatly impacts crop yield due to the panicle-bearing traits of tillers. The emergence of the AM is essential for the incipient bud formation, and then the bud is dormant or outgrowth immediately to form a branch or tiller. While numerous reviews have focused on plant branching and tillering development networks, fewer specifically address AM initiation and its regulatory mechanisms. This review synthesizes the significant advancements in the genetic and hormonal factors governing AM initiation, with a primary focus on studies conducted in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.). In particular, by elaborating on critical genes like LATERAL SUPPRESSOR (LAS), which specifically regulates AM initiation and the networks in which they are involved, we attempt to unify the cascades through which they are positioned. We concentrate on clarifying the precise mutual regulation between shoot apical meristem (SAM) and AM-related factors. Additionally, we examine challenges in elucidating AM formation mechanisms alongside opportunities provided by emerging omics approaches to identify AM-specific genes. By expanding our comprehension of the genetic and hormonal regulation of AM development, we can develop strategies to optimize crop production and address global food challenges effectively.
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Affiliation(s)
- Yundong Yuan
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Yanfang Du
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Pierre Delaplace
- Plant Sciences, Gembloux Agro-Bio Tech, TERRA-Teaching and Research Center, Université de Liège, 5030, Gembloux, Belgium
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11
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Xu X, Passalacqua M, Rice B, Demesa-Arevalo E, Kojima M, Takebayashi Y, Harris B, Sakakibara H, Gallavotti A, Gillis J, Jackson D. Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583414. [PMID: 38496543 PMCID: PMC10942292 DOI: 10.1101/2024.03.04.583414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Stem cells in plant shoots are a rare population of cells that produce leaves, fruits and seeds, vital sources for food and bioethanol. Uncovering regulators expressed in these stem cells will inform crop engineering to boost productivity. Single-cell analysis is a powerful tool for identifying regulators expressed in specific groups of cells. However, accessing plant shoot stem cells is challenging. Recent single-cell analyses of plant shoots have not captured these cells, and failed to detect stem cell regulators like CLAVATA3 and WUSCHEL . In this study, we finely dissected stem cell-enriched shoot tissues from both maize and arabidopsis for single-cell RNA-seq profiling. We optimized protocols to efficiently recover thousands of CLAVATA3 and WUSCHEL expressed cells. A cross-species comparison identified conserved stem cell regulators between maize and arabidopsis. We also performed single-cell RNA-seq on maize stem cell overproliferation mutants to find additional candidate regulators. Expression of candidate stem cell genes was validated using spatial transcriptomics, and we functionally confirmed roles in shoot development. These candidates include a family of ribosome-associated RNA-binding proteins, and two families of sugar kinase genes related to hypoxia signaling and cytokinin hormone homeostasis. These large-scale single-cell profiling of stem cells provide a resource for mining stem cell regulators, which show significant association with yield traits. Overall, our discoveries advance the understanding of shoot development and open avenues for manipulating diverse crops to enhance food and energy security.
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12
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Kaur H, Jha P, Ochatt SJ, Kumar V. Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research: recent advances and future opportunities. Crit Rev Biotechnol 2024; 44:202-217. [PMID: 36775666 DOI: 10.1080/07388551.2023.2165900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/04/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
Single-cell approaches are a promising way to obtain high-resolution transcriptomics data and have the potential to revolutionize the study of plant growth and development. Recent years have seen the advent of unprecedented technological advances in the field of plant biology to study the transcriptional information of individual cells by single-cell RNA sequencing (scRNA-seq). This review focuses on the modern advancements of single-cell transcriptomics in plants over the past few years. In addition, it also offers a new insight of how these emerging methods will expedite advance research in plant biotechnology in the near future. Lastly, the various technological hurdles and inherent limitations of single-cell technology that need to be conquered to develop such outstanding possible knowledge gain is critically analyzed and discussed.
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Affiliation(s)
- Harmeet Kaur
- Division of Research and Development, Plant Biotechnology Lab, Lovely Professional University, Phagwara, Punjab, India
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Priyanka Jha
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
- Department of Research Facilitation, Division of Research and Development, Lovely Professional University, Phagwara, Punjab, India
| | - Sergio J Ochatt
- Agroécologie, InstitutAgro Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Vijay Kumar
- Division of Research and Development, Plant Biotechnology Lab, Lovely Professional University, Phagwara, Punjab, India
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
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13
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Islam MT, Liu Y, Hassan MM, Abraham PE, Merlet J, Townsend A, Jacobson D, Buell CR, Tuskan GA, Yang X. Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0029. [PMID: 38435807 PMCID: PMC10905259 DOI: 10.34133/bdr.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/28/2024] [Indexed: 03/05/2024] Open
Abstract
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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Affiliation(s)
- Md Torikul Islam
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding,
Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jean Merlet
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education,
University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Alice Townsend
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education,
University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C. Robin Buell
- Center for Applied Genetic Technologies,
University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences,
University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics, and Genomics,
University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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14
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Ali M, Yang T, He H, Zhang Y. Plant biotechnology research with single-cell transcriptome: recent advancements and prospects. PLANT CELL REPORTS 2024; 43:75. [PMID: 38381195 DOI: 10.1007/s00299-024-03168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
KEY MESSAGE Single-cell transcriptomic techniques have emerged as powerful tools in plant biology, offering high-resolution insights into gene expression at the individual cell level. This review highlights the rapid expansion of single-cell technologies in plants, their potential in understanding plant development, and their role in advancing plant biotechnology research. Single-cell techniques have emerged as powerful tools to enhance our understanding of biological systems, providing high-resolution transcriptomic analysis at the single-cell level. In plant biology, the adoption of single-cell transcriptomics has seen rapid expansion of available technologies and applications. This review article focuses on the latest advancements in the field of single-cell transcriptomic in plants and discusses the potential role of these approaches in plant development and expediting plant biotechnology research in the near future. Furthermore, inherent challenges and limitations of single-cell technology are critically examined to overcome them and enhance our knowledge and understanding.
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Affiliation(s)
- Muhammad Ali
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China
- Peking University-Institute of Advanced Agricultural Sciences, Weifang, China
| | - Tianxia Yang
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Hai He
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Yu Zhang
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China.
