1
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Rutowicz K, Lüthi J, de Groot R, Holtackers R, Yakimovich Y, Pazmiño DM, Gandrillon O, Pelkmans L, Baroux C. Multiscale chromatin dynamics and high entropy in plant iPSC ancestors. J Cell Sci 2024; 137:jcs261703. [PMID: 38738286 PMCID: PMC11234377 DOI: 10.1242/jcs.261703] [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: 10/10/2023] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Plant protoplasts provide starting material for of inducing pluripotent cell masses that are competent for tissue regeneration in vitro, analogous to animal induced pluripotent stem cells (iPSCs). Dedifferentiation is associated with large-scale chromatin reorganisation and massive transcriptome reprogramming, characterised by stochastic gene expression. How this cellular variability reflects on chromatin organisation in individual cells and what factors influence chromatin transitions during culturing are largely unknown. Here, we used high-throughput imaging and a custom supervised image analysis protocol extracting over 100 chromatin features of cultured protoplasts. The analysis revealed rapid, multiscale dynamics of chromatin patterns with a trajectory that strongly depended on nutrient availability. Decreased abundance in H1 (linker histones) is hallmark of chromatin transitions. We measured a high heterogeneity of chromatin patterns indicating intrinsic entropy as a hallmark of the initial cultures. We further measured an entropy decline over time, and an antagonistic influence by external and intrinsic factors, such as phytohormones and epigenetic modifiers, respectively. Collectively, our study benchmarks an approach to understand the variability and evolution of chromatin patterns underlying plant cell reprogramming in vitro.
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Affiliation(s)
- Kinga Rutowicz
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Joel Lüthi
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Reinoud de Groot
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - René Holtackers
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Yauhen Yakimovich
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Diana M. Pazmiño
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Olivier Gandrillon
- Laboratory of Biology and Modeling of the Cell, University of Lyon, ENS de Lyon,69342 Lyon, France
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Célia Baroux
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
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2
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Serivichyaswat PT, Kareem A, Feng M, Melnyk CW. Auxin signaling in the cambium promotes tissue adhesion and vascular formation during Arabidopsis graft healing. PLANT PHYSIOLOGY 2024; 196:754-762. [PMID: 38701036 PMCID: PMC11444275 DOI: 10.1093/plphys/kiae257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/21/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
The strong ability of plants to regenerate wounds is exemplified by grafting when two plants are cut and joined together to grow as one. During graft healing, tissues attach, cells proliferate, and the vasculatures connect to form a graft union. The plant hormone auxin plays a central role, and auxin-related mutants perturb grafting success. Here, we investigated the role of individual cell types and their response to auxin during Arabidopsis (Arabidopsis thaliana) graft formation. By employing a cell-specific inducible misexpression system, we blocked auxin response in individual cell types using the bodenlos mutation. We found that auxin signaling in procambial tissues was critical for successful tissue attachment and vascular differentiation. In addition, we found that auxin signaling was required for cell divisions of the procambial cells during graft formation. Loss of function mutants in cambial pathways also perturbed attachment and phloem reconnection. We propose that cambial and procambial tissues drive tissue attachment and vascular differentiation during successful grafting. Our study thus refines our knowledge of graft development and furthers our understanding of the regenerative role of the cambium.
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Affiliation(s)
- Phanu T Serivichyaswat
- Department of Plant Biology, Swedish University of Agricultural Sciences, Ulls gränd 1, 765 51 Uppsala, Sweden
| | - Abdul Kareem
- Department of Plant Biology, Swedish University of Agricultural Sciences, Ulls gränd 1, 765 51 Uppsala, Sweden
| | - Ming Feng
- Department of Plant Biology, Swedish University of Agricultural Sciences, Ulls gränd 1, 765 51 Uppsala, Sweden
| | - Charles W Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences, Ulls gränd 1, 765 51 Uppsala, Sweden
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3
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Chen Y, Ince YÇ, Kawamura A, Favero DS, Suzuki T, Sugimoto K. ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana. PLANT PHYSIOLOGY 2024:kiae474. [PMID: 39315875 DOI: 10.1093/plphys/kiae474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/09/2024] [Indexed: 09/25/2024]
Abstract
Injured plant somatic tissues regenerate themselves by establishing shoot or root meristems. In Arabidopsis (Arabidopsis thaliana), a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, whether and how environmental factors influence this process remains elusive. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyls as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristems through the regulatory network governed by HY5, thus highlighting the influence of light signals on plant developmental plasticity.
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Affiliation(s)
- Yu Chen
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan
- RIKEN, Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yetkin Çaka Ince
- RIKEN, Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ayako Kawamura
- RIKEN, Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - David S Favero
- RIKEN, Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Keiko Sugimoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan
- RIKEN, Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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4
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Huang Y, Yue E, Lian G, Lu J, Ran L, Ma S, Wang K, Bai Y, Han N, Bian H, Guo F. Novel mechanism of MicroRNA408 in callus formation from rice mature embryo. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39265046 DOI: 10.1111/tpj.17019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/14/2024]
Abstract
Mature embryos are the main explants of tissue culture used in rice transgenic technology. However, the mechanism of mature embryo callus formation remains unclear. In this study, a microRNA-mediated gene regulatory network of rice calli was established using degradome sequencing. We identified a microRNA, OsmiR408, that regulates the formation of the callus derived from the mature rice embryo. OsUCLACYANIN 30 (OsUCL 30), a target gene of OsmiR408, was the most abundant cleavage mRNA in rice callus. OsUCL17 was verified as a target gene of OsmiR408 using RNA ligase-mediated 5'-RACE. In analysis of the OsmiR408 promoter reporter line and pri-miR408 transcript level, the promoter activity and transcript level of MIR408 were increased dramatically during callus formation. In phenotypic observations, OsmiR408 knockout caused severe defects in mature embryo callus formation, whereas OsmiR408 overexpression promoted callus formation. Transcriptome analysis demonstrated that OsUCLs and certain genes related to the plant hormone signal transduction and phenylpropanoid-flavonoid biosynthesis pathway had different differential expression patterns between OsmiR408 knockout and overexpression calli. Thus, OsmiR408 may regulate callus formation mainly by affecting plant hormone signal transduction and phenylpropanoid-flavonoid biosynthesis pathway. Our findings provide insight into OsmiR408/UCLs module function in callus formation.
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Affiliation(s)
- Yizi Huang
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Erkui Yue
- Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Guiwei Lian
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinhan Lu
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Le Ran
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Shengyun Ma
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kaiqiang Wang
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Yu Bai
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Han
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hongwu Bian
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fu Guo
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Seed Industry Laboratory, Yazhou Bay Science and Technology City, Sanya, 572025, China
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5
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Ziemmer JK, Dos Reis de Oliveira T, Santa-Catarina C, do Nascimento Vieira L, Goldenberg R, Pacheco de Freitas Fraga H. Plant regeneration capacity in seeds of three species of Miconia (Melastomataceae) may be related to endogenous polyamine profiles. PROTOPLASMA 2024; 261:937-950. [PMID: 38530427 DOI: 10.1007/s00709-024-01945-y] [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: 11/05/2023] [Accepted: 03/16/2024] [Indexed: 03/28/2024]
Abstract
In plant tissue culture, differences in endogenous levels of species-specific plant growth regulators (PGRs) may explain differences in regenerative capacity. In the case of polyamines (PAs), their dynamics and distribution may vary between species, genotypes, tissues, and developmental pathways, such as sexual reproduction and apomixis. In this study, for the first time, we aimed to assess the impact of varying endogenous PAs levels in seeds from distinct reproductive modes in Miconia spp. (Melastomataceae), on their in vitro regenerative capacity. We quantified the free PAs endogenous content in seeds of Miconia australis (obligate apomictic), Miconia hyemalis (facultative apomictic), and Miconia sellowiana (sexual) and evaluated their in vitro regenerative potential in WPM culture medium supplemented with a combination of 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-benzylaminopurine (BAP). The morphogenic responses were characterized by light microscopy and scanning electron microscopy and discussed regarding the endogenous PAs profiles found. Seeds of M. sellowiana presented approximately eight times more putrescine than M. australis, which was associated with a higher percentage of regenerated calluses (76.67%) than M. australis (5.56%). On the other hand, spermine levels were significantly higher in M. australis. Spermine is indicated as an inhibitor of auxin-carrying gene expression, which may have contributed to its lower regenerative capacity under the tested conditions. These findings provide important insights into in vitro morphogenesis mechanisms in Miconia and highlight the significance of endogenous PA levels in plant regeneration. These discoveries can potentially optimize future regeneration protocols in Miconia, a plant group still underexplored in this area.
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Affiliation(s)
- Juliana Klostermann Ziemmer
- Programa de Pós-Graduação em Biologia Vegetal, Campinas, Universidade Estadual de Campinas, São Paulo, 13083-862, Brazil.
| | - Tadeu Dos Reis de Oliveira
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | | | - Renato Goldenberg
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, 81531-970, Brazil
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6
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Kumar M, Ayzenshtat D, Rather GA, Zemach H, Belausov E, Eshed Williams L, Bocobza S. A dynamic WUSCHEL/Layer 1 interplay directs shoot apical meristem formation during regeneration in tobacco. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39215624 DOI: 10.1111/tpj.17002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 08/11/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
De novo shoot apical meristem (SAM) organogenesis during regeneration in tissue culture has been investigated for several decades, but the precise mechanisms governing early-stage cell fate specification remain elusive. In contrast to SAM establishment during embryogenesis, in vitro SAM formation occurs without positional cues and is characterized by autonomous initiation of cellular patterning. Here, we report on the initial stages of SAM organogenesis and on the molecular mechanisms that orchestrate gene patterning to establish SAM homeostasis. We found that SAM organogenesis in tobacco calli starts with protuberance formation followed by the formation of an intact L1 layer covering the nascent protuberance. We also exposed a complex interdependent relationship between L1 and WUS expression and revealed that any disruption in this interplay compromises shoot formation. Silencing WUS in nascent protuberances prevented L1 formation and caused the disorganization of the outer cell layers exhibiting both anticlinal and periclinal divisions, suggesting WUS plays a critical role in the proper establishment and organization of L1 during SAM organogenesis. We further discovered that silencing TONNEAU1 prevents the exclusive occurrence of anticlinal divisions in the outermost layer of the protuberances and suppresses the acquisition of L1 cellular identity and L1 formation, ultimately impeding SAM formation and regeneration. This study provides a novel molecular framework for the characterization of a WUS/L1 interplay that mediates SAM formation during regeneration.
