101
|
Seyfferth C, Renema J, Wendrich JR, Eekhout T, Seurinck R, Vandamme N, Blob B, Saeys Y, Helariutta Y, Birnbaum KD, De Rybel B. Advances and Opportunities in Single-Cell Transcriptomics for Plant Research. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:847-866. [PMID: 33730513 PMCID: PMC7611048 DOI: 10.1146/annurev-arplant-081720-010120] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell. The field of plant biology has fully embraced single-cell transcriptomics and is rapidly expanding the portfolio of available technologies and applications. In this review, we give an overview of the main advances in plant single-cell transcriptomics over the past few years and provide the reader with an accessible guideline covering all steps, from sample preparation to data analysis. We end by offering a glimpse of how these technologies will shape and accelerate plant-specific research in the near future.
Collapse
Affiliation(s)
- Carolin Seyfferth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jim Renema
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jos R Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Viikki Plant Science Centre, HiLIFE/Organismal and Evolutionary Biology Research Program, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Yrjo Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Viikki Plant Science Centre, HiLIFE/Organismal and Evolutionary Biology Research Program, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA;
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| |
Collapse
|
102
|
Kausch AP, Wang K, Kaeppler HF, Gordon-Kamm W. Maize transformation: history, progress, and perspectives. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:38. [PMID: 37309443 PMCID: PMC10236110 DOI: 10.1007/s11032-021-01225-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/14/2021] [Indexed: 06/14/2023]
Abstract
Maize functional genomics research and genetic improvement strategies have been greatly accelerated and refined through the development and utilization of genetic transformation systems. Maize transformation is a composite technology based on decades' efforts in optimizing multiple factors involving microbiology and physical/biochemical DNA delivery, as well as cellular and molecular biology. This review provides a historical reflection on the development of maize transformation technology including the early failures and successful milestones. It also provides a current perspective on the understanding of tissue culture responses and their impact on plant regeneration, the pros and cons of different DNA delivery methods, the identification of a palette of selectable/screenable markers, and most recently the development of growth-stimulating or morphogenic genes to improve efficiencies and extend the range of transformable genotypes. Steady research progress in these interdependent components has been punctuated by benchmark reports celebrating the progress in maize transformation, which invariably relied on a large volume of supporting research that contributed to each step and to the current state of the art. The recent explosive use of CRISPR/Cas9-mediated genome editing has heightened the demand for higher transformation efficiencies, especially for important inbreds, to support increasingly sophisticated and complicated genomic modifications, in a manner that is widely accessible. These trends place an urgent demand on taking maize transformation to the next level, presaging a new generation of improvements on the horizon. Once realized, we anticipate a near-future where readily accessible, genotype-independent maize transformation, together with advanced genomics, genome editing, and accelerated breeding, will contribute to world agriculture and global food security.
Collapse
Affiliation(s)
- Albert P. Kausch
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, RI 02892 USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
| | | |
Collapse
|
103
|
Bobrovskikh A, Doroshkov A, Mazzoleni S, Cartenì F, Giannino F, Zubairova U. A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis. Front Genet 2021; 12:652974. [PMID: 34093652 PMCID: PMC8176226 DOI: 10.3389/fgene.2021.652974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023] Open
Abstract
Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants' features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem's solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells' spatial localization in the initial plant organ-one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities.
Collapse
Affiliation(s)
- Aleksandr Bobrovskikh
- Laboratory of Plant Growth Biomechanics, Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia.,Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Alexey Doroshkov
- Laboratory of Plant Growth Biomechanics, Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Fabrizio Cartenì
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Francesco Giannino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Ulyana Zubairova
- Laboratory of Plant Growth Biomechanics, Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
104
|
Ke Y, Podio M, Conner J, Ozias-Akins P. Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures. Sci Rep 2021; 11:9880. [PMID: 33972603 PMCID: PMC8110759 DOI: 10.1038/s41598-021-89170-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 12/04/2022] Open
Abstract
Apomixis, a type of asexual reproduction in angiosperms, results in progenies that are genetically identical to the mother plant. It is a highly desirable trait in agriculture due to its potential to preserve heterosis of F1 hybrids through subsequent generations. However, no major crops are apomictic. Deciphering mechanisms underlying apomixis becomes one of the alternatives to engineer self-reproducing capability into major crops. Parthenogenesis, a major component of apomixis, commonly described as the ability to initiate embryo formation from the egg cell without fertilization, also can be valuable in plant breeding for doubled haploid production. A deeper understanding of transcriptional differences between parthenogenetic and sexual or non-parthenogenetic eggs can assist with pathway engineering. By conducting laser capture microdissection-based RNA-seq on sexual and parthenogenetic egg cells on the day of anthesis, a de novo transcriptome for the Cenchrus ciliaris egg cells was created, transcriptional profiles that distinguish the parthenogenetic egg from its sexual counterpart were identified, and functional roles for a few transcription factors in promoting natural parthenogenesis were suggested. These transcriptome data expand upon previous gene expression studies and will be a resource for future research on the transcriptome of egg cells in parthenogenetic and sexual genotypes.