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15
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Xiao W, Jiang N, Ji Z, Ni M, Zhang Z, Zhao Q, Huang R, Li P, Hou L. Single-Cell RNA Sequencing Reveals the Cellular Landscape of Longissimus Dorsi in a Newborn Suhuai Pig. Int J Mol Sci 2024; 25:1204. [PMID: 38256277 PMCID: PMC10816681 DOI: 10.3390/ijms25021204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The introduction of single-cell RNA sequencing (scRNA-seq) technology has spurred additional advancements in analyzing the cellular composition of tissues. The longissimus dorsi (LD) in pigs serves as the primary skeletal muscle for studying meat quality in the pig industry. However, the single-cell profile of porcine LD is still in its infancy stage. In this study, we profiled the transcriptomes of 16,018 cells in the LD of a newborn Suhuai pig at single-cell resolution. Subsequently, we constructed a cellular atlas of the LD, identifying 11 distinct cell populations, including endothelial cells (24.39%), myotubes (18.82%), fibro-adipogenic progenitors (FAPs, 18.11%), satellite cells (16.74%), myoblasts (3.99%), myocytes (5.74%), Schwann cells (3.81%), smooth muscle cells (3.22%), dendritic cells (2.99%), pericytes (1.86%), and neutrophils (0.33%). CellChat was employed to deduce the cell-cell interactions by evaluating the gene expression of receptor-ligand pairs across different cell types. The results show that FAPs and pericytes are the primary signal contributors in LD. In addition, we delineated the developmental trajectory of myogenic cells and examined alterations in the expression of various marker genes and molecular events throughout various stages of differentiation. Moreover, we found that FAPs can be divided into three subclusters (NR2F2-FAPs, LPL-FAPs, and TNMD-FAPs) according to their biological functions, suggesting that the FAPs could be associated with the differentiation of tendon cell. Taken together, we constructed the cellular atlas and cell communication network in LD of a newborn Suhuai pig, and analyzed the developmental trajectory of myogenic cells and the heterogeneity of FAPs subpopulation cells. This enhances our comprehension of the molecular features involved in skeletal muscle development and the meat quality control in pigs.
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Affiliation(s)
- Wei Xiao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Nengjing Jiang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengyu Ji
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengru Ni
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaobo Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingbo Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- Huai’an Academy, Nanjing Agricultural University, Huai’an 223001, China
| | - Ruihua Huang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- Huai’an Academy, Nanjing Agricultural University, Huai’an 223001, China
| | - Pinghua Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- Huai’an Academy, Nanjing Agricultural University, Huai’an 223001, China
| | - Liming Hou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- Huai’an Academy, Nanjing Agricultural University, Huai’an 223001, China
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16
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Zhang Y, Shen C, Shi J, Shi J, Zhang D. Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:17-35. [PMID: 37935244 DOI: 10.1093/jxb/erad386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
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17
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Lindsay P, Swentowsky KW, Jackson D. Cultivating potential: Harnessing plant stem cells for agricultural crop improvement. MOLECULAR PLANT 2024; 17:50-74. [PMID: 38130059 DOI: 10.1016/j.molp.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.
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Affiliation(s)
- Penelope Lindsay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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18
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Liu H, Guo Z, Gangurde SS, Garg V, Deng Q, Du P, Lu Q, Chitikineni A, Xiao Y, Wang W, Hong Y, Varshney RK, Chen X. A Single-Nucleus Resolution Atlas of Transcriptome and Chromatin Accessibility for Peanut (Arachis Hypogaea L.) Leaves. Adv Biol (Weinh) 2024; 8:e2300410. [PMID: 37828417 DOI: 10.1002/adbi.202300410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/02/2023] [Indexed: 10/14/2023]
Abstract
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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Affiliation(s)
- Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Zenhua Guo
- Rice Research Institute of Heilongjiang Academy of Agriculture Sciences, Heilongjiang Province, Jiamusi, 154026, China
| | - Sunil S Gangurde
- USDA-ARS, Crop Genetics and Breeding Research Unit, Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - Vanika Garg
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, Western Australia, 6150, Australia
| | - Quanqing Deng
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Puxuan Du
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Annapurna Chitikineni
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, Western Australia, 6150, Australia
| | - Yuan Xiao
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Wenyi Wang
- College of Agriculture, South China Agriculture University, Guangzhou, Guangdong Province, 510642, China
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, Western Australia, 6150, Australia
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
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19
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Shen X, Xiao B, Kaderbek T, Lin Z, Tan K, Wu Q, Yuan L, Lai J, Zhao H, Song W. Dynamic transcriptome landscape of developing maize ear. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1856-1870. [PMID: 37731154 DOI: 10.1111/tpj.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/19/2023] [Accepted: 08/26/2023] [Indexed: 09/22/2023]
Abstract
Seed number and harvesting ability in maize (Zea mays L.) are primarily determined by the architecture of female inflorescence, namely the ear. Therefore, ear morphogenesis contributes to grain yield and as such is one of the key target traits during maize breeding. However, the molecular networks of this highly dynamic and complex grain-bearing inflorescence remain largely unclear. As a first step toward characterizing these networks, we performed a high-spatio-temporal-resolution investigation of transcriptomes using 130 ear samples collected from developing ears with length from 0.1 mm to 19.0 cm. Comparisons of these mRNA populations indicated that these spatio-temporal transcriptomes were clearly separated into four distinct stages stages I, II, III, and IV. A total of 23 793 genes including 1513 transcription factors (TFs) were identified in the investigated developing ears. During the stage I of ear morphogenesis, 425 genes were predicted to be involved in a co-expression network established by eight hub TFs. Moreover, 9714 ear-specific genes were identified in the seven kinds of meristems. Additionally, 527 genes including 59 TFs were identified as especially expressed in ear and displayed high temporal specificity. These results provide a high-resolution atlas of gene activity during ear development and help to unravel the regulatory modules associated with the differentiation of the ear in maize.
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Affiliation(s)
- Xiaomeng Shen
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Bing Xiao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P.R. China
| | - Tangnur Kaderbek
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Zhen Lin
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Kaiwen Tan
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Qingyu Wu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Lixing Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P.R. China
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
| | - Haiming Zhao
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
| | - Weibin Song
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
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20
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Minow MAA, Marand AP, Schmitz RJ. Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. Annu Rev Genet 2023; 57:297-319. [PMID: 37562412 PMCID: PMC10775913 DOI: 10.1146/annurev-genet-022123-110824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.
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Affiliation(s)
- Mark A A Minow
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
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21
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Wu Z, Zhang G, Zhao R, Gao Q, Zhao J, Zhu X, Wang F, Kang Z, Wang X. Transcriptomic analysis of wheat reveals possible resistance mechanism mediated by Yr10 to stripe rust. STRESS BIOLOGY 2023; 3:44. [PMID: 37870601 PMCID: PMC10593697 DOI: 10.1007/s44154-023-00115-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/09/2023] [Indexed: 10/24/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a catastrophic disease that threatens global wheat yield. Yr10 is a race-specific all-stage disease resistance gene in wheat. However, the resistance mechanism of Yr10 is poorly characterized. Therefore, to elucidate the potential molecular mechanism mediated by Yr10, transcriptomic sequencing was performed at 0, 18, and 48 h post-inoculation (hpi) of compatible wheat Avocet S (AvS) and incompatible near-isogenic line (NIL) AvS + Yr10 inoculated with Pst race CYR32. Respectively, 227, 208, and 4050 differentially expressed genes (DEGs) were identified at 0, 18, and 48 hpi between incompatible and compatible interaction. The response of Yr10 to stripe rust involved various processes and activities, as indicated by the results of Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Specifically, the response included photosynthesis, defense response to fungus, metabolic processes related to salicylic acid (SA) and jasmonic acid (JA), and activities related to reactive oxygen species (ROS). Ten candidate genes were selected for qRT-PCR verification and the results showed that the transcriptomic data was reliable. Through the functional analysis of candidate genes by the virus-induced gene silencing (VIGS) system, it was found that the gene TaHPPD (4-hydroxyphenylpyruvate dioxygenase) negatively regulated the resistance of wheat to stripe rust by affecting SA signaling, pathogenesis-related (PR) gene expression, and ROS clearance. Our study provides insight into Yr10-mediated resistance in wheat.