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Affiliation(s)
- Manoj Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Dana Ayzenshtat
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Gulzar A Rather
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Hanita Zemach
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Eduard Belausov
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
| | - Leor Eshed Williams
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Samuel Bocobza
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeTsiyon, Israel
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7
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Bao J, O’Donohue B, Sommerville KD, Mitter N, O’Brien C, Hayward A. Tissue Culture Innovations for Propagation and Conservation of Myrteae-A Globally Important Myrtaceae Tribe. PLANTS (BASEL, SWITZERLAND) 2024; 13:2244. [PMID: 39204680 PMCID: PMC11359692 DOI: 10.3390/plants13162244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Myrteae is the most species-rich tribe in the Myrtaceae family, represented by a range of socioeconomically and ecologically significant species. Many of these species, including commercially relevant ones, have become increasingly threatened in the wild, and now require conservation actions. Tissue culture presents an appropriate in vitro tool to facilitate medium-term and long-term wild germplasm conservation, as well as for commercial propagation to maintain desirable traits of commercial cultivars. So far, tissue culture has not been extensively achieved for Myrteae. Here, tissue culture for Eugenia, one of the most species-rich genera in Myrteae, is reviewed, giving directions for other related Myrteae. This review also focuses on ex situ conservation of Australian Myrteae, including using seed banking and field banking. Despite some progress, challenges to conserve these species remain, mostly due to the increasing threats in the wild and limited research. Research into in vitro methods (tissue culture and cryopreservation) is paramount given that at least some of the species are 'non-orthodox'. There is an urgent need to develop long-term in vitro conservation for capturing the remaining germplasm of threatened Myrteae.
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Affiliation(s)
- Jingyin Bao
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (B.O.); (N.M.); (C.O.)
| | - Billy O’Donohue
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (B.O.); (N.M.); (C.O.)
| | - Karen D. Sommerville
- Australian Institute of Botanical Science, The Royal Botanic Gardens and Domain Trust, Mount Annan, NSW 2567, Australia;
| | - Neena Mitter
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (B.O.); (N.M.); (C.O.)
| | - Chris O’Brien
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (B.O.); (N.M.); (C.O.)
| | - Alice Hayward
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (B.O.); (N.M.); (C.O.)
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8
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Yin R, Chen R, Xia K, Xu X. A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis. PLANT COMMUNICATIONS 2024; 5:100941. [PMID: 38720464 PMCID: PMC11369778 DOI: 10.1016/j.xplc.2024.100941] [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: 11/18/2023] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/16/2024]
Abstract
The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement. This developmental process incorporates a series of cell fate transitions and reprogramming. However, our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited. Here, we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0, 1, and 4 days, and the construction of a detailed single-cell transcriptional atlas of the callus induction process. We identify the cell types responsible for initiating the early callus: lateral root primordium-initiating (LRPI)-like cells and quiescent center (QC)-like cells. LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia. We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells. QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration. We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions. Overall, our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation, significantly improving our understanding of callus formation.
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Affiliation(s)
- Ruilian Yin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 10049, China; BGI Research, Beijing 102601, China
| | - Ruiying Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 10049, China; BGI Research, Beijing 102601, China
| | - Keke Xia
- BGI Research, Beijing 102601, China.
| | - Xun Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 10049, China; BGI Research, Beijing 102601, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China.
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9
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Wittmer J, Heidstra R. Appreciating animal induced pluripotent stem cells to shape plant cell reprogramming strategies. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4373-4393. [PMID: 38869461 PMCID: PMC11263491 DOI: 10.1093/jxb/erae264] [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: 12/23/2023] [Accepted: 06/12/2024] [Indexed: 06/14/2024]
Abstract
Animals and plants have developed resilience mechanisms to effectively endure and overcome physical damage and environmental challenges throughout their life span. To sustain their vitality, both animals and plants employ mechanisms to replenish damaged cells, either directly, involving the activity of adult stem cells, or indirectly, via dedifferentiation of somatic cells that are induced to revert to a stem cell state and subsequently redifferentiate. Stem cell research has been a rapidly advancing field in animal studies for many years, driven by its promising potential in human therapeutics, including tissue regeneration and drug development. A major breakthrough was the discovery of induced pluripotent stem cells (iPSCs), which are reprogrammed from somatic cells by expressing a limited set of transcription factors. This discovery enabled the generation of an unlimited supply of cells that can be differentiated into specific cell types and tissues. Equally, a keen interest in the connection between plant stem cells and regeneration has been developed in the last decade, driven by the demand to enhance plant traits such as yield, resistance to pathogens, and the opportunities provided by CRISPR/Cas-mediated gene editing. Here we discuss how knowledge of stem cell biology benefits regeneration technology, and we speculate on the creation of a universal genotype-independent iPSC system for plants to overcome regenerative recalcitrance.
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Affiliation(s)
- Jana Wittmer
- Cell and Developmental Biology, cluster Plant Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Renze Heidstra
- Cell and Developmental Biology, cluster Plant Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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10
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Chen C, Hu Y, Ikeuchi M, Jiao Y, Prasad K, Su YH, Xiao J, Xu L, Yang W, Zhao Z, Zhou W, Zhou Y, Gao J, Wang JW. Plant regeneration in the new era: from molecular mechanisms to biotechnology applications. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1338-1367. [PMID: 38833085 DOI: 10.1007/s11427-024-2581-2] [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: 01/31/2024] [Accepted: 03/26/2024] [Indexed: 06/06/2024]
Abstract
Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.
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Affiliation(s)
- Chunli Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences (CAS), China National Botanical Garden, Beijing, 100093, China.
| | - Momoko Ikeuchi
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
| | - 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.
| | - Kalika Prasad
- Indian Institute of Science Education and Research, Pune, 411008, India.
- , Thiruvananthapuram, 695551, India.
| | - Ying Hua Su
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology (IGDB), CAS, Beijing, 100101, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), IGDB, CAS, Beijing, 100101, China.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- CEPAMS, SIPPE, CAS, Shanghai, 200032, China.
| | - Zhong Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, CEMPS, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Wenkun Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Yun Zhou
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, 47907, USA.
| | - Jian Gao
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai, 200032, China.
- New Cornerstone Science Laboratory, Shanghai, 200032, China.
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11
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Lee HS, Han JE, Bae EK, Jie EY, Kim SW, Kwon HJ, Lee HS, Yeon SH, Murthy HN, Park SY. Response surface methodology mediated optimization of phytosulfokine and plant growth regulators for enhanced protoplast division, callus induction, and somatic embryogenesis in Angelica Gigas Nakai. BMC PLANT BIOLOGY 2024; 24:527. [PMID: 38858674 PMCID: PMC11165744 DOI: 10.1186/s12870-024-05243-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: 02/22/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Angelica Gigas (Purple parsnip) is an important medicinal plant that is cultivated and utilized in Korea, Japan, and China. It contains bioactive substances especially coumarins with anti-inflammatory, anti-platelet aggregation, anti-cancer, anti-diabetic, antimicrobial, anti-obesity, anti-oxidant, immunomodulatory, and neuroprotective properties. This medicinal crop can be genetically improved, and the metabolites can be obtained by embryonic stem cells. In this context, we established the protoplast-to-plant regeneration methodology in Angelica gigas. RESULTS In the present investigation, we isolated the protoplast from the embryogenic callus by applying methods that we have developed earlier and established protoplast cultures using Murashige and Skoog (MS) liquid medium and by embedding the protoplast in thin alginate layer (TAL) methods. We supplemented the culture medium with growth regulators namely 2,4-dichlorophenoxyaceticacid (2,4-D, 0, 0.75, 1.5 mg L- 1), kinetin (KN, 0, 0.5, and 1.0 mg L- 1) and phytosulfokine (PSK, 0, 50, 100 nM) to induce protoplast division, microcolony formation, and embryogenic callus regeneration. We applied central composite design (CCD) and response surface methodology (RSM) for the optimization of 2,4-D, KN, and PSK levels during protoplast division, micro-callus formation, and induction of embryogenic callus stages. The results revealed that 0.04 mg L- 1 2,4-D + 0.5 mg L- 1 KN + 2 nM PSK, 0.5 mg L- 1 2,4-D + 0.9 mg L- 1 KN and 90 nM PSK, and 1.5 mg L- 1 2,4-D and 1 mg L- 1 KN were optimum for protoplast division, micro-callus formation and induction embryogenic callus. MS basal semi-solid medium without growth regulators was good for the development of embryos and plant regeneration. CONCLUSIONS This study demonstrated successful protoplast culture, protoplast division, micro-callus formation, induction embryogenic callus, somatic embryogenesis, and plant regeneration in A. gigas. The methodologies developed here are quite useful for the genetic improvement of this important medicinal plant.
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Affiliation(s)
- Han-Sol Lee
- Department of Horticultural Science, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jong-Eun Han
- Department of Horticultural Science, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Eun-Kyung Bae
- Department of Forest Bioresources, National Institute of Forest Science, 39 Onjeong-ro, Suwon, 16631, Republic of Korea
| | - Eun Yee Jie
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea.
| | - Hyuk Joon Kwon
- Food Science R&D Center, Kolmar BNH Co., Seocho-gu, Seoul, 30003, Republic of Korea
| | - Hak Sung Lee
- Food Science R&D Center, Kolmar BNH Co., Seocho-gu, Seoul, 30003, Republic of Korea
| | - Soo-Ho Yeon
- Food Science R&D Center, Kolmar BNH Co., Seocho-gu, Seoul, 30003, Republic of Korea
| | - Hosakatte Niranjana Murthy
- Department of Horticultural Science, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
- Department of Botany, Karnatak University, Dharwad, 580003, India
- Department of Biotechnology, KLE Technological University, Hubballi, 580039, India
| | - So-Young Park
- Department of Horticultural Science, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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12
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Yang W, Zhai H, Wu F, Deng L, Chao Y, Meng X, Chen Q, Liu C, Bie X, Sun C, Yu Y, Zhang X, Zhang X, Chang Z, Xue M, Zhao Y, Meng X, Li B, Zhang X, Zhang D, Zhao X, Gao C, Li J, Li C. Peptide REF1 is a local wound signal promoting plant regeneration. Cell 2024; 187:3024-3038.e14. [PMID: 38781969 DOI: 10.1016/j.cell.2024.04.040] [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: 01/09/2024] [Revised: 03/10/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Plants frequently encounter wounding and have evolved an extraordinary regenerative capacity to heal the wounds. However, the wound signal that triggers regenerative responses has not been identified. Here, through characterization of a tomato mutant defective in both wound-induced defense and regeneration, we demonstrate that in tomato, a plant elicitor peptide (Pep), REGENERATION FACTOR1 (REF1), acts as a systemin-independent local wound signal that primarily regulates local defense responses and regenerative responses in response to wounding. We further identified PEPR1/2 ORTHOLOG RECEPTOR-LIKE KINASE1 (PORK1) as the receptor perceiving REF1 signal for plant regeneration. REF1-PORK1-mediated signaling promotes regeneration via activating WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), a master regulator of wound-induced cellular reprogramming in plants. Thus, REF1-PORK1 signaling represents a conserved phytocytokine pathway to initiate, amplify, and stabilize a signaling cascade that orchestrates wound-triggered organ regeneration. Application of REF1 provides a simple method to boost the regeneration and transformation efficiency of recalcitrant crops.