Collapse
Affiliation(s)
- Yuji Ke
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Maricel Podio
- Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA
| | - Joann Conner
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA.,Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA. .,Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA.
| |
Collapse
|
105
|
Serrano-Ron L, Cabrera J, Perez-Garcia P, Moreno-Risueno MA. Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks. FRONTIERS IN PLANT SCIENCE 2021; 12:661361. [PMID: 34017350 PMCID: PMC8129646 DOI: 10.3389/fpls.2021.661361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/25/2021] [Indexed: 05/30/2023]
Abstract
Over the last decades, research on postembryonic root development has been facilitated by "omics" technologies. Among these technologies, microarrays first, and RNA sequencing (RNA-seq) later, have provided transcriptional information on the underlying molecular processes establishing the basis of System Biology studies in roots. Cell fate specification and development have been widely studied in the primary root, which involved the identification of many cell type transcriptomes and the reconstruction of gene regulatory networks (GRN). The study of lateral root (LR) development has not been an exception. However, the molecular mechanisms regulating cell fate specification during LR formation remain largely unexplored. Recently, single-cell RNA-seq (scRNA-seq) studies have addressed the specification of tissues from stem cells in the primary root. scRNA-seq studies are anticipated to be a useful approach to decipher cell fate specification and patterning during LR formation. In this review, we address the different scRNA-seq strategies used both in plants and animals and how we could take advantage of scRNA-seq to unravel new regulatory mechanisms and reconstruct GRN. In addition, we discuss how to integrate scRNA-seq results with previous RNA-seq datasets and GRN. We also address relevant findings obtained through single-cell based studies and how LR developmental studies could be facilitated by scRNA-seq approaches and subsequent GRN inference. The use of single-cell approaches to investigate LR formation could help to decipher fundamental biological mechanisms such as cell memory, synchronization, polarization, or pluripotency.
Collapse
Affiliation(s)
| | | | | | - Miguel A. Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
| |
Collapse
|
106
|
Lopez-Anido CB, Vatén A, Smoot NK, Sharma N, Guo V, Gong Y, Anleu Gil MX, Weimer AK, Bergmann DC. Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf. Dev Cell 2021; 56:1043-1055.e4. [PMID: 33823130 DOI: 10.1101/2020.09.08.288498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 05/22/2023]
Abstract
Dynamic cell identities underlie flexible developmental programs. The stomatal lineage in the Arabidopsis leaf epidermis features asynchronous and indeterminate divisions that can be modulated by environmental cues. The products of the lineage, stomatal guard cells and pavement cells, regulate plant-atmosphere exchanges, and the epidermis as a whole influences overall leaf growth. How flexibility is encoded in development of the stomatal lineage and how cell fates are coordinated in the leaf are open questions. Here, by leveraging single-cell transcriptomics and molecular genetics, we uncovered models of cell differentiation within Arabidopsis leaf tissue. Profiles across leaf tissues identified points of regulatory congruence. In the stomatal lineage, single-cell resolution resolved underlying cell heterogeneity within early stages and provided a fine-grained profile of guard cell differentiation. Through integration of genome-scale datasets and spatiotemporally precise functional manipulations, we also identified an extended role for the transcriptional regulator SPEECHLESS in reinforcing cell fate commitment.
Collapse
Affiliation(s)
- Camila B Lopez-Anido
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Anne Vatén
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Nicole K Smoot
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Nidhi Sharma
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Victoria Guo
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Yan Gong
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - M Ximena Anleu Gil
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Annika K Weimer
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA.
| |
Collapse
|
107
|
Wang C, Yang X, Li G. Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops. Int J Mol Sci 2021; 22:3508. [PMID: 33805287 PMCID: PMC8037405 DOI: 10.3390/ijms22073508] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Flowering plants develop new organs throughout their life cycle. The vegetative shoot apical meristem (SAM) generates leaf whorls, branches and stems, whereas the reproductive SAM, called the inflorescence meristem (IM), forms florets arranged on a stem or an axis. In cereal crops, the inflorescence producing grains from fertilized florets makes the major yield contribution, which is determined by the numbers and structures of branches, spikelets and florets within the inflorescence. The developmental progression largely depends on the activity of IM. The proper regulations of IM size, specification and termination are outcomes of complex interactions between promoting and restricting factors/signals. Here, we focus on recent advances in molecular mechanisms underlying potential pathways of IM identification, maintenance and differentiation in cereal crops, including rice (Oryza sativa), maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare), highlighting the researches that have facilitated grain yield by, for example, modifying the number of inflorescence branches. Combinatorial functions of key regulators and crosstalk in IM determinacy and specification are summarized. This review delivers the knowledge to crop breeding applications aiming to the improvements in yield performance and productivity.
Collapse
Affiliation(s)
- Chengyu Wang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Campus, The University of Adelaide, Glen Osmond, SA 5064, Australia;
| | - Gang Li
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Campus, The University of Adelaide, Glen Osmond, SA 5064, Australia;
| |
Collapse
|
108
|
Zheng HX, Wu FH, Li SM, Zhang XS, Sui N. Single-cell profiling lights different cell trajectories in plants. ABIOTECH 2021; 2:64-78. [PMID: 36304478 PMCID: PMC9590582 DOI: 10.1007/s42994-021-00040-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/13/2021] [Indexed: 11/29/2022]
Abstract
The molecular mechanism of the maintenance and differentiation of plant stem cells is an eternal theme in studies on plant growth and development. Recent advances in single-cell RNA sequencing (scRNA-seq) methods have completely changed the understanding of cell heterogeneity and cell function, allowing research precision to identify the differentiation trajectory of stem cells maintained and differentiated at the cellular level. This review aimed to mainly discuss the novel insights provided by scRNA-seq for the maintenance and initiation of plant stem cells, cell differentiation, cell response to environmental changes, and improvement strategies for scRNA-seq. In addition, it highlighted additional perspectives beyond scRNA-seq, such as spatial transcriptomes, epigenomes, and single-cell multiomics, for a renewed understanding of stem cell maintenance and cell differentiation, thus providing potential targets and theoretical foundations for crop improvement.
Collapse
Affiliation(s)
- Hong-Xiang Zheng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, 250014 Shandong China
| | - Feng-Hui Wu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, 250014 Shandong China
| | - Si-Min Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, 250014 Shandong China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018 Shandong China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, 250014 Shandong China
| |
Collapse
|