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Hao H, Xie B, Zhao D, Kang J, Jiang X, Gai Y. Proteomic insights into adventitious root formation in Larix kaempferi. J Proteomics 2024; 307:105288. [PMID: 39173904 DOI: 10.1016/j.jprot.2024.105288] [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: 04/06/2024] [Revised: 08/09/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
The adventitious root formaton (ARF) in excised plant parts is essential for the survival of isolated plant fragments. In this study, we explored the complex mechanisms of ARF in Larix kaempferi by conducting a comprehensive proteomic analysis across three distinct stages: the induction of adventitious root primordia (C1, 0-25 d), the formation of adventitious root primordia (C2, 25-35 d), and the elongation of adventitious roots (C3, 35-45 d). We identified 1976 proteins, with 263 and 156 proteins exhibiting increased abundance in the C2/C1 and C3/C2 transitions, respectively. In contrast, a decrease in the abundance of 106 and 132 proteins suggests a significant demand for metabolic processes during the C2/C1 phase. The abundance of IAA-amino acid hydrolase and S-adenosylmethionine synthase were increased in the C2/C1 phase, underscoring the role of auxin in adventitious root induction. The decrease in abundance of photosynthesis-related proteins during the C2/C1 phase highlights the significance of initial light conditions in adventitious root induction. Moreover, variation in cell wall synthesis and metabolic proteins in the C2/C1 and C3/C2 stages suggests that cell wall metabolism is integral to adventitious root regeneration. Gene Ontology enrichment analysis revealed pathways related to protein modification enzymes, including deubiquitinases and kinases, which are crucial for modulating protein modifications to promote ARF. Furthermore, the increased abundance of antioxidant enzymes, such as peroxidases and glutathione peroxidases, indicates a potential approach for enhancing ARF by supplementing the culture medium with antioxidants. Our study provides insights into metabolic changes during ARF in L. kaempferi, offering strategies to enhance adventitious root regeneration. These findings have the potential to refine plant propagation techniques and expedite breeding processes. SIGNFICANCE: The main challenge in the asexual reproduction technology of Larix kaempferi lies in adventitious root formation (ARF). While numerous studies have concentrated on the efficiency of ARF, proteomic data are currently scarce. In this study, we collected samples from three stages of ARF in L. kaempferi and subsequently performed proteomic analysis. The data generated not only reveal changes in protein abundance but also elucidate key metabolic processes involved in ARF. These insights offer a novel perspective on addressing the challenge of adventurous root regeneration.
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Affiliation(s)
- Haifei Hao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Baohui Xie
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Dadi Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Jiaqi Kang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Xiangning Jiang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Ying Gai
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China.
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2
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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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García-Gómez ML, Ten Tusscher K. Multi-scale mechanisms driving root regeneration: From regeneration competence to tissue repatterning. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38824611 DOI: 10.1111/tpj.16860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024]
Abstract
Plants possess an outstanding capacity to regenerate enabling them to repair damages caused by suboptimal environmental conditions, biotic attacks, or mechanical damages impacting the survival of these sessile organisms. Although the extent of regeneration varies greatly between localized cell damage and whole organ recovery, the process of regeneration can be subdivided into a similar sequence of interlinked regulatory processes. That is, competence to regenerate, cell fate reprogramming, and the repatterning of the tissue. Here, using root tip regeneration as a paradigm system to study plant regeneration, we provide a synthesis of the molecular responses that underlie both regeneration competence and the repatterning of the root stump. Regarding regeneration competence, we discuss the role of wound signaling, hormone responses and synthesis, and rapid changes in gene expression observed in the cells close to the cut. Then, we consider how this rapid response is followed by the tissue repatterning phase, where cells experience cell fate changes in a spatial and temporal order to recreate the lost stem cell niche and columella. Lastly, we argue that a multi-scale modeling approach is fundamental to uncovering the mechanisms underlying root regeneration, as it allows to integrate knowledge of cell-level gene expression, cell-to-cell transport of hormones and transcription factors, and tissue-level growth dynamics to reveal how the bi-directional feedbacks between these processes enable self-organized repatterning of the root apex.