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Affiliation(s)
- Wentao Yang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Huawei Zhai
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Fangming Wu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Deng
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Yu Chao
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianwen Meng
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Qian Chen
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Chenhuan Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Bie
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Chuanlong Sun
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yang Yu
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiaofei Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyue Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeqian Chang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Xue
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yajie Zhao
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiangbing Meng
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Boshu Li
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiansheng Zhang
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Dajian Zhang
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiangyu Zhao
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Caixia Gao
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuanyou Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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13
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Omori M, Yamane H, Tao R. Comparative transcriptome and functional analyses provide insights into the key factors regulating shoot regeneration in highbush blueberry. HORTICULTURE RESEARCH 2024; 11:uhae114. [PMID: 38919558 PMCID: PMC11197304 DOI: 10.1093/hr/uhae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/09/2024] [Indexed: 06/27/2024]
Abstract
Establishing an efficient plant regeneration system is a crucial prerequisite for genetic engineering technology in plants. However, the regeneration rate exhibits considerable variability among genotypes, and the key factors underlying shoot regeneration capacity remain largely elusive. Blueberry leaf explants cultured on a medium rich in cytokinins exhibit direct shoot organogenesis without prominent callus formation, which holds promise for expediting genetic transformation while minimizing somatic mutations during culture. The objective of this study is to unravel the molecular and genetic determinants that govern cultivar-specific shoot regeneration potential in highbush blueberry (Vaccinium corymbosum L.). We conducted comparative transcriptome analysis using two highbush blueberry genotypes: 'Blue Muffin' ('BM') displaying a high regeneration rate (>80%) and 'O'Neal' ('ON') exhibiting a low regeneration rate (<10%). The findings revealed differential expression of numerous auxin-related genes; notably, 'BM' exhibited higher expression of auxin signaling genes compared to 'ON'. Among blueberry orthologs of transcription factors involved in meristem formation in Arabidopsis, expression of VcENHANCER OF SHOOT REGENERATION (VcESR), VcWUSCHEL (VcWUS), and VcCUP-SHAPED COTYLEDON 2.1 were significantly higher in 'BM' relative to 'ON'. Exogenous application of auxin promoted regeneration, as well as VcESR and VcWUS expression, whereas inhibition of auxin biosynthesis yielded the opposite effects. Overexpression of VcESR in 'BM' promoted shoot regeneration under phytohormone-free conditions by activating the expression of cytokinin- and auxin-related genes. These findings provide new insights into the molecular mechanisms underlying blueberry regeneration and have practical implications for enhancing plant regeneration and transformation techniques.
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Affiliation(s)
| | | | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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14
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Jiang P, Han P, He M, Shui G, Guo C, Shah S, Wang Z, Wu H, Li J, Pan Z. Appropriate mowing can promote the growth of Anabasis aphylla through the auxin metabolism pathway. BMC PLANT BIOLOGY 2024; 24:482. [PMID: 38822275 PMCID: PMC11141038 DOI: 10.1186/s12870-024-05204-3] [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: 04/09/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Anabasis aphylla (A. aphylla), a species of the Amaranthaceae family, is widely distributed in northwestern China and has high pharmacological value and ecological functions. However, the growth characteristics are poorly understood, impeding its industrial development for biopesticide development. Here, we explored the regenerative capacity of A. aphylla. To this end, different lengths of the secondary branches of perennial branches were mowed at the end of March before sprouting. The four treatments were no mowing (M0) and mowing 1/3, 2/3, and the entire length of the secondary branches of perennial branches (M1-M3, respectively). Next, to evaluate the compensatory growth after mowing, new assimilate branches' related traits were recorded every 30 days, and the final biomass was recorded. The mowed plants showed a greater growth rate of assimilation branches than un-mowed plants. Additionally, with the increasing mowing degree, the growth rate and the final biomass of assimilation branches showed a decreasing trend, with the greatest growth rate and final biomass in response to M1. To evaluate the mechanism of the compensatory growth after mowing, a combination of dynamic (0, 1, 5, and 8 days after mowing) plant hormone-targeted metabolomics and transcriptomics was performed for the M0 and M1 treatment. Overall, 26 plant hormone metabolites were detected, 6 of which significantly increased after mowing compared with control: Indole-3-acetyl-L-valine methyl ester, Indole-3-carboxylic acid, Indole-3-carboxaldehyde, Gibberellin A24, Gibberellin A4, and cis (+)-12-oxo-phytodienoic acid. Additionally, 2,402 differentially expressed genes were detected between the mowed plants and controls. By combining clustering analysis based on expression trends after mowing and gene ontology analysis of each cluster, 18 genes related to auxin metabolism were identified, 6 of which were significantly related to auxin synthesis. Our findings suggest that appropriate mowing can promote A. aphylla growth, regulated by the auxin metabolic pathway, and lays the foundation for the development of the industrial value of A. aphylla.
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Affiliation(s)
- Ping Jiang
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China
- Key Laboratory of Special Fruit and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China
| | - Peng Han
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Mengyao He
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China
- Key Laboratory of Special Fruit and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China
| | - Guangling Shui
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Chunping Guo
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Sulaiman Shah
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China
- Key Laboratory of Special Fruit and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China
| | - Zixuan Wang
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China
- Key Laboratory of Special Fruit and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China
| | - Haokai Wu
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China
- Key Laboratory of Special Fruit and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China
| | - Jian Li
- Southern Xinjiang Research Institute, Shihezi University, Tumushuk, 843806, Xinjiang, China.
| | - Zhenyuan Pan
- Agricultural College, Shihezi University, Shihezi, 832003, Xinjiang, China.
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15
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Hoermayer L, Montesinos JC, Trozzi N, Spona L, Yoshida S, Marhava P, Caballero-Mancebo S, Benková E, Heisenberg CP, Dagdas Y, Majda M, Friml J. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. Dev Cell 2024; 59:1333-1344.e4. [PMID: 38579717 DOI: 10.1016/j.devcel.2024.03.009] [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: 04/09/2023] [Revised: 11/13/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.
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Affiliation(s)
- Lukas Hoermayer
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria; Department of Plant Molecular Biology (DMBV), University of Lausanne, 1015 Lausanne, Switzerland; Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Juan Carlos Montesinos
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria; Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Departamento de Bioquímica y Biología Molecular, Universitat de València, 46100 Burjassot, Spain
| | - Nicola Trozzi
- Department of Plant Molecular Biology (DMBV), University of Lausanne, 1015 Lausanne, Switzerland
| | - Leonhard Spona
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Saiko Yoshida
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria; Max Planck Institute for Plant Breeding Research, 50829 Carl-von-Linné-Weg 10, Cologne, Germany
| | - Petra Marhava
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria; Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, University of Agricultural Sciences (SLU), 90183 Umeå, Sweden
| | | | - Eva Benková
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | | | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Mateusz Majda
- Department of Plant Molecular Biology (DMBV), University of Lausanne, 1015 Lausanne, Switzerland
| | - Jiří Friml
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria.
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16
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Zhang C, Tang Y, Tang S, Chen L, Li T, Yuan H, Xu Y, Zhou Y, Zhang S, Wang J, Wen H, Jiang W, Pang Y, Deng X, Cao X, Zhou J, Song X, Liu Q. An inducible CRISPR activation tool for accelerating plant regeneration. PLANT COMMUNICATIONS 2024; 5:100823. [PMID: 38243597 PMCID: PMC11121170 DOI: 10.1016/j.xplc.2024.100823] [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: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
The inducible CRISPR activation (CRISPR-a) system offers unparalleled precision and versatility for regulating endogenous genes, making it highly sought after in plant research. In this study, we developed a chemically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system. We systematically compared different induction strategies and achieved high efficiency in target gene activation. We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration. Further experiments showed that induced activation of these morphogenic genes can accelerate regeneration and improve regeneration efficiency in both eudicot and monocot plants, including alfalfa, woodland strawberry, and sheepgrass. Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.
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Affiliation(s)
- Cuimei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yajun Tang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China
| | - Shanjie Tang
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Chen
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tong Li
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haidi Yuan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China
| | - Yujun Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yangyan Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Shuaibin Zhang
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianli Wang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang 150086, China
| | - Hongyu Wen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xian Deng
- Key Laboratory of Seed Innovation and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China.
| | - Xianwei Song
- Key Laboratory of Seed Innovation and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China.
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17
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Domínguez-Figueroa J, Gómez-Rojas A, Escobar C. Functional studies of plant transcription factors and their relevance in the plant root-knot nematode interaction. FRONTIERS IN PLANT SCIENCE 2024; 15:1370532. [PMID: 38784063 PMCID: PMC11113014 DOI: 10.3389/fpls.2024.1370532] [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: 01/14/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Root-knot nematodes are polyphagous parasitic nematodes that cause severe losses in the agriculture worldwide. They enter the root in the elongation zone and subtly migrate to the root meristem where they reach the vascular cylinder and establish a feeding site called gall. Inside the galls they induce a group of transfer cells that serve to nurture them along their parasitic stage, the giant cells. Galls and giant cells develop through a process of post-embryogenic organogenesis that involves manipulating different genetic regulatory networks within the cells, some of them through hijacking some molecular transducers of established plant developmental processes, such as lateral root formation or root regeneration. Galls/giant cells formation involves different mechanisms orchestrated by the nematode´s effectors that generate diverse plant responses in different plant tissues, some of them include sophisticated mechanisms to overcome plant defenses. Yet, the plant-nematode interaction is normally accompanied to dramatic transcriptomic changes within the galls and giant cells. It is therefore expected a key regulatory role of plant-transcription factors, coordinating both, the new organogenesis process induced by the RKNs and the plant response against the nematode. Knowing the role of plant-transcription factors participating in this process becomes essential for a clear understanding of the plant-RKNs interaction and provides an opportunity for the future development and design of directed control strategies. In this review, we present the existing knowledge of the TFs with a functional role in the plant-RKN interaction through a comprehensive analysis of current scientific literature and available transcriptomic data.
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Affiliation(s)
- Jose Domínguez-Figueroa
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
- Centro de Biotecnologia y Genomica de Plantas (CBGP), Universidad Politecnica de Madrid and Instituto de Investigacion y Tecnologia Agraria y Alimentaria-Consejo Superior de investigaciones Cientificas (UPM-INIA/CSIC), Madrid, Spain
| | - Almudena Gómez-Rojas
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Carolina Escobar
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
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18
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Xu P, Zhong Y, Xu A, Liu B, Zhang Y, Zhao A, Yang X, Ming M, Cao F, Fu F. Application of Developmental Regulators for Enhancing Plant Regeneration and Genetic Transformation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1272. [PMID: 38732487 PMCID: PMC11085514 DOI: 10.3390/plants13091272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Establishing plant regeneration systems and efficient genetic transformation techniques plays a crucial role in plant functional genomics research and the development of new crop varieties. The inefficient methods of transformation and regeneration of recalcitrant species and the genetic dependence of the transformation process remain major obstacles. With the advancement of plant meristematic tissues and somatic embryogenesis research, several key regulatory genes, collectively known as developmental regulators, have been identified. In the field of plant genetic transformation, the application of developmental regulators has recently garnered significant interest. These regulators play important roles in plant growth and development, and when applied in plant genetic transformation, they can effectively enhance the induction and regeneration capabilities of plant meristematic tissues, thus providing important opportunities for improving genetic transformation efficiency. This review focuses on the introduction of several commonly used developmental regulators. By gaining an in-depth understanding of and applying these developmental regulators, it is possible to further enhance the efficiency and success rate of plant genetic transformation, providing strong support for plant breeding and genetic engineering research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fangfang Fu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (P.X.); (Y.Z.); (A.X.); (B.L.); (Y.Z.); (A.Z.); (X.Y.); (M.M.); (F.C.)