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Affiliation(s)
- Zhongyi Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Gaohua Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ran Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jinchen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoxu Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangyan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiaojing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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22
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Hong L, Fletcher JC. Stem Cells: Engines of Plant Growth and Development. Int J Mol Sci 2023; 24:14889. [PMID: 37834339 PMCID: PMC10573764 DOI: 10.3390/ijms241914889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
The development of both animals and plants relies on populations of pluripotent stem cells that provide the cellular raw materials for organ and tissue formation. Plant stem cell reservoirs are housed at the shoot and root tips in structures called meristems, with the shoot apical meristem (SAM) continuously producing aerial leaf, stem, and flower organs throughout the life cycle. Thus, the SAM acts as the engine of plant development and has unique structural and molecular features that allow it to balance self-renewal with differentiation and act as a constant source of new cells for organogenesis while simultaneously maintaining a stem cell reservoir for future organ formation. Studies have identified key roles for intercellular regulatory networks that establish and maintain meristem activity, including the KNOX transcription factor pathway and the CLV-WUS stem cell feedback loop. In addition, the plant hormones cytokinin and auxin act through their downstream signaling pathways in the SAM to integrate stem cell activity and organ initiation. This review discusses how the various regulatory pathways collectively orchestrate SAM function and touches on how their manipulation can alter stem cell activity to improve crop yield.
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Affiliation(s)
- Liu Hong
- Plant Gene Expression Center, United States Department of Agriculture—Agricultural Research Service, Albany, CA 94710, USA;
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jennifer C. Fletcher
- Plant Gene Expression Center, United States Department of Agriculture—Agricultural Research Service, Albany, CA 94710, USA;
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
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23
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Oliva M, Lister R. Exploring the identity of individual plant cells in space and time. THE NEW PHYTOLOGIST 2023; 240:61-67. [PMID: 37483019 PMCID: PMC10952157 DOI: 10.1111/nph.19153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/17/2023] [Indexed: 07/25/2023]
Abstract
In recent years, single-cell genomics, coupled to imaging techniques, have become the state-of-the-art approach for characterising biological systems. In plant sciences, a variety of tissues and species have been profiled, providing an enormous quantity of data on cell identity at an unprecedented resolution, but what biological insights can be gained from such data sets? Using recently published studies in plant sciences, we will highlight how single-cell technologies have enabled a better comprehension of tissue organisation, cell fate dynamics in development or in response to various stimuli, as well as identifying key transcriptional regulators of cell identity. We discuss the limitations and technical hurdles to overcome, as well as future directions, and the promising use of single-cell omics to understand, predict, and manipulate plant development and physiology.
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Affiliation(s)
- Marina Oliva
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular SciencesUniversity of Western AustraliaPerthWA6009Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular SciencesUniversity of Western AustraliaPerthWA6009Australia
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical ResearchThe University of Western AustraliaPerthWA6009Australia
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24
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Zhang J, Ahmad M, Gao H. Application of single-cell multi-omics approaches in horticulture research. MOLECULAR HORTICULTURE 2023; 3:18. [PMID: 37789394 PMCID: PMC10521458 DOI: 10.1186/s43897-023-00067-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
Cell heterogeneity shapes the morphology and function of various tissues and organs in multicellular organisms. Elucidation of the differences among cells and the mechanism of intercellular regulation is essential for an in-depth understanding of the developmental process. In recent years, the rapid development of high-throughput single-cell transcriptome sequencing technologies has influenced the study of plant developmental biology. Additionally, the accuracy and sensitivity of tools used to study the epigenome and metabolome have significantly increased, thus enabling multi-omics analysis at single-cell resolution. Here, we summarize the currently available single-cell multi-omics approaches and their recent applications in plant research, review the single-cell based studies in fruit, vegetable, and ornamental crops, and discuss the potential of such approaches in future horticulture research.
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Affiliation(s)
- Jun Zhang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mayra Ahmad
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Gao
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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25
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Sanchez Carrillo IB, Hoffmann PC, Barff T, Beck M, Germain H. Preparing Arabidopsis thaliana root protoplasts for cryo electron tomography. FRONTIERS IN PLANT SCIENCE 2023; 14:1261180. [PMID: 37810374 PMCID: PMC10556516 DOI: 10.3389/fpls.2023.1261180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
The use of protoplasts in plant biology has become a convenient tool for the application of transient gene expression. This model system has allowed the study of plant responses to biotic and abiotic stresses, protein location and trafficking, cell wall dynamics, and single-cell transcriptomics, among others. Although well-established protocols for isolating protoplasts from different plant tissues are available, they have never been used for studying plant cells using cryo electron microscopy (cryo-EM) and cryo electron tomography (cryo-ET). Here we describe a workflow to prepare root protoplasts from Arabidopsis thaliana plants for cryo-ET. The process includes protoplast isolation and vitrification on EM grids, and cryo-focused ion beam milling (cryo-FIB), with the aim of tilt series acquisition. The whole workflow, from growing the plants to the acquisition of the tilt series, may take a few months. Our protocol provides a novel application to use plant protoplasts as a tool for cryo-ET.
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Affiliation(s)
| | - Patrick C. Hoffmann
- Department of Molecular Sociology, Max-Planck-Institute for Biophysics, Frankfurt, Germany
| | - Teura Barff
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Martin Beck
- Department of Molecular Sociology, Max-Planck-Institute for Biophysics, Frankfurt, Germany
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Hugo Germain
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
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26
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Cao S, He Z, Chen R, Luo Y, Fu LY, Zhou X, He C, Yan W, Zhang CY, Chen D. scPlant: A versatile framework for single-cell transcriptomic data analysis in plants. PLANT COMMUNICATIONS 2023; 4:100631. [PMID: 37254480 PMCID: PMC10504592 DOI: 10.1016/j.xplc.2023.100631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/13/2023] [Accepted: 05/24/2023] [Indexed: 06/01/2023]
Abstract
Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth, development, and responses to external stimuli. However, single-cell transcriptomic data analysis in plants is not trivial, given that there is currently no end-to-end solution and that integration of various bioinformatics tools involves a large number of required dependencies. Here, we present scPlant, a versatile framework for exploring plant single-cell atlases with minimum input data provided by users. The scPlant pipeline is implemented with numerous functions for diverse analytical tasks, ranging from basic data processing to advanced demands such as cell-type annotation and deconvolution, trajectory inference, cross-species data integration, and cell-type-specific gene regulatory network construction. In addition, a variety of visualization tools are bundled in a built-in Shiny application, enabling exploration of single-cell transcriptomic data on the fly.