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Affiliation(s)
- Monica L García-Gómez
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Experimental and Computational Plant Development Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- CropXR Institute, Utrecht, The Netherlands
- Translational Plant Biology Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Kirsten Ten Tusscher
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Experimental and Computational Plant Development Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- CropXR Institute, Utrecht, The Netherlands
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4
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Raha P, Khatua I, Saha G, Adhikari S, Gantait S, Bandyopadhyay TK. Morpho-histology of co-occurrence of somatic embryos, shoots, and inflorescences within a callus of Limonium 'Misty Blue'. PHYSIOLOGIA PLANTARUM 2024; 176:e14389. [PMID: 38887935 DOI: 10.1111/ppl.14389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/11/2024] [Accepted: 05/29/2024] [Indexed: 06/20/2024]
Abstract
This is the first attempt to report the co-occurrence of somatic embryos, shoots, and inflorescences and their sequential development from stem cell niches of an individual callus mass through morpho-histological study of any angiosperm. In the presence of a proper auxin/cytokinin combination, precambial stem cells from the middle layer of a compact callus, which was derived from the thin cell layer of the inflorescence rachis of Limonium, expressed the highest level of totipotency and pluripotency and simultaneously developed somatic embryos, shoots, and inflorescences. This study also proposed the concept of programmed cell death during bipolar somatic embryo and unipolar shoot bud pattern formation. The unique feature of this research was the stepwise histological description of in vitro racemose inflorescence development. Remarkably, during the initiation of inflorescence development, either a unipolar structure with open vascular elements or an independent bipolar structure with closed vascular elements were observed. The protocol predicted the production of 6.6 ± 0.24 and 7.4 ± 0.24 somatic embryos and shoots, respectively, from 400 mg of callus, which again multiplied, rooted, and acclimatised. The plants' ploidy level and genetic fidelity were assessed randomly before acclimatisation by flow cytometry and inter simple sequence repeats (ISSR) marker analysis. Finally, the survivability and flower quality of the regenerated plants were evaluated in the field.
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Affiliation(s)
- Priyanka Raha
- Department of Molecular Biology and Biotechnology, University of Kalyani, Nadia, West Bengal, India
| | - Ishita Khatua
- Department of Molecular Biology and Biotechnology, University of Kalyani, Nadia, West Bengal, India
| | - Gourab Saha
- Department of Molecular Biology and Biotechnology, University of Kalyani, Nadia, West Bengal, India
| | - Sinchan Adhikari
- Department of Botany, University of Kalyani, Nadia, West Bengal, India
| | - Saikat Gantait
- Crop Research Unit (Genetics and Plant Breeding), Bidhan Chandra Krishi Viswavidyalaya, Nadia, West Bengal, India
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5
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Cardi T, Murovec J, Bakhsh A, Boniecka J, Bruegmann T, Bull SE, Eeckhaut T, Fladung M, Galovic V, Linkiewicz A, Lukan T, Mafra I, Michalski K, Kavas M, Nicolia A, Nowakowska J, Sági L, Sarmiento C, Yıldırım K, Zlatković M, Hensel G, Van Laere K. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. TRENDS IN PLANT SCIENCE 2023; 28:1144-1165. [PMID: 37331842 DOI: 10.1016/j.tplants.2023.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023]
Abstract
The discovery of the CRISPR/Cas genome-editing system has revolutionized our understanding of the plant genome. CRISPR/Cas has been used for over a decade to modify plant genomes for the study of specific genes and biosynthetic pathways as well as to speed up breeding in many plant species, including both model and non-model crops. Although the CRISPR/Cas system is very efficient for genome editing, many bottlenecks and challenges slow down further improvement and applications. In this review we discuss the challenges that can occur during tissue culture, transformation, regeneration, and mutant detection. We also review the opportunities provided by new CRISPR platforms and specific applications related to gene regulation, abiotic and biotic stress response improvement, and de novo domestication of plants.
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Affiliation(s)
- Teodoro Cardi
- Consiglio Nazionale delle Ricerche (CNR), Institute of Biosciences and Bioresources (IBBR), Portici, Italy; CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Jana Murovec
- University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Allah Bakhsh
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey; Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Justyna Boniecka
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | | | - Simon E Bull
- Molecular Plant Breeding, Institute of Agricultural Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Switzerland; Plant Biochemistry, Institute of Molecular Plant Biology, ETH, Zurich, Switzerland
| | - Tom Eeckhaut
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium
| | | | - Vladislava Galovic
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Anna Linkiewicz
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Tjaša Lukan
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Isabel Mafra
- Rede de Química e Tecnologia