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19
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Hong C, Lee HG, Shim S, Park OS, Kim JH, Lee K, Oh E, Kim J, Jung YJ, Seo PJ. Histone modification-dependent production of peptide hormones facilitates acquisition of pluripotency during leaf-to-callus transition in Arabidopsis. THE NEW PHYTOLOGIST 2024; 242:1068-1083. [PMID: 38406998 DOI: 10.1111/nph.19637] [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: 11/30/2023] [Accepted: 01/07/2024] [Indexed: 02/27/2024]
Abstract
Chromatin configuration is critical for establishing tissue identity and changes substantially during tissue identity transitions. The crucial scientific and agricultural technology of in vitro tissue culture exploits callus formation from diverse tissue explants and tissue regeneration via de novo organogenesis. We investigated the dynamic changes in H3ac and H3K4me3 histone modifications during leaf-to-callus transition in Arabidopsis thaliana. We analyzed changes in the global distribution of H3ac and H3K4me3 during the leaf-to-callus transition, focusing on transcriptionally active regions in calli relative to leaf explants, defined by increased accumulation of both H3ac and H3K4me3. Peptide signaling was particularly activated during callus formation; the peptide hormones RGF3, RGF8, PIP1 and PIPL3 were upregulated, promoting callus proliferation and conferring competence for de novo shoot organogenesis. The corresponding peptide receptors were also implicated in peptide-regulated callus proliferation and regeneration capacity. The effect of peptide hormones in plant regeneration is likely at least partly conserved in crop plants. Our results indicate that chromatin-dependent regulation of peptide hormone production not only stimulates callus proliferation but also establishes pluripotency, improving the overall efficiency of two-step regeneration in plant systems.
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Affiliation(s)
- Cheljong Hong
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Sangrea Shim
- Department of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Ok-Sun Park
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Jong Hee Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Korea
| | - Kyounghee Lee
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Eunkyoo Oh
- Department of Life Sciences, Korea University, Seoul, 08826, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Yu Jin Jung
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong, 17579, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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20
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Wang Y, Jiang L, Kong D, Meng J, Song M, Cui W, Song Y, Wang X, Liu J, Wang R, He Y, Chang C, Ju C. Ethylene controls three-dimensional growth involving reduced auxin levels in the moss Physcomitrium patens. THE NEW PHYTOLOGIST 2024. [PMID: 38571393 DOI: 10.1111/nph.19728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
The conquest of land by plants was concomitant with, and possibly enabled by, the evolution of three-dimensional (3D) growth. The moss Physcomitrium patens provides a model system for elucidating molecular mechanisms in the initiation of 3D growth. Here, we investigate whether the phytohormone ethylene, which is believed to have been a signal before land plant emergence, plays a role in 3D growth regulation in P. patens. We report ethylene controls 3D gametophore formation, based on results from exogenously applied ethylene and genetic manipulation of PpEIN2, which is a central component in the ethylene signaling pathway. Overexpression (OE) of PpEIN2 activates ethylene responses and leads to earlier formation of gametophores with fewer gametophores produced thereafter, phenocopying ethylene-treated wild-type. Conversely, Ppein2 knockout mutants, which are ethylene insensitive, show initially delayed gametophore formation with more gametophores produced later. Furthermore, pharmacological and biochemical analyses reveal auxin levels are decreased in the OE lines but increased in the knockout mutants. Our results suggest that evolutionarily, ethylene and auxin molecular networks were recruited to build the plant body plan in ancestral land plants. This might have played a role in enabling ancient plants to acclimate to the continental surfaces of the planet.
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Affiliation(s)
- Yidong Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Lanlan Jiang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Dongdong Kong
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Jie Meng
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Meifang Song
- Institute of Radiation Technology, Beijing Academy of Science and Technology, Beijing, 100050, China
| | - Wenxiu Cui
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yaqi Song
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiaofan Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Jiao Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Rui Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yikun He
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Caren Chang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Chuanli Ju
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
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21
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Cao L, Wang G, Ye X, Li F, Wang S, Li H, Wang P, Wang J. Physiological, Metabolic, and Transcriptomic Analyses Reveal Mechanisms of Proliferation and Somatic Embryogenesis of Litchi ( Litchi chinensis Sonn.) Embryogenic Callus Promoted by D-Arginine Treatment. Int J Mol Sci 2024; 25:3965. [PMID: 38612774 PMCID: PMC11012067 DOI: 10.3390/ijms25073965] [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: 01/31/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
D-arginine (D-Arg) can promote embryogenic callus (EC) proliferation and increase the rate of somatic embryo induction of litchi (Litchi chinensis Sonn.), yet the mechanism underlying the processes is incompletely understood. To investigate the mechanism, physiological responses of polyamines (PAs) [putrescine (Put), spermidine (Spd), and spermine (Spm)] were investigated for D-Arg-treated litchi EC and enzyme activity related to polyamine metabolism, plant endogenous hormones, and polyamine- and embryogenic-related genes were explored. Results showed that the exogenous addition of D-Arg reduces the activity of diamine oxidase (DAO) and polyamine oxidase (PAO) in EC, reduces the production of H2O2, promotes EC proliferation, and increases the (Spd + Spm)/Put ratio to promote somatic embryo induction. Exogenous D-Arg application promoted somatic embryogenesis (SE) by increasing indole-3-acetyl glycine (IAA-Gly), kinetin-9-glucoside (K9G), and dihydrozeatin-7-glucoside (DHZ7G) levels and decreasing trans-zeatin riboside (tZR), N-[(-)-jasmonoyl]-(L)-valine (JA-Val), jasmonic acid (JA), and jasmonoyl-L-isoleucine (Ja-ILE) levels on 18 d, as well as promoting cell division and differentiation. The application of exogenous D-Arg regulated EC proliferation and somatic embryo induction by altering gene expression levels of the WRKY family, AP2/ERF family, C3H family, and C2H2 family. These results indicate that exogenous D-Arg could regulate the proliferation of EC and the SE induction of litchi by changing the biosynthesis of PAs through the alteration of gene expression pattern and endogenous hormone metabolism.
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Affiliation(s)
- Ludan Cao
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China;
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Guo Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Fang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Shujun Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Huanling Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Jiabao Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
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22
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Li J, Zhang Q, Wang Z, Liu Q. The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions. PLANT PHYSIOLOGY 2024; 194:2022-2038. [PMID: 38290051 PMCID: PMC10980418 DOI: 10.1093/plphys/kiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.
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Affiliation(s)
- Jiawen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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23
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Castro-Camba R, Vielba JM, Rico S, Covelo P, Cernadas MJ, Vidal N, Sánchez C. Wounding-Related Signaling Is Integrated within the Auxin-Response Framework to Induce Adventitious Rooting in Chestnut. Genes (Basel) 2024; 15:388. [PMID: 38540447 PMCID: PMC10970416 DOI: 10.3390/genes15030388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 06/14/2024] Open
Abstract
Wounding and exogenous auxin are needed to induce adventitious roots in chestnut microshoots. However, the specific inductive role of wounding has not been characterized in this species. In the present work, two main goals were established: First, we prompted to optimize exogenous auxin treatments to improve the overall health status of the shoots at the end of the rooting cycle. Second, we developed a time-series transcriptomic analysis to compare gene expression in response to wounding alone and wounding plus auxin, focusing on the early events within the first days after treatments. Results suggest that the expression of many genes involved in the rooting process is under direct or indirect control of both stimuli. However, specific levels of expression of relevant genes are only attained when both treatments are applied simultaneously, leading to the successful development of roots. In this sense, we have identified four transcription factors upregulated by auxin (CsLBD16, CsERF113, Cs22D and CsIAA6), with some of them also being induced by wounding. The highest expression levels of these genes occurred when wounding and auxin treatments were applied simultaneously, correlating with the rooting response of the shoots. The results of this work clarify the genetic nature of the wounding response in chestnut, its relation to adventitious rooting, and might be helpful in the development of more specific protocols for the vegetative propagation of this species.
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Affiliation(s)
| | | | | | | | | | | | - Conchi Sánchez
- Department of Plant Production, Misión Biológica de Galicia (CSIC), Avda de Vigo s/n, 15705 Santiago de Compostela, Spain; (R.C.-C.); (J.M.V.); (S.R.); (P.C.); (M.J.C.); (N.V.)
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24
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Petersen M, Ebstrup E, Rodriguez E. Going through changes - the role of autophagy during reprogramming and differentiation. J Cell Sci 2024; 137:jcs261655. [PMID: 38393817 DOI: 10.1242/jcs.261655] [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: 02/25/2024] Open
Abstract
Somatic cell reprogramming is a complex feature that allows differentiated cells to undergo fate changes into different cell types. This process, which is conserved between plants and animals, is often achieved via dedifferentiation into pluripotent stem cells, which have the ability to generate all other types of cells and tissues of a given organism. Cellular reprogramming is thus a complex process that requires extensive modification at the epigenetic and transcriptional level, unlocking cellular programs that allow cells to acquire pluripotency. In addition to alterations in the gene expression profile, cellular reprogramming requires rearrangement of the proteome, organelles and metabolism, but these changes are comparatively less studied. In this context, autophagy, a cellular catabolic process that participates in the recycling of intracellular constituents, has the capacity to affect different aspects of cellular reprogramming, including the removal of protein signatures that might hamper reprogramming, mitophagy associated with metabolic reprogramming, and the supply of energy and metabolic building blocks to cells that undergo fate changes. In this Review, we discuss advances in our understanding of the role of autophagy during cellular reprogramming by drawing comparisons between plant and animal studies, as well as highlighting aspects of the topic that warrant further research.
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Affiliation(s)
- Morten Petersen
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Elise Ebstrup
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Eleazar Rodriguez
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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25
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Jeong YY, Noh YS, Kim SW, Seo PJ. Efficient regeneration of protoplasts from Solanum lycopersicum cultivar Micro-Tom. Biol Methods Protoc 2024; 9:bpae008. [PMID: 38414647 PMCID: PMC10898868 DOI: 10.1093/biomethods/bpae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024] Open
Abstract
Protoplast regeneration has become a key platform for genetic and genome engineering. However, we lack reliable and reproducible methods for efficient protoplast regeneration for tomato (Solanum lycopersicum) cultivars. Here, we optimized cell and tissue culture methods for protoplast isolation, microcallus proliferation, shoot regeneration, and plantlet establishment of the tomato cultivar Micro-Tom. A thin layer of alginate was applied to protoplasts isolated from third to fourth true leaves and cultured at an optimal density of 1 × 105 protoplasts/ml. We determined the optimal culture media for protoplast proliferation, callus formation, de novo shoot regeneration, and root regeneration. Regenerated plantlets exhibited morphologically normal growth and sexual reproduction. The entire regeneration process, from protoplasts to flowering plants, was accomplished within 5 months. The optimized protoplast regeneration platform enables biotechnological applications, such as genome engineering, as well as basic research on plant regeneration in Solanaceae species.