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Affiliation(s)
- Shanni Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhaohui He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ruidong Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yuting Luo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Liang-Yu Fu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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27
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Zhang S, Zhu C, Zhang X, Liu M, Xue X, Lai C, Xuhan X, Chen Y, Zhang Z, Lai Z, Lin Y. Single-cell RNA sequencing analysis of the embryogenic callus clarifies the spatiotemporal developmental trajectories of the early somatic embryo in Dimocarpus longan. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1277-1297. [PMID: 37235696 DOI: 10.1111/tpj.16319] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023]
Abstract
Plant embryogenic calli (ECs) can undergo somatic embryogenesis to regenerate plants. This process is mediated by regulatory factors, such as transcription factors and specifically expressed genes, but the precise molecular mechanisms underlying somatic embryogenesis at the single-cell level remain unclear. In this study, we performed high-resolution single-cell RNA sequencing analysis to determine the cellular changes in the EC of the woody plant species Dimocarpus longan (longan) and clarify the continuous cell differentiation trajectories at the transcriptome level. The highly heterogeneous cells in the EC were divided into 12 putative clusters (e.g., proliferating, meristematic, vascular, and epidermal cell clusters). We determined cluster-enriched expression marker genes and found that overexpression of the epidermal cell marker gene GDSL ESTERASE/LIPASE-1 inhibited the hydrolysis of triacylglycerol. In addition, the stability of autophagy was critical for the somatic embryogenesis of longan. The pseudo-timeline analysis elucidated the continuous cell differentiation trajectories from early embryonic cell division to vascular and epidermal cell differentiation during the somatic embryogenesis of longan. Moreover, key transcriptional regulators associated with cell fates were revealed. We found that ETHYLENE RESPONSIVE FACTOR 6 was characterized as a heat-sensitive factor that negatively regulates longan somatic embryogenesis under high-temperature stress conditions. The results of this study provide new spatiotemporal insights into cell division and differentiation during longan somatic embryogenesis at single-cell resolution.
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Affiliation(s)
- Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengyu Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaodong Xue
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, Toulouse, 31300, France
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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28
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Cao Y, Ma J, Han S, Hou M, Wei X, Zhang X, Zhang ZJ, Sun S, Ku L, Tang J, Dong Z, Zhu Z, Wang X, Zhou X, Zhang L, Li X, Long Y, Wan X, Duan C. Single-cell RNA sequencing profiles reveal cell type-specific transcriptional regulation networks conditioning fungal invasion in maize roots. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1839-1859. [PMID: 37349934 PMCID: PMC10440994 DOI: 10.1111/pbi.14097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/24/2023] [Accepted: 05/29/2023] [Indexed: 06/24/2023]
Abstract
Stalk rot caused by Fusarium verticillioides (Fv) is one of the most destructive diseases in maize production. The defence response of root system to Fv invasion is important for plant growth and development. Dissection of root cell type-specific response to Fv infection and its underlying transcription regulatory networks will aid in understanding the defence mechanism of maize roots to Fv invasion. Here, we reported the transcriptomes of 29 217 single cells derived from root tips of two maize inbred lines inoculated with Fv and mock condition, and identified seven major cell types with 21 transcriptionally distinct cell clusters. Through the weighted gene co-expression network analysis, we identified 12 Fv-responsive regulatory modules from 4049 differentially expressed genes (DEGs) that were activated or repressed by Fv infection in these seven cell types. Using a machining-learning approach, we constructed six cell type-specific immune regulatory networks by integrating Fv-induced DEGs from the cell type-specific transcriptomes, 16 known maize disease-resistant genes, five experimentally validated genes (ZmWOX5b, ZmPIN1a, ZmPAL6, ZmCCoAOMT2, and ZmCOMT), and 42 QTL or QTN predicted genes that are associated with Fv resistance. Taken together, this study provides not only a global view of maize cell fate determination during root development but also insights into the immune regulatory networks in major cell types of maize root tips at single-cell resolution, thus laying the foundation for dissecting molecular mechanisms underlying disease resistance in maize.
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Affiliation(s)
- Yanyong Cao
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
- Zhongzhi International Institute of Agricultural Biosciences, Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- The Shennong LaboratoryZhengzhouChina
| | - Juan Ma
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Shengbo Han
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Mengwei Hou
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Xun Wei
- Zhongzhi International Institute of Agricultural Biosciences, Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
| | - Xingrui Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhanyuan J. Zhang
- Division of Plant Sciences, Plant Transformation Core FacilityUniversity of MissouriColumbiaMissouriUSA
- Present address:
Inari Agriculture, Inc.West LafayetteIndiana47906USA
| | - Suli Sun
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Lixia Ku
- The Shennong LaboratoryZhengzhouChina
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Jihua Tang
- The Shennong LaboratoryZhengzhouChina
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zhenying Dong
- Zhongzhi International Institute of Agricultural Biosciences, Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
| | - Zhendong Zhu
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoming Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoxiao Zhou
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Lili Zhang
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiangdong Li
- Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Yan Long
- Zhongzhi International Institute of Agricultural Biosciences, Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
| | - Canxing Duan
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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29
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Wang Y, Jiao Y. Cell signaling in the shoot apical meristem. PLANT PHYSIOLOGY 2023; 193:70-82. [PMID: 37224874 DOI: 10.1093/plphys/kiad309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/24/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023]
Abstract
Distinct from animals, plants maintain organogenesis from specialized tissues termed meristems throughout life. In the shoot apex, the shoot apical meristem (SAM) produces all aerial organs, such as leaves, from its periphery. For this, the SAM needs to precisely balance stem cell renewal and differentiation, which is achieved through dynamic zonation of the SAM, and cell signaling within functional domains is key for SAM functions. The WUSCHEL-CLAVATA feedback loop plays a key role in SAM homeostasis, and recent studies have uncovered new components, expanding our understanding of the spatial expression and signaling mechanism. Advances in polar auxin transport and signaling have contributed to knowledge of the multifaceted roles of auxin in the SAM and organogenesis. Finally, single-cell techniques have expanded our understanding of the cellular functions within the shoot apex at single-cell resolution. In this review, we summarize the most up-to-date understanding of cell signaling in the SAM and focus on the multiple levels of regulation of SAM formation and maintenance.
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Affiliation(s)
- Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
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30
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Chen C, Ge Y, Lu L. Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1185377. [PMID: 37636094 PMCID: PMC10453814 DOI: 10.3389/fpls.2023.1185377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023]
Abstract
Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.
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Affiliation(s)
- Ce Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yining Ge
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lingli Lu
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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31
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Wang L, Wan MC, Liao RY, Xu J, Xu ZG, Xue HC, Mai YX, Wang JW. The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution. Dev Cell 2023; 58:1429-1444.e6. [PMID: 37321217 DOI: 10.1016/j.devcel.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/13/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023]
Abstract
Bryophytes represent a sister to the rest of land plants. Despite their evolutionary importance and relatively simple body plan, a comprehensive understanding of the cell types and transcriptional states that underpin the temporal development of bryophytes has not been achieved. Using time-resolved single-cell RNA sequencing, we define the cellular taxonomy of Marchantia polymorpha across asexual reproduction phases. We identify two maturation and aging trajectories of the main plant body of M. polymorpha at single-cell resolution: the gradual maturation of tissues and organs along the tip-to-base axis of the midvein and the progressive decline of meristem activities in the tip along the chronological axis. Specifically, we observe that the latter aging axis is temporally correlated with the formation of clonal propagules, suggesting an ancient strategy to optimize allocation of resources to producing offspring. Our work thus provides insights into the cellular heterogeneity that underpins the temporal development and aging of bryophytes.
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Affiliation(s)
- Long Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Mu-Chun Wan
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ren-Yu Liao
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Jie Xu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Hao-Chen Xue
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Yan-Xia Mai
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; Core Facility Center of CEMPS, SIPPE, CAS, Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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Liao RY, Wang JW. Analysis of meristems and plant regeneration at single-cell resolution. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102378. [PMID: 37172363 DOI: 10.1016/j.pbi.2023.102378] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/12/2023] [Indexed: 05/14/2023]
Abstract
Rapid development of high-throughput single-cell RNA sequencing (scRNA-seq) technologies offers exciting opportunities to reveal new and rare cell types, previously hidden cell states, and continuous developmental trajectories. In this review, we first illustrate the ways in which scRNA-seq enables researchers to distinguish between distinct plant cell populations, delineate cell cycle continuums, and infer continuous differentiation trajectories of diverse cell types in shoots, roots, and floral and vascular meristems with unprecedented resolution. We then highlight the emerging power of scRNA-seq to dissect cell heterogeneity in regenerating tissues and uncover the cellular basis of cell reprogramming and stem cell commitment during plant regeneration. We conclude by discussing related outstanding questions in the field.
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Affiliation(s)
- Ren-Yu Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China; University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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Liang X, Ma Z, Ke Y, Wang J, Wang L, Qin B, Tang C, Liu M, Xian X, Yang Y, Wang M, Zhang Y. Single-cell transcriptomic analyses reveal cellular and molecular patterns of rubber tree response to early powdery mildew infection. PLANT, CELL & ENVIRONMENT 2023; 46:2222-2237. [PMID: 36929646 DOI: 10.1111/pce.14585] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 06/08/2023]
Abstract
As a perennial woody plant, the rubber tree (Hevea brasiliensis) must adapt to various environmental challenges through gene expression in multiple cell types. It is still unclear how genes in this species are expressed at the cellular level and the precise mechanisms by which cells respond transcriptionally to environmental stimuli, especially in the case of pathogen infection. Here, we characterized the transcriptomes in Hevea leaves during early powdery mildew infection using single-cell RNA sequencing. We identified 10 cell types and constructed the first single-cell atlas of Hevea leaves. Distinct gene expression patterns of the cell clusters were observed under powdery mildew infection, which was especially significant in the epidermal cells. Most of the genes involved in host-pathogen interactions in epidermal cells exhibited a pattern of dramatically increased expression with increasing pseudotime. Interestingly, we found that the HbCNL2 gene, encoding a nucleotide-binding leucine-rich repeat protein, positively modulated the defence of rubber leaves against powdery mildew. Overexpression of the HbCNL2 gene triggered a typical cell death phenotype in tobacco leaves and a higher level of reactive oxygen species in the protoplasts of Hevea leaves. The HbCNL2 protein was located in the cytomembrane and nucleus, and its leucine-rich repeat domain interacted with the histidine kinase-like ATPase domain of the molecular chaperone HbHSP90 in the nucleus. Collectively, our results provide the first observation of the cellular and molecular responses of Hevea leaves to biotrophic pathogen infection and can guide the identification of disease-resistance genes in this important tree species.
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Affiliation(s)
- Xiaoyu Liang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Zhan Ma
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Yuhang Ke
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Jiali Wang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Lifeng Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bi Qin
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chaorong Tang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Mingyang Liu
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Xuemei Xian
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Ye Yang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Meng Wang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Yu Zhang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
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D'Agostino LW, Yong-Villalobos L, Herrera-Estrella L, Patil GB. Development of High-Quality Nuclei Isolation to Study Plant Root-Microbe Interaction for Single-Nuclei Transcriptomic Sequencing in Soybean. PLANTS (BASEL, SWITZERLAND) 2023; 12:2466. [PMID: 37447027 DOI: 10.3390/plants12132466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
Single-nucleus RNA sequencing (sNucRNA-seq) is an emerging technology that has been rapidly adopted and demonstrated to be a powerful tool for detailed characterization of each cell- and sub cell-types in complex tissues of higher eukaryotes. sNucRNA-seq has also been used to dissect cell-type-specific transcriptional responses to environmental or developmental signals. In plants, this technology is being utilized to identify cell-type-specific trajectories for the study of several tissue types and important traits, including the single-cell dissection of the genetic determinants regulating plant-microbe interactions. The isolation of high-quality nuclei is one of the prerequisite steps to obtain high-quality sNucRNA-seq results. Although nuclei isolation from several plant tissues is well established, this process is highly troublesome when plant tissues are associated with beneficial or pathogenic microbes. For example, root tissues colonized with rhizobium bacteria (nodules), leaf tissue infected with bacterial or fungal pathogens, or roots infected with nematodes pose critical challenges to the isolation of high-quality nuclei and use for downstream application. Therefore, isolation of microbe-free, high-quality nuclei from plant tissues are necessary to avoid clogging or interference with the microfluidic channel (e.g., 10× Genomics) or particle-templated emulsion that are used in sNucRNA-seq platforms. Here, we developed a simple, effective, and efficient method to isolate high-quality nuclei from soybean roots and root nodules, followed by washing out bacterial contamination. This protocol has been designed to be easily implemented into any lab environment, and it can also be scaled up for use with multiple samples and applicable to a variety of samples with the presence of microbes. We validated this protocol by successfully generating a barcoded library using the 10× Genomics microfluidic platform from tissue subjected to this procedure. This workflow was developed to provide an accessible alternative to instrument-based approaches (e.g., fluorescent cell sorting) and will expand the ability of researchers to perform experiments such as sNucRNA-seq and sNucATAC-seq on inherently heterogeneous plant tissue samples.