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Affiliation(s)
- Yeong Yeop Jeong
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Yoo-Sun Noh
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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26
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Park SJ, Park JS, Yang JH, Moon KB, Shin SY, Jeon JH, Kim HS, Lee HJ. MicroRNA396 negatively regulates shoot regeneration in tomato. HORTICULTURE RESEARCH 2024; 11:uhad291. [PMID: 38371631 PMCID: PMC10873581 DOI: 10.1093/hr/uhad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024]
Abstract
Numerous studies have been dedicated to genetically engineering crops to enhance their yield and quality. One of the key requirements for generating genetically modified plants is the reprogramming of cell fate. However, the efficiency of shoot regeneration during this process is highly dependent on genotypes, and the underlying molecular mechanisms remain poorly understood. Here, we identified microRNA396 (miR396) as a negative regulator of shoot regeneration in tomato. By selecting two genotypes with contrasting shoot regeneration efficiencies and analyzing their transcriptome profiles, we found that miR396 and its target transcripts, which encode GROWTH-REGULATING FACTORs (GRFs), exhibit differential abundance between high- and low-efficiency genotypes. Suppression of miR396 functions significantly improved shoot regeneration rates along with increased expression of GRFs in transformed T0 explants, suggesting that miR396 is a key molecule involved in the determination of regeneration efficiency. Notably, we also showed that co-expression of a miR396 suppressor with the gene-editing tool can be employed to generate gene-edited plants in the genotype with a low capacity for shoot regeneration. Our findings show the critical role of miR396 as a molecular barrier to shoot regeneration in tomato and suggest that regeneration efficiency can be improved by blocking this single microRNA.
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Affiliation(s)
- Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Jin Ho Yang
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Seung Yong Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Korea
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27
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Luo D, Shi L, Sun Z, Qi F, Liu H, Xue L, Li X, Liu H, Qu P, Zhao H, Dai X, Dong W, Zheng Z, Huang B, Fu L, Zhang X. Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut ( Arachis hypogaea L.). Genes (Basel) 2024; 15:160. [PMID: 38397150 PMCID: PMC10887910 DOI: 10.3390/genes15020160] [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: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The capability of embryogenic callus induction is a prerequisite for in vitro plant regeneration. However, embryogenic callus induction is strongly genotype-dependent, thus hindering the development of in vitro plant genetic engineering technology. In this study, to examine the genetic variation in embryogenic callus induction rate (CIR) in peanut (Arachis hypogaea L.) at the seventh, eighth, and ninth subcultures (T7, T8, and T9, respectively), we performed genome-wide association studies (GWAS) for CIR in a population of 353 peanut accessions. The coefficient of variation of CIR among the genotypes was high in the T7, T8, and T9 subcultures (33.06%, 34.18%, and 35.54%, respectively), and the average CIR ranged from 1.58 to 1.66. A total of 53 significant single-nucleotide polymorphisms (SNPs) were detected (based on the threshold value -log10(p) = 4.5). Among these SNPs, SNPB03-83801701 showed high phenotypic variance and neared a gene that encodes a peroxisomal ABC transporter 1. SNPA05-94095749, representing a nonsynonymous mutation, was located in the Arahy.MIX90M locus (encoding an auxin response factor 19 protein) at T8, which was associated with callus formation. These results provide guidance for future elucidation of the regulatory mechanism of embryogenic callus induction in peanut.
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Affiliation(s)
- Dandan Luo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Shi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Ziqi Sun
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Feiyan Qi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Hongfei Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lulu Xue
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiaona Li
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Han Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Pengyu Qu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Huanhuan Zhao
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiaodong Dai
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Wenzhao Dong
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Zheng Zheng
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Bingyan Huang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinyou Zhang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
- National Innovation Center for Bio-Breeding Industry, Xinxiang 453500, China
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Kaňuková Š, Lenkavská K, Gubišová M, Kraic J. Suspension culture of stem cells established of Calendula officinalis L. Sci Rep 2024; 14:441. [PMID: 38172230 PMCID: PMC10764935 DOI: 10.1038/s41598-023-50945-0] [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: 07/25/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Plant stem cell cultures have so far been established in only a few plant species using cambial meristematic cells. The presence of stem cells or stem cell-like cells in other organs and tissues of the plant body, as well as the possibility of de novo generation of meristematic cells from differentiated cells, allow to consider the establishment of stem cell cultures in a broader range of species. This study aimed to establish a stem cell culture of the medicinal plant Calendula officinalis L. Callus tissues were induced from leaf and root explants, and already at this stage, stem and dedifferentiated cells could be identified. The cell suspension cultures established both from the root- and leaf-derived calli contained a high proportion of stem cells (92-93% and 72-73%, respectively). The most effective combination of growth regulators for the development of stem cells in calli as well as cell cultures was 1.0 mg/L 2,4-D and 0.5 mg/L BAP. The highest amount of stem cells (5.60-5.72 × 105) was in cell suspension derived from the roots. An effective protocol for the establishment of marigold stem cell suspension culture was developed. The ratio of root-derived stem cells against dedifferentiated cells exceeded 90%.
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Affiliation(s)
- Šarlota Kaňuková
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 917 01, Trnava, Slovakia
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, 921 68, Piešťany, Slovakia
| | - Klaudia Lenkavská
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 917 01, Trnava, Slovakia
| | - Marcela Gubišová
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, 921 68, Piešťany, Slovakia
| | - Ján Kraic
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 917 01, Trnava, Slovakia.
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, 921 68, Piešťany, Slovakia.
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29
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Cao S, Sawettalake N, Shen L. Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce. Gigascience 2024; 13:giae043. [PMID: 38991853 PMCID: PMC11238431 DOI: 10.1093/gigascience/giae043] [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: 02/26/2024] [Revised: 04/24/2024] [Accepted: 06/22/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Lettuce, an important member of the Asteraceae family, is a globally cultivated cash vegetable crop. With a highly complex genome (∼2.5 Gb; 2n = 18) rich in repeat sequences, current lettuce reference genomes exhibit thousands of gaps, impeding a comprehensive understanding of the lettuce genome. FINDINGS Here, we present a near-complete gapless reference genome for cutting lettuce with high transformability, using long-read PacBio HiFi and Nanopore sequencing data. In comparison to stem lettuce genome, we identify 127,681 structural variations (SVs, present in 0.41 Gb of sequence), reflecting the divergence of leafy and stem lettuce. Interestingly, these SVs are related to transposons and DNA methylation states. Furthermore, we identify 4,612 whole-genome triplication genes exhibiting high expression levels associated with low DNA methylation levels and high N6-methyladenosine RNA modifications. DNA methylation changes are also associated with activation of genes involved in callus formation. CONCLUSIONS Our gapless lettuce genome assembly, an unprecedented achievement in the Asteraceae family, establishes a solid foundation for functional genomics, epigenomics, and crop breeding and sheds new light on understanding the complexity of gene regulation associated with the dynamics of DNA and RNA epigenetics in genome evolution.
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Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Nunchanoke Sawettalake
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
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30
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Meira FS, Ribeiro DG, de Campos SS, Falcão LL, Gomes ACMM, de Alencar Dusi DM, Marcellino LH, Mehta A, Scherwinski-Pereira JE. Differential expression of genes potentially related to the callogenesis and in situ hybridization of SERK gene in macaw palm (Acrocomia aculeata Jacq.) Lodd. ex Mart. PROTOPLASMA 2024; 261:89-101. [PMID: 37482557 DOI: 10.1007/s00709-023-01881-3] [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: 01/05/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
For the purpose of understanding the molecular processes triggered during callus formation in macaw palm, the expression of seven genes potentially involved in this process, identified in previous studies and from the literature, was investigated by RT-qPCR. In addition, in situ hybridization of the SERK gene was performed. Leaf tissues from adult plants from two macaw palm accession were inoculated in a medium combined with Picloram at a concentration of 450 μM to induce callus. The expression analysis was performed from leaf samples from two accessions of different origins (Municipalities of Tiros, MG, and Buriti Vermelho, DF, Brazil), which are characterized as non-responsive (NR) and responsive (R), respectively. The material was collected before callus induction (0 DAI, initial day) and 120 days after callus induction (120 DAI). Genes related to development (SERK, OASA, EF1, ANN1) and stress (LEA, CAT2, and MDAR5) were evaluated. The results obtained showed that all the genes involved with the development had their expressions downregulated at 0 DAI when the accession R was compared with the accession NR. On the other hand, it was possible to observe that these genes were upregulated at 120 DAI. The LEA stress gene showed a tendency to increase expression in the NR accession, while the R accession showed decreased expression and the CAT2 and MDAR5 genes showed upregulation in both accessions. In situ hybridization showed SERK transcripts in the vascular bundles, indicating the expression of SERK in this region, in addition to its expression in calluses. The results obtained in this study support our hypothesis that the regulation of genes involved in the control of oxidative stress and development is crucial for the formation of calluses in macaw palm.
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Affiliation(s)
- Filipe Sathler Meira
- Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Daiane Gonzaga Ribeiro
- Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Samanta Siqueira de Campos
- Universidade Federal do Rio Grande do Sul, Departamento de Horticultura e Silvicultura, Porto Alegre, RS, 91540-000, Brazil
| | - Loeni Ludke Falcão
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
| | | | | | - Lucilia Helena Marcellino
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
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31
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Ince YÇ, Sugimoto K. Illuminating the path to shoot meristem regeneration: Molecular insights into reprogramming cells into stem cells. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102452. [PMID: 37709567 DOI: 10.1016/j.pbi.2023.102452] [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: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Plant cells possess the ability to dedifferentiate and reprogram into stem cell-like populations, enabling the regeneration of new organs. However, the maintenance of stem cells relies on specialized microenvironments composed of distinct cell populations with specific functions. Consequently, the regeneration process necessitates the orchestrated regulation of multiple pathways across diverse cellular populations. One crucial pathway involves the transcription factor WUSCHEL HOMEOBOX 5 (WOX5), which plays a pivotal role in reprogramming cells into stem cells and promoting their conversion into shoot meristems through WUSCHEL (WUS). Additionally, cell and tissue mechanics, including cell wall modifications and mechanical stress, critically contribute to de novo shoot organogenesis by regulating polar auxin transport. Furthermore, light signaling emerges as a key regulator of plant regeneration, directly influencing expression of meristem genes and potentially influencing aforementioned pathways as well.
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Affiliation(s)
- Yetkin Çaka Ince
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan.
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan.