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Affiliation(s)
- Leonidas W D'Agostino
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Lenin Yong-Villalobos
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
- Unidad de Genomica Avanzada, Centro de Investigacion y de Estudios Avanzados, Instituto Politecnico Nacional, Irapuato 36821, Mexico
| | - Gunvant B Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
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35
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Zha W, Li C, Wu Y, Chen J, Li S, Sun M, Wu B, Shi S, Liu K, Xu H, Li P, Liu K, Yang G, Chen Z, Xu D, Zhou L, You A. Single-Cell RNA sequencing of leaf sheath cells reveals the mechanism of rice resistance to brown planthopper ( Nilaparvata lugens). FRONTIERS IN PLANT SCIENCE 2023; 14:1200014. [PMID: 37404541 PMCID: PMC10316026 DOI: 10.3389/fpls.2023.1200014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/26/2023] [Indexed: 07/06/2023]
Abstract
The brown planthopper (BPH) (Nilaparvata lugens) sucks rice sap causing leaves to turn yellow and wither, often leading to reduced or zero yields. Rice co-evolved to resist damage by BPH. However, the molecular mechanisms, including the cells and tissues, involved in the resistance are still rarely reported. Single-cell sequencing technology allows us to analyze different cell types involved in BPH resistance. Here, using single-cell sequencing technology, we compared the response offered by the leaf sheaths of the susceptible (TN1) and resistant (YHY15) rice varieties to BPH (48 hours after infestation). We found that the 14,699 and 16,237 cells (identified via transcriptomics) in TN1 and YHY15 could be annotated using cell-specific marker genes into nine cell-type clusters. The two rice varieties showed significant differences in cell types (such as mestome sheath cells, guard cells, mesophyll cells, xylem cells, bulliform cells, and phloem cells) in the rice resistance mechanism to BPH. Further analysis revealed that although mesophyll, xylem, and phloem cells are involved in the BPH resistance response, the molecular mechanism used by each cell type is different. Mesophyll cell may regulate the expression of genes related to vanillin, capsaicin, and ROS production, phloem cell may regulate the cell wall extension related genes, and xylem cell may be involved in BPH resistance response by controlling the expression of chitin and pectin related genes. Thus, rice resistance to BPH is a complicated process involving multiple insect resistance factors. The results presented here will significantly promote the investigation of the molecular mechanisms underlying the resistance of rice to insects and accelerate the breeding of insect-resistant rice varieties.
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Affiliation(s)
- Wenjun Zha
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Changyan Li
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yan Wu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Junxiao Chen
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Sanhe Li
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Minshan Sun
- Henan Assist Research Biotechnology Co., Ltd., Zhengzhou, China
| | - Bian Wu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Shaojie Shi
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Kai Liu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Huashan Xu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Peide Li
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Kai Liu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guocai Yang
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zhijun Chen
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Deze Xu
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Lei Zhou
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Aiqing You
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Jin J, Yu S, Lu P, Cao P. Deciphering plant cell-cell communications using single-cell omics data. Comput Struct Biotechnol J 2023; 21:3690-3695. [PMID: 37576747 PMCID: PMC10412842 DOI: 10.1016/j.csbj.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 08/15/2023] Open
Abstract
Plants have various cell types that respond to different environmental factors, and cell-cell communication is the fundamental process that controls these plant responses. The emergence of single-cell techniques provides opportunities to explore features unique to each cell type and construct a comprehensive cell-cell communication (CCC) network. Although the most current successes of CCC inference were achieved in animal research, computational methods can also be directly applied to plants. This review describes the current major models for cell-cell communication inference and summarizes the computational tools based on single-cell omics datasets. In addition, we discuss the limitations of plant cell-cell communication research and propose new directions to expand the field in meaningful ways.
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Affiliation(s)
- Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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37
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Tu M, Du C, Yu B, Wang G, Deng Y, Wang Y, Chen M, Chang J, Yang G, He G, Xiong Z, Li Y. Current advances in the molecular regulation of abiotic stress tolerance in sorghum via transcriptomic, proteomic, and metabolomic approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1147328. [PMID: 37235010 PMCID: PMC10206308 DOI: 10.3389/fpls.2023.1147328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
Sorghum (Sorghum bicolor L. Moench), a monocot C4 crop, is an important staple crop for many countries in arid and semi-arid regions worldwide. Because sorghum has outstanding tolerance and adaptability to a variety of abiotic stresses, including drought, salt, and alkaline, and heavy metal stressors, it is valuable research material for better understanding the molecular mechanisms of stress tolerance in crops and for mining new genes for their genetic improvement of abiotic stress tolerance. Here, we compile recent progress achieved using physiological, transcriptome, proteome, and metabolome approaches; discuss the similarities and differences in how sorghum responds to differing stresses; and summarize the candidate genes involved in the process of responding to and regulating abiotic stresses. More importantly, we exemplify the differences between combined stresses and a single stress, emphasizing the necessity to strengthen future studies regarding the molecular responses and mechanisms of combined abiotic stresses, which has greater practical significance for food security. Our review lays a foundation for future functional studies of stress-tolerance-related genes and provides new insights into the molecular breeding of stress-tolerant sorghum genotypes, as well as listing a catalog of candidate genes for improving the stress tolerance for other key monocot crops, such as maize, rice, and sugarcane.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Canghao Du
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Boju Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guoli Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yanbin Deng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyong Xiong
- Laboratory of Forage and Endemic Crop Biology (Inner Mongolia University), Ministry of Education, School of Life Sciences, Hohhot, China
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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38
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Satterlee JW, Evans LJ, Conlon BR, Conklin P, Martinez-Gomez J, Yen JR, Wu H, Sylvester AW, Specht CD, Cheng J, Johnston R, Coen E, Scanlon MJ. A Wox3-patterning module organizes planar growth in grass leaves and ligules. NATURE PLANTS 2023; 9:720-732. [PMID: 37142751 DOI: 10.1038/s41477-023-01405-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/28/2023] [Indexed: 05/06/2023]
Abstract
Grass leaves develop from a ring of primordial initial cells within the periphery of the shoot apical meristem, a pool of organogenic stem cells that generates all of the organs of the plant shoot. At maturity, the grass leaf is a flattened, strap-like organ comprising a proximal supportive sheath surrounding the stem and a distal photosynthetic blade. The sheath and blade are partitioned by a hinge-like auricle and the ligule, a fringe of epidermally derived tissue that grows from the adaxial (top) leaf surface. Together, the ligule and auricle comprise morphological novelties that are specific to grass leaves. Understanding how the planar outgrowth of grass leaves and their adjoining ligules is genetically controlled can yield insight into their evolutionary origins. Here we use single-cell RNA-sequencing analyses to identify a 'rim' cell type present at the margins of maize leaf primordia. Cells in the leaf rim have a distinctive identity and share transcriptional signatures with proliferating ligule cells, suggesting that a shared developmental genetic programme patterns both leaves and ligules. Moreover, we show that rim function is regulated by genetically redundant Wuschel-like homeobox3 (WOX3) transcription factors. Higher-order mutations in maize Wox3 genes greatly reduce leaf width and disrupt ligule outgrowth and patterning. Together, these findings illustrate the generalizable use of a rim domain during planar growth of maize leaves and ligules, and suggest a parsimonious model for the homology of the grass ligule as a distal extension of the leaf sheath margin.
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Affiliation(s)
- James W Satterlee
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Lukas J Evans
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Brianne R Conlon
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Phillip Conklin
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Jeffery R Yen
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Hao Wu
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Anne W Sylvester
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Chelsea D Specht
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Jie Cheng
- John Innes Centre, Norwich Research Park, Norwich, UK
- State Key Laboratory of Systematic and Evolutionary Botany, Chinese Academy of Sciences, Beijing, China
| | - Robyn Johnston
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- The Elshire Group Ltd., Palmerston North, New Zealand
| | - Enrico Coen
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Michael J Scanlon
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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39
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Guillotin B, Rahni R, Passalacqua M, Mohammed MA, Xu X, Raju SK, Ramírez CO, Jackson D, Groen SC, Gillis J, Birnbaum KD. A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature 2023; 617:785-791. [PMID: 37165193 PMCID: PMC10657638 DOI: 10.1038/s41586-023-06053-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits1. Key traits that distinguish these species are mediated by specialized cell types2. Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others-driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops.
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Affiliation(s)
- Bruno Guillotin
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ramin Rahni
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Mohammed Ateequr Mohammed
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Xiaosa Xu
- Cold Spring Harbor Laboratory, New York, NY, USA
| | - Sunil Kenchanmane Raju
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Carlos Ortiz Ramírez
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- UGA-LANGEBIO Cinvestav, Guanajuato, México
| | | | - Simon C Groen
- Department of Nematology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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Zhang L, He C, Lai Y, Wang Y, Kang L, Liu A, Lan C, Su H, Gao Y, Li Z, Yang F, Li Q, Mao H, Chen D, Chen W, Kaufmann K, Yan W. Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis. Genome Biol 2023; 24:65. [PMID: 37016448 PMCID: PMC10074895 DOI: 10.1186/s13059-023-02908-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. RESULTS Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. CONCLUSIONS Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.
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Affiliation(s)
- Lihua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yating Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Kang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwen Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zeqing Li
- Wuhan Igenebook Biotechnology Co., Ltd, Wuhan, 430014, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Sun Y, Han Y, Sheng K, Yang P, Cao Y, Li H, Zhu QH, Chen J, Zhu S, Zhao T. Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii. MOLECULAR PLANT 2023; 16:694-708. [PMID: 36772793 DOI: 10.1016/j.molp.2023.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/31/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Comprehensive utilization of cottonseeds is limited by the presence of pigment glands and its inclusion gossypol. The ideal cotton has glandless seeds but a glanded plant, a trait found in only a few Australian wild cotton species, including Gossypium bickii. Introgression of this trait into cultivated species has proved to be difficult. Understanding the biological processes toward pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding of cultivated cotton varieties with the trait of glandless seeds and glanded plant. In this study, single-cell RNA sequencing (scRNA-seq) was performed on 12 222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48 h after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. By integrating the pigment gland cell developmental trajectory, transcription factor regulatory networks, and core transcription factor functional validation, we established a model for pigment gland formation. In this model, light and gibberellin were verified to promote the formation of pigment glands. In addition, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11), and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. Collectively, these findings provide new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations.
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Affiliation(s)
- Yue Sun
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yifei Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kuang Sheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ping Yang
- Agricultural Experiment Station, Zhejiang University, Hangzhou 310058, China
| | - Yuefen Cao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Huazu Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Jinhong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Institute of Hainan, Zhejiang University, Hangzhou 310058, China
| | - Shuijin Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Institute of Hainan, Zhejiang University, Hangzhou 310058, China.
| | - Tianlun Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Institute of Hainan, Zhejiang University, Hangzhou 310058, China.
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Rojas BE, Tonetti T, Figueroa CM. Trehalose 6-phosphate metabolism in C 4 species. CURRENT OPINION IN PLANT BIOLOGY 2023; 72:102347. [PMID: 36806837 DOI: 10.1016/j.pbi.2023.102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, is an essential signal metabolite in plants, linking growth and development to carbon status. Our current understanding of Tre6P metabolism and signaling pathways in plants is based almost entirely on studies performed with Arabidopsis thaliana, a model plant that performs C3 photosynthesis. Conversely, our knowledge on the molecular mechanisms involved in Tre6P regulation of carbon partitioning and metabolism in C4 plants is scarce. This topic is especially relevant due to the agronomic importance of crops performing C4 photosynthesis, such as maize, sorghum and sugarcane. In this review, we focused our attention on recent developments related to Tre6P metabolism in C4 species and raised some open questions that should be addressed in the near future to improve the yield of economically important crops.
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Affiliation(s)
- Bruno E Rojas
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Tomás Tonetti
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina.
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Depuydt T, De Rybel B, Vandepoele K. Charting plant gene functions in the multi-omics and single-cell era. TRENDS IN PLANT SCIENCE 2023; 28:283-296. [PMID: 36307271 DOI: 10.1016/j.tplants.2022.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology.
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Affiliation(s)
- Thomas Depuydt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium; Ghent University, Bioinformatics Institute Ghent, Ghent, Belgium.
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44
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Xu X, Jackson D. Single-cell analysis opens a goldmine for plant functional studies. Curr Opin Biotechnol 2023; 79:102858. [PMID: 36493588 DOI: 10.1016/j.copbio.2022.102858] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022]
Abstract
Functional studies in biology require the identification of genes, regulatory elements, and networks, followed by a deep understanding of how they orchestrate to specify cell types, mediate signaling, and respond to internal and external cues over evolutionary timescales. Advances in single-cell analysis have enabled biologists to tackle these questions at the resolution of the individual cell. Here, we highlight recent studies in plants that have embraced single-cell analyses to facilitate functional studies. This review will provide guidance and perspectives for incorporating these advanced approaches in plant research for the coming decades.