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32
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Yin R, Xia K, Xu X. Spatial transcriptomics drives a new era in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1571-1581. [PMID: 37651723 DOI: 10.1111/tpj.16437] [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: 05/05/2023] [Revised: 07/25/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
SUMMARYThe plant community lags far behind the animal and human fields concerning the application of single‐cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single‐cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell‐fate lineages, and reveal cell‐to‐cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple‐omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology.
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Affiliation(s)
- Ruilian Yin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- BGI Research, Shenzhen, 518083, China
| | - Keke Xia
- BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518120, China
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33
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Okazaki K, Ito S, Nakamura H, Asami T, Shimomura K, Umehara M. Increase in ENHANCER OF SHOOT REGENERATION2 expression by treatment with strigolactone-related inhibitors and kinetin during adventitious shoot formation in ipecac. PLANT CELL REPORTS 2023; 42:1927-1936. [PMID: 37803214 DOI: 10.1007/s00299-023-03073-y] [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: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
KEY MESSAGE Increase of ENHANCER OF SHOOT REGENERATION 2 expression was consistent to treatment with kinetin, TIS108, and KK094 in adventitious shoot formation of ipecac. Unlike many plant species, ipecac (Carapichea ipecacuanha (Brot.) L. Andersson) can form adventitious shoots in tissue culture without cytokinin (CK) treatment. Strigolactone (SL) biosynthesis and signaling inhibitors stimulate adventitious shoot formation in ipecac, suggesting their potential use as novel growth regulators in plant tissue culture, but the molecular mechanism of their action is unclear. In this study, we compared the effects of SL-related inhibitors (TIS108 and KK094) and CKs (2iP, tZ, and kinetin) on adventitious shoot formation in ipecac. Exogenously applied SL-related inhibitors and CKs stimulated adventitious shoot formation. Combinations of SL-related inhibitors and kinetin also promoted adventitious shoot formation, but without additive effects. We also analyzed the expression of CK biosynthesis genes in ipecac. TIS108 increased the expression of the ipecac homolog of ISOPENTENYL TRANSFERASE 3 (CiIPT3) but decreased that of LONELY GUY 7 homolog (CiLOG7), presumably resulting in no change in 2iP-type CK levels. KK094 and kinetin increased CiLOG7 expression, elevating 2iP-type CK levels. Among pluripotency- and meristem-related genes, TIS108, KK094, and kinetin consistently increased the expression of ENHANCER OF SHOOT REGENERATION 2 homolog (CiESR2), which has a key role in shoot regeneration, in the internodal segment region that formed adventitious shoots. We propose that CiESR2 might be a key stimulator of adventitious shoot formation in ipecac.
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Affiliation(s)
- Karin Okazaki
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-Machi, Ora-Gun, Gunma, 374-0193, Japan
| | - Shinsaku Ito
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Hidemitsu Nakamura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Tadao Asami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Koichiro Shimomura
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-Machi, Ora-Gun, Gunma, 374-0193, Japan
| | - Mikihisa Umehara
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-Machi, Ora-Gun, Gunma, 374-0193, Japan.
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34
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Sanchez-Corrionero A, Sánchez-Vicente I, Arteaga N, Manrique-Gil I, Gómez-Jiménez S, Torres-Quezada I, Albertos P, Lorenzo O. Fine-tuned nitric oxide and hormone interface in plant root development and regeneration. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6104-6118. [PMID: 36548145 PMCID: PMC10575706 DOI: 10.1093/jxb/erac508] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Plant root growth and developmental capacities reside in a few stem cells of the root apical meristem (RAM). Maintenance of these stem cells requires regenerative divisions of the initial stem cell niche (SCN) cells, self-maintenance, and proliferative divisions of the daughter cells. This ensures sufficient cell diversity to guarantee the development of complex root tissues in the plant. Damage in the root during growth involves the formation of a new post-embryonic root, a process known as regeneration. Post-embryonic root development and organogenesis processes include primary root development and SCN maintenance, plant regeneration, and the development of adventitious and lateral roots. These developmental processes require a fine-tuned balance between cell proliferation and maintenance. An important regulator during root development and regeneration is the gasotransmitter nitric oxide (NO). In this review we have sought to compile how NO regulates cell rate proliferation, cell differentiation, and quiescence of SCNs, usually through interaction with phytohormones, or other molecular mechanisms involved in cellular redox homeostasis. NO exerts a role on molecular components of the auxin and cytokinin signaling pathways in primary roots that affects cell proliferation and maintenance of the RAM. During root regeneration, a peak of auxin and cytokinin triggers specific molecular programs. Moreover, NO participates in adventitious root formation through its interaction with players of the brassinosteroid and cytokinin signaling cascade. Lately, NO has been implicated in root regeneration under hypoxia conditions by regulating stem cell specification through phytoglobins.
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Affiliation(s)
- Alvaro Sanchez-Corrionero
- Departamento de Botánica y Fisiología Vegetal, Instituto de Investigación en Agrobiotecnología (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
- Universidad Politécnica de Madrid, Madrid, Spain
| | - Inmaculada Sánchez-Vicente
- Departamento de Botánica y Fisiología Vegetal, Instituto de Investigación en Agrobiotecnología (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
| | - Noelia Arteaga
- Departamento de Botánica y Fisiología Vegetal, Instituto de Investigación en Agrobiotecnología (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
| | - Isabel Manrique-Gil
- Departamento de Botánica y Fisiología Vegetal, Instituto de Investigación en Agrobiotecnología (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
| | - Sara Gómez-Jiménez
- Departamento de Botánica y Fisiología Vegetal, Instituto de Investigación en Agrobiotecnología (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
| | - Isabel Torres-Quezada
- Departamento de Botánica y Fisiología Vegetal, Instituto de Investigación en Agrobiotecnología (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
| | - Pablo Albertos
- Departamento de Botánica y Fisiología Vegetal, Instituto de Investigación en Agrobiotecnología (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
| | - Oscar Lorenzo
- Departamento de Botánica y Fisiología Vegetal, Instituto de Investigación en Agrobiotecnología (CIALE), Facultad de Biología, Universidad de Salamanca, C/ Río Duero 12, 37185 Salamanca, Spain
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35
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Hesami M, Pepe M, de Ronne M, Yoosefzadeh-Najafabadi M, Adamek K, Torkamaneh D, Jones AMP. Transcriptomic Profiling of Embryogenic and Non-Embryogenic Callus Provides New Insight into the Nature of Recalcitrance in Cannabis. Int J Mol Sci 2023; 24:14625. [PMID: 37834075 PMCID: PMC10572465 DOI: 10.3390/ijms241914625] [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: 07/31/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Differential gene expression profiles of various cannabis calli including non-embryogenic and embryogenic (i.e., rooty and embryonic callus) were examined in this study to enhance our understanding of callus development in cannabis and facilitate the development of improved strategies for plant regeneration and biotechnological applications in this economically valuable crop. A total of 6118 genes displayed significant differential expression, with 1850 genes downregulated and 1873 genes upregulated in embryogenic callus compared to non-embryogenic callus. Notably, 196 phytohormone-related genes exhibited distinctly different expression patterns in the calli types, highlighting the crucial role of plant growth regulator (PGRs) signaling in callus development. Furthermore, 42 classes of transcription factors demonstrated differential expressions among the callus types, suggesting their involvement in the regulation of callus development. The evaluation of epigenetic-related genes revealed the differential expression of 247 genes in all callus types. Notably, histone deacetylases, chromatin remodeling factors, and EMBRYONIC FLOWER 2 emerged as key epigenetic-related genes, displaying upregulation in embryogenic calli compared to non-embryogenic calli. Their upregulation correlated with the repression of embryogenesis-related genes, including LEC2, AGL15, and BBM, presumably inhibiting the transition from embryogenic callus to somatic embryogenesis. These findings underscore the significance of epigenetic regulation in determining the developmental fate of cannabis callus. Generally, our results provide comprehensive insights into gene expression dynamics and molecular mechanisms underlying the development of diverse cannabis calli. The observed repression of auxin-dependent pathway-related genes may contribute to the recalcitrant nature of cannabis, shedding light on the challenges associated with efficient cannabis tissue culture and regeneration protocols.
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Affiliation(s)
- Mohsen Hesami
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.H.)
| | - Marco Pepe
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.H.)
| | - Maxime de Ronne
- Département de Phytologie, Université Laval, Quebec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC G1V 0A6, Canada
- Centre de Recherche et d’innovation sur les Végétaux (CRIV), Université Laval, Quebec, QC G1V 0A6, Canada
| | | | - Kristian Adamek
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.H.)
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC G1V 0A6, Canada
- Centre de Recherche et d’innovation sur les Végétaux (CRIV), Université Laval, Quebec, QC G1V 0A6, Canada
- Institut Intelligence et Données (IID), Université Laval, Quebec, QC G1V 0A6, Canada
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Kim SH, Zebro M, Jang DC, Sim JE, Park HK, Kim KY, Bae HM, Tilahun S, Park SM. Optimization of Plant Growth Regulators for In Vitro Mass Propagation of a Disease-Free 'Shine Muscat' Grapevine Cultivar. Curr Issues Mol Biol 2023; 45:7721-7733. [PMID: 37886931 PMCID: PMC10605919 DOI: 10.3390/cimb45100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
This study addresses the propagation challenges faced by 'Shine Muscat', a newly introduced premium grapevine cultivar in South Korea, where multiple viral infections pose considerable economic loss. The primary objective was to establish a robust in vitro propagation method for producing disease-free grapes and to identify effective plant growth regulators to facilitate large-scale mass cultivation. After experimentation, 2.0 µM 6-benzyladenine (BA) exhibited superior shoot formation in the Murashige and Skoog medium compared with kinetin and thidiazuron. Conversely, α-naphthaleneacetic acid (NAA) hindered shoot growth and induced callus formation, while indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA) demonstrated favorable root formation, with IBA showing better results overall. Furthermore, inter simple sequence repeat analysis confirmed the genetic stability of in vitro-cultivated seedlings using 2.0 μM BA and 1.0 μM IBA, validating the suitability of the developed propagation method for generating disease-free 'Shine Muscat' grapes. These findings offer promising prospects for commercial grape cultivation, ensuring a consistent supply of healthy grapes in the market.
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Affiliation(s)
- Si-Hong Kim
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea; (S.-H.K.); (D.-C.J.); (H.-K.P.); (K.-Y.K.)
- Smart Farm Research Center, KIST Gangneung, Institute of National Products, 679 Saimdang-ro, Gangneung 25451, Republic of Korea
| | - Mewuleddeg Zebro
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea; (M.Z.); (J.-E.S.)
| | - Dong-Cheol Jang
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea; (S.-H.K.); (D.-C.J.); (H.-K.P.); (K.-Y.K.)
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jeong-Eun Sim
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea; (M.Z.); (J.-E.S.)
| | - Han-Kyeol Park
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea; (S.-H.K.); (D.-C.J.); (H.-K.P.); (K.-Y.K.)
| | - Kyeong-Yeon Kim
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea; (S.-H.K.); (D.-C.J.); (H.-K.P.); (K.-Y.K.)
| | - Hyung-Min Bae
- Novagreen Business Centre, Kangwon National University, Chunchen 24341, Republic of Korea;
| | - Shimeles Tilahun
- Agriculture and Life Science Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
- Department of Horticulture and Plant Sciences, Jimma University, Jimma 378, Ethiopia
| | - Sung-Min Park
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea; (S.-H.K.); (D.-C.J.); (H.-K.P.); (K.-Y.K.)
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Republic of Korea
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37
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Song X, Guo P, Xia K, Wang M, Liu Y, Chen L, Zhang J, Xu M, Liu N, Yue Z, Xu X, Gu Y, Li G, Liu M, Fang L, Deng XW, Li B. Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus. Proc Natl Acad Sci U S A 2023; 120:e2310163120. [PMID: 37703282 PMCID: PMC10515167 DOI: 10.1073/pnas.2310163120] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/09/2023] [Indexed: 09/15/2023] Open
Abstract
Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation in crop engineering. Pluripotent callus cells develop into fertile shoots through shoot regeneration. The molecular basis of the shoot regeneration process in crop callus remains largely elusive. This study pioneers the exploration of the spatial transcriptome of tomato callus during shoot regeneration. The findings reveal the presence of highly heterogeneous cell populations within the callus, including epidermis, vascular tissue, shoot primordia, inner callus, and outgrowth shoots. By characterizing the spatially resolved molecular features of shoot primordia and surrounding cells, specific factors essential for shoot primordia formation are identified. Notably, chlorenchyma cells, enriched in photosynthesis-related processes, play a crucial role in promoting shoot primordia formation and subsequent shoot regeneration. Light is shown to promote shoot regeneration by inducing chlorenchyma cell development and coordinating sugar signaling. These findings significantly advance our understanding of the cellular and molecular aspects of shoot regeneration in tomato callus and demonstrate the immense potential of spatial transcriptomics in plant biology.
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Affiliation(s)
- Xiehai Song
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Pengru Guo
- Beijing Genomics Institute Research, Beijing102601, China
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Keke Xia
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Meiling Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Yongqi Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Lichuan Chen
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Jinhui Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Mengyuan Xu
- Beijing Genomics Institute Research, Beijing102601, China
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Naixu Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Zhiliang Yue
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Xun Xu
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Ying Gu
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong271018, China
| | - Min Liu
- Baimaike Intelligent Manufacturing, Qingdao, Shandong266500, China
| | - Liang Fang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong518005, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
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Park JS, Park KH, Park SJ, Ko SR, Moon KB, Koo H, Cho HS, Park SU, Jeon JH, Kim HS, Lee HJ. WUSCHEL controls genotype-dependent shoot regeneration capacity in potato. PLANT PHYSIOLOGY 2023; 193:661-676. [PMID: 37348867 DOI: 10.1093/plphys/kiad345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023]
Abstract
Plant cells can reprogram their fate. The combinatorial actions of auxin and cytokinin dedifferentiate somatic cells to regenerate organs, which can develop into individual plants. As transgenic plants can be generated from genetically modified somatic cells through these processes, cell fate transition is an unavoidable step in crop genetic engineering. However, regeneration capacity closely depends on the genotype, and the molecular events underlying these variances remain elusive. In the present study, we demonstrated that WUSCHEL (WUS)-a homeodomain transcription factor-determines regeneration capacity in different potato (Solanum tuberosum) genotypes. Comparative analysis of shoot regeneration efficiency and expression of genes related to cell fate transition revealed that WUS expression coincided with regeneration rate in different potato genotypes. Moreover, in a high-efficiency genotype, WUS silencing suppressed shoot regeneration. Meanwhile, in a low-efficiency genotype, regeneration could be enhanced through the supplementation of a different type of cytokinin that promoted WUS expression. Computational modeling of cytokinin receptor-ligand interactions suggested that the docking pose of cytokinins mediated by hydrogen bonding with the core residues may be pivotal for WUS expression and shoot regeneration in potatoes. Furthermore, our whole-genome sequencing analysis revealed core sequence variations in the WUS promoters that differentiate low- and high-efficiency genotypes. The present study revealed that cytokinin responses, particularly WUS expression, determine shoot regeneration efficiency in different potato genotypes.
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Affiliation(s)
- Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Crop Science, Chungnam National University, Daejeon 34134, South Korea
| | - Kwang Hyun Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 34141, South Korea
| | - Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, South Korea
| | - Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, South Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, Daejeon 34134, South Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, South Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, South Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea
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39
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Fehér A. A Common Molecular Signature Indicates the Pre-Meristematic State of Plant Calli. Int J Mol Sci 2023; 24:13122. [PMID: 37685925 PMCID: PMC10488067 DOI: 10.3390/ijms241713122] [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: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
In response to different degrees of mechanical injury, certain plant cells re-enter the division cycle to provide cells for tissue replenishment, tissue rejoining, de novo organ formation, and/or wound healing. The intermediate tissue formed by the dividing cells is called a callus. Callus formation can also be induced artificially in vitro by wounding and/or hormone (auxin and cytokinin) treatments. The callus tissue can be maintained in culture, providing starting material for de novo organ or embryo regeneration and thus serving as the basis for many plant biotechnology applications. Due to the biotechnological importance of callus cultures and the scientific interest in the developmental flexibility of somatic plant cells, the initial molecular steps of callus formation have been studied in detail. It was revealed that callus initiation can follow various ways, depending on the organ from which it develops and the inducer, but they converge on a seemingly identical tissue. It is not known, however, if callus is indeed a special tissue with a defined gene expression signature, whether it is a malformed meristem, or a mass of so-called "undifferentiated" cells, as is mostly believed. In this paper, I review the various mechanisms of plant regeneration that may converge on callus initiation. I discuss the role of plant hormones in the detour of callus formation from normal development. Finally, I compare various Arabidopsis gene expression datasets obtained a few days, two weeks, or several years after callus induction and identify 21 genes, including genes of key transcription factors controlling cell division and differentiation in meristematic regions, which were upregulated in all investigated callus samples. I summarize the information available on all 21 genes that point to the pre-meristematic nature of callus tissues underlying their wide regeneration potential.
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Affiliation(s)
- Attila Fehér
- Institute of Plant Biology, Biological Research Centre, 62 Temesvári Körút, 6726 Szeged, Hungary; or
- Department of Plant Biology, University of Szeged, 52 Közép Fasor, 6726 Szeged, Hungary
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40
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Wamhoff D, Patzer L, Schulz DF, Debener T, Winkelmann T. GWAS of adventitious root formation in roses identifies a putative phosphoinositide phosphatase (SAC9) for marker-assisted selection. PLoS One 2023; 18:e0287452. [PMID: 37595005 PMCID: PMC10437954 DOI: 10.1371/journal.pone.0287452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/06/2023] [Indexed: 08/20/2023] Open
Abstract
Rose propagation by cuttings is limited by substantial genotypic differences in adventitious root formation. To identify possible genetic factors causing these differences and to develop a marker for marker-assisted selection for high rooting ability, we phenotyped 95 cut and 95 garden rose genotypes in a hydroponic rooting system over 6 weeks. Data on rooting percentage after 3 to 6 weeks, root number, and root fresh mass were highly variable among genotypes and used in association mappings performed on genotypic information from the WagRhSNP 68 K Axiom SNP array for roses. GWAS analyses revealed only one significantly associated SNP for rooting percentage after 3 weeks. Nevertheless, prominent genomic regions/peaks were observed and further analysed for rooting percentage after 6 weeks, root number and root fresh mass. Some of the SNPs in these peak regions were associated with large effects on adventitious root formation traits. Very prominent were ten SNPs, which were all located in a putative phosphoinositide phosphatase SAC9 on chromosome 2 and showed very high effects on rooting percentage after 6 weeks of more than 40% difference between nulliplex and quadruplex genotypes. SAC9 was reported to be involved in the regulation of endocytosis and in combination with other members of the SAC gene family to regulate the translocation of auxin-efflux PIN proteins via the dephosphorylation of phosphoinositides. For one SNP within SAC9, a KASP marker was successfully derived and used to select genotypes with a homozygous allele configuration. Phenotyping these homozygous genotypes for adventitious root formation verified the SNP allele dosage effect on rooting. Hence, the presented KASP derived from a SNP located in SAC9 can be used for marker-assisted selection in breeding programs for high rooting ability in the future.
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Affiliation(s)
- David Wamhoff
- Institute of Horticultural Production Systems, Section Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Hannover, Germany
| | - Laurine Patzer
- Institute of Plant Genetics, Section Molecular Plant Breeding, Leibniz Universität Hannover, Hannover, Germany
| | - Dietmar Frank Schulz
- Institute of Plant Genetics, Section Molecular Plant Breeding, Leibniz Universität Hannover, Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Section Molecular Plant Breeding, Leibniz Universität Hannover, Hannover, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Section Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Hannover, Germany
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41
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Park JS, Choi Y, Jeong MG, Jeong YI, Han JH, Choi HK. Uncovering transcriptional reprogramming during callus development in soybean: insights and implications. FRONTIERS IN PLANT SCIENCE 2023; 14:1239917. [PMID: 37600197 PMCID: PMC10436568 DOI: 10.3389/fpls.2023.1239917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023]
Abstract
Callus, a valuable tool in plant genetic engineering, originates from dedifferentiated cells. While transcriptional reprogramming during callus formation has been extensively studied in Arabidopsis thaliana, our knowledge of this process in other species, such as Glycine max, remains limited. To bridge this gap, our study focused on conducting a time-series transcriptome analysis of soybean callus cultured for various durations (0, 1, 7, 14, 28, and 42 days) on a callus induction medium following wounding with the attempt of identifying genes that play key roles during callus formation. As the result, we detected a total of 27,639 alterations in gene expression during callus formation, which could be categorized into eight distinct clusters. Gene ontology analysis revealed that genes associated with hormones, cell wall modification, and cell cycle underwent transcriptional reprogramming throughout callus formation. Furthermore, by scrutinizing the expression patterns of genes related to hormones, cell cycle, cell wall, and transcription factors, we discovered that auxin, cytokinin, and brassinosteroid signaling pathways activate genes involved in both root and shoot meristem development during callus formation. In summary, our transcriptome analysis provides significant insights into the molecular mechanisms governing callus formation in soybean. The information obtained from this study contributes to a deeper understanding of this intricate process and paves the way for further investigation in the field.