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Affiliation(s)
- Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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45
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Zhang K, Liu S, Fu Y, Wang Z, Yang X, Li W, Zhang C, Zhang D, Li J. Establishment of an efficient cotton root protoplast isolation protocol suitable for single-cell RNA sequencing and transient gene expression analysis. PLANT METHODS 2023; 19:5. [PMID: 36653863 PMCID: PMC9850602 DOI: 10.1186/s13007-023-00983-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Cotton has tremendous economic value worldwide; however, its allopolyploid nature and time-consuming transformation methods have hampered the development of cotton functional genomics. The protoplast system has proven to be an important and versatile tool for functional genomics, tissue-specific marker gene identification, tracking developmental trajectories, and genome editing in plants. Nevertheless, the isolation of abundant viable protoplasts suitable for single-cell RNA sequencing (scRNA-seq) and genome editing remains a challenge in cotton. RESULTS We established an efficient transient gene expression system using protoplasts isolated from cotton taproots. The system enables the isolation of large numbers of viable protoplasts and uses an optimized PEG-mediated transfection protocol. The highest yield (3.55 × 105/g) and viability (93.3%) of protoplasts were obtained from cotton roots grown in hydroponics for 72 h. The protoplasts isolated were suitable for scRNA-seq. The highest transfection efficiency (80%) was achieved when protoplasts were isolated as described above and transfected with 20 μg of plasmid for 20 min in a solution containing 200 mM Ca2+. Our protoplast-based transient expression system is suitable for various applications, including validation the efficiency of CRISPR vectors, protein subcellular localization analysis, and protein-protein interaction studies. CONCLUSIONS The protoplast isolation and transfection protocol developed in this study is stable, versatile, and time-saving. It will accelerate functional genomics and molecular breeding in cotton.
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Affiliation(s)
- Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Shanhe Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Yunze Fu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Zixuan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, 071001, China
| | - Xiubo Yang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Wenjing Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Caihua Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Dongmei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
- Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, 071001, China.
| | - Jun Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China.
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Song J, Fan B, Shao X, Zang Y, Wang D, Min Y. Single-cell transcriptome sequencing atlas of cassava tuberous root. FRONTIERS IN PLANT SCIENCE 2023; 13:1053669. [PMID: 36684718 PMCID: PMC9848496 DOI: 10.3389/fpls.2022.1053669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Single-cell transcriptome sequencing (ScRNA-seq) has emerged as an effective method for examining cell differentiation and development. In non-model plants, it hasn't been employed very much, especially in sink organs that are abundant in secondary metabolites. RESULTS In this study, we sequenced the single-cell transcriptomes at two developmental phases of cassava tuberous roots using the technology known as 10x Genomics (S1, S2). In total, 14,566 cells were grouped into 15 different cell types, primarily based on the marker genes of model plants known to exist. In the pseudotime study, the cell differentiation trajectory was defined, and the difference in gene expression between the two stages on the pseudotime axis was compared. The differentiation process of the vascular tissue and cerebral tissue was identified by the trajectory. We discovered the rare cell type known as the casparian strip via the use of up-regulated genes and pseudotime analysis, and we explained how it differentiates from endodermis. The successful creation of a protoplast isolation technique for organs rich in starch was also described in our study. DISCUSSION Together, we created the first high-resolution single-cell transcriptome atlas of cassava tuberous roots, which made significant advancements in our understanding of how these roots differentiate and develop.
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Affiliation(s)
- Jinjia Song
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
| | - Benji Fan
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
| | - Xiaodie Shao
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
| | - Yuwei Zang
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
| | - Dayong Wang
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
| | - Yi Min
- Department of Biotechnology, School of Life Sciences, Hainan University, Haikou, Hainan, China
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Abstract
Droplet-based single-cell RNA-sequencing (scRNA-seq) empowers transcriptomic profiling with an unprecedented resolution, facilitating insights into the cellular heterogeneity of tissues, developmental progressions, stress-response dynamics, and more at single-cell level. In this chapter, we describe the experimental workflow of processing Arabidopsis root tissue into protoplasts and generating single-cell transcriptomes. We also describe the general computational workflow of visualizing and utilizing scRNA-seq data. This protocol can be used as a starting point for establishing a scRNA-seq workflow.
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Affiliation(s)
- Yuji Ke
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Max Minne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas Eekhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Single Cell Core, VIB, Ghent/Leuven, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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Tyagi P, Singh D, Mathur S, Singh A, Ranjan R. Upcoming progress of transcriptomics studies on plants: An overview. FRONTIERS IN PLANT SCIENCE 2022; 13:1030890. [PMID: 36589087 PMCID: PMC9798009 DOI: 10.3389/fpls.2022.1030890] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and developmental stages. RNA-Seq is a significant technique for identifying gene predictions and mining functional analysis that improves gene ontology understanding mechanisms of biological processes, molecular functions, and cellular components, but there is limited information available on this topic. Transcriptomics research on different types of plants can assist researchers to understand functional genes in better ways and regulatory processes to improve breeding selection and cultivation practices. In recent years, several advancements in RNA-Seq technology have been made for the characterization of the transcriptomes of distinct cell types in biological tissues in an efficient manner. RNA-Seq technologies are briefly introduced and examined in terms of their scientific applications. In a nutshell, it introduces all transcriptome sequencing and analysis techniques, as well as their applications in plant biology research. This review will focus on numerous existing and forthcoming strategies for improving transcriptome sequencing technologies for functional gene mining in various plants using RNA- Seq technology, based on the principles, development, and applications.
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Thibivilliers S, Farmer A, Schroeder S, Libault M. Plant Single-Cell/Nucleus RNA-seq Workflow. Methods Mol Biol 2022; 2584:165-181. [PMID: 36495448 DOI: 10.1007/978-1-0716-2756-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-cell transcriptomics technologies allow researchers to investigate how individual cells, in complex multicellular organisms, differentially use their common genomic DNA. In plant biology, these technologies were recently applied to reveal the transcriptomes of various plant cells isolated from different organs and different species and in response to environmental stresses. These first studies support the potential of single-cell transcriptomics technology to decipher the biological function of plant cells, their developmental programs, cell-type-specific gene networks, programs controlling plant cell response to environmental stresses, etc. In this chapter, we provide information regarding the critical steps and important information to consider when developing an experimental design in plant single-cell biology. We also describe the current status of bioinformatics tools used to analyze single-cell RNA-seq datasets and how additional emerging technologies such as spatial transcriptomics and long-read sequencing technologies will provide additional information on the differential use of the genome by plant cells.
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Affiliation(s)
- Sandra Thibivilliers
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Susan Schroeder
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, OK, USA
- Department of Microbiology & Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Marc Libault
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE, USA.
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Tu M, Zeng J, Zhang J, Fan G, Song G. Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1038109. [PMID: 36570898 PMCID: PMC9773216 DOI: 10.3389/fpls.2022.1038109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Juntao Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guozhi Fan
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guangsen Song
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
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