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Affiliation(s)
- Joo-Seok Park
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Yoram Choi
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Min-Gyun Jeong
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Yeong-Il Jeong
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Ji-Hyun Han
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Hong-Kyu Choi
- Department of Molecular Genetics, Dong-A University, Busan, Republic of Korea
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42
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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: 8] [Impact Index Per Article: 8.0] [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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43
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Bekalu ZE, Panting M, Bæksted Holme I, Brinch-Pedersen H. Opportunities and Challenges of In Vitro Tissue Culture Systems in the Era of Crop Genome Editing. Int J Mol Sci 2023; 24:11920. [PMID: 37569295 PMCID: PMC10419073 DOI: 10.3390/ijms241511920] [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: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Currently, the development of genome editing (GE) tools has provided a wide platform for targeted modification of plant genomes. However, the lack of versatile DNA delivery systems for a large variety of crop species has been the main bottleneck for improving crops with beneficial traits. Currently, the generation of plants with heritable mutations induced by GE tools mostly goes through tissue culture. Unfortunately, current tissue culture systems restrict successful results to only a limited number of plant species and genotypes. In order to release the full potential of the GE tools, procedures need to be species and genotype independent. This review provides an in-depth summary and insights into the various in vitro tissue culture systems used for GE in the economically important crops barley, wheat, rice, sorghum, soybean, maize, potatoes, cassava, and millet and uncovers new opportunities and challenges of already-established tissue culture platforms for GE in the crops.
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44
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Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. SCIENCE ADVANCES 2023; 9:eadg6983. [PMID: 37418524 PMCID: PMC10328406 DOI: 10.1126/sciadv.adg6983] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2-based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency.
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Affiliation(s)
- Nao Ogura
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
| | - Yohei Sasagawa
- Department of Functional Genome Informatics, Division of Medical Genomics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan
| | - Tasuku Ito
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Toshiaki Tameshige
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Yokohama 244-0813, Japan
| | - Satomi Kawai
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
| | - Masaki Sano
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
| | - Yuki Doll
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ayako Kawamura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Biosciences and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Itoshi Nikaido
- Department of Functional Genome Informatics, Division of Medical Genomics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 119-0033, Japan
| | - Momoko Ikeuchi
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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Vu QT, Song K, Park S, Xu L, Nam HG, Hong S. An auxin-mediated ultradian rhythm positively influences root regeneration via EAR1/EUR1 in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1136445. [PMID: 37351216 PMCID: PMC10282773 DOI: 10.3389/fpls.2023.1136445] [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: 01/03/2023] [Accepted: 04/04/2023] [Indexed: 06/24/2023]
Abstract
Ultradian rhythms have been proved to be critical for diverse biological processes. However, comprehensive understanding of the short-period rhythms remains limited. Here, we discover that leaf excision triggers a gene expression rhythm with ~3-h periodicity, named as the excision ultradian rhythm (UR), which is regulated by the plant hormone auxin. Promoter-luciferase analyses showed that the spatiotemporal patterns of the excision UR were positively associated with de novo root regeneration (DNRR), a post-embryonic developmental process. Transcriptomic analysis indicated more than 4,000 genes including DNRR-associated genes were reprogramed toward ultradian oscillation. Genetic studies showed that EXCISION ULTRADIAN RHYTHM 1 (EUR1) encoding ENHANCER OF ABSCISIC ACID CO-RECEPTOR1 (EAR1), an abscisic acid signaling regulator, was required to generate the excision ultradian rhythm and enhance root regeneration. The eur1 mutant exhibited the absence of auxin-induced excision UR generation and partial failure during rescuing root regeneration. Our results demonstrate a link between the excision UR and adventitious root formation via EAR1/EUR1, implying an additional regulatory layer in plant regeneration.
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Affiliation(s)
- Quy Thi Vu
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Kitae Song
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Sungjin Park
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Sunghyun Hong
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
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46
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Liu X, Bie XM, Lin X, Li M, Wang H, Zhang X, Yang Y, Zhang C, Zhang XS, Xiao J. Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation. NATURE PLANTS 2023; 9:908-925. [PMID: 37142750 DOI: 10.1038/s41477-023-01406-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/29/2023] [Indexed: 05/06/2023]
Abstract
Genetic transformation is important for gene functional study and crop improvement. However, it is less effective in wheat. Here we employed a multi-omic analysis strategy to uncover the transcriptional regulatory network (TRN) responsible for wheat regeneration. RNA-seq, ATAC-seq and CUT&Tag techniques were utilized to profile the transcriptional and chromatin dynamics during early regeneration from the scutellum of immature embryos in the wheat variety Fielder. Our results demonstrate that the sequential expression of genes mediating cell fate transition during regeneration is induced by auxin, in coordination with changes in chromatin accessibility, H3K27me3 and H3K4me3 status. The built-up TRN driving wheat regeneration was found to be dominated by 446 key transcription factors (TFs). Further comparisons between wheat and Arabidopsis revealed distinct patterns of DNA binding with one finger (DOF) TFs in the two species. Experimental validations highlighted TaDOF5.6 (TraesCS6A02G274000) and TaDOF3.4 (TraesCS2B02G592600) as potential enhancers of transformation efficiency in different wheat varieties.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Min Bie
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Menglu Li
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Hongzhe Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Nanjing Agricultural University, Nanjing, China
| | - Chunyan Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xian Sheng Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing, China.
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47
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Neves M, Correia S, Canhoto J. Ethylene Inhibition Reduces De Novo Shoot Organogenesis and Subsequent Plant Development from Leaf Explants of Solanum betaceum Cav. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091854. [PMID: 37176912 PMCID: PMC10180641 DOI: 10.3390/plants12091854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
In de novo shoot organogenesis (DNSO) plant cells develop into new shoots, without the need of an existing meristem. Generally, this process is triggered by wounding and specific growth regulators, such as auxins and cytokinins. Despite the potential significance of the plant hormone ethylene in DNSO, its effect in regeneration processes of woody species has not been thoroughly investigated. To address this gap, Solanum betaceum Cav. was used as an experimental model to explore the role of this hormone on DNSO and potentially extend the findings to other woody species. In this work it was shown that ethylene positively regulates DNSO from tamarillo leaf explants. Ethylene precursors ACC and ethephon stimulated shoot regeneration by increasing the number of buds and shoots regenerated. In contrast, the inhibition of ethylene biosynthesis or perception by AVG and AgNO3 decreased shoot regeneration. Organogenic callus induced in the presence of ethylene precursors showed an upregulated expression of the auxin efflux carrier gene PIN1, suggesting that ethylene may enhance shoot regeneration by affecting auxin distribution prior to shoot development. Additionally, it was found that the de novo shoot meristems induced in explants in which ethylene biosynthesis and perception was suppressed were unable to further develop into elongated shoots. Overall, these results imply that altering ethylene levels and perception could enhance shoot regeneration efficiency in tamarillo. Moreover, we offer insights into the possible molecular mechanisms involved in ethylene-induced shoot regeneration.
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Affiliation(s)
- Mariana Neves
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
- InnovPlantProtect CoLab, 7350-478 Elvas, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
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48
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Guo F, Wang H, Lian G, Cai G, Liu W, Zhang H, Li D, Zhou C, Han N, Zhu M, Su Y, Seo PJ, Xu L, Bian H. Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice. Commun Biol 2023; 6:457. [PMID: 37100819 PMCID: PMC10130139 DOI: 10.1038/s42003-023-04835-w] [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: 10/19/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
In rice (Oryza sativa) tissue culture, callus can be induced from the scutellum in embryo or from the vasculature of non-embryonic organs such as leaves, nodes, or roots. Here we show that the auxin signaling pathway triggers cell division in the epidermis of the scutellum to form an embryo-like structure, which leads to callus formation. Our transcriptome data show that embryo-, stem cell-, and auxin-related genes are upregulated during scutellum-derived callus initiation. Among those genes, the embryo-specific gene OsLEC1 is activated by auxin and involved in scutellum-derived callus initiation. However, OsLEC1 is not required for vasculature-derived callus initiation from roots. In addition, OsIAA11 and OsCRL1, which are involved in root development, are required for vasculature-derived callus formation but not for scutellum-derived callus formation. Overall, our data indicate that scutellum-derived callus initiation is regulated by an embryo-like development program, and this is different from vasculature-derived callus initiation which borrows a root development program.
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Affiliation(s)
- Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guiwei Lian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Haidao Zhang
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Chun Zhou
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Muyuan Zhu
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinghua Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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49
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Bisht A, Eekhout T, Canher B, Lu R, Vercauteren I, De Jaeger G, Heyman J, De Veylder L. PAT1-type GRAS-domain proteins control regeneration by activating DOF3.4 to drive cell proliferation in Arabidopsis roots. THE PLANT CELL 2023; 35:1513-1531. [PMID: 36747478 PMCID: PMC10118276 DOI: 10.1093/plcell/koad028] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 05/22/2023]
Abstract
Plant roots possess remarkable regenerative potential owing to their ability to replenish damaged or lost stem cells. ETHYLENE RESPONSE FACTOR 115 (ERF115), one of the key molecular elements linked to this potential, plays a predominant role in the activation of regenerative cell divisions. However, the downstream operating molecular machinery driving wound-activated cell division is largely unknown. Here, we biochemically and genetically identified the GRAS-domain transcription factor SCARECROW-LIKE 5 (SCL5) as an interaction partner of ERF115 in Arabidopsis thaliana. Although nonessential under control growth conditions, SCL5 acts redundantly with the related PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) and SCL21 transcription factors to activate the expression of the DNA-BINDING ONE FINGER 3.4 (DOF3.4) transcription factor gene. DOF3.4 expression is wound-inducible in an ERF115-dependent manner and, in turn, activates D3-type cyclin expression. Accordingly, ectopic DOF3.4 expression drives periclinal cell division, while its downstream D3-type cyclins are essential for the regeneration of a damaged root. Our data highlight the importance and redundant roles of the SCL5, SCL21, and PAT1 transcription factors in wound-activated regeneration processes and pinpoint DOF3.4 as a key downstream element driving regenerative cell division.
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Affiliation(s)
- Anchal Bisht
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Balkan Canher
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
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50
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Loupit G, Brocard L, Ollat N, Cookson SJ. Grafting in plants: recent discoveries and new applications. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2433-2447. [PMID: 36846896 DOI: 10.1093/jxb/erad061] [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: 10/13/2022] [Accepted: 02/14/2023] [Indexed: 06/06/2023]
Abstract
Grafting is a traditional horticultural technique that makes use of plant wound healing mechanisms to join two different genotypes together to form one plant. In many agricultural systems, grafting with rootstocks controls the vigour of the scion and/or provides tolerance to deleterious soil conditions such as the presence of soil pests or pathogens or limited or excessive water or mineral nutrient supply. Much of our knowledge about the limits to grafting different genotypes together comes from empirical knowledge of horticulturalists. Until recently, researchers believed that grafting monocotyledonous plants was impossible, because they lack a vascular cambium, and that graft compatibility between different scion/rootstock combinations was restricted to closely related genotypes. Recent studies have overturned these ideas and open up the possibility of new research directions and applications for grafting in agriculture. The objective of this review is to describe and assess these recent advances in the field of grafting and, in particular, the molecular mechanisms underlining graft union formation and graft compatibility between different genotypes. The challenges of characterizing the different stages of graft union formation and phenotyping graft compatibility are examined.
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Affiliation(s)
- Grégoire Loupit
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Lysiane Brocard
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US4, F-33000 Bordeaux, France
| | - Nathalie Ollat
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Sarah Jane Cookson
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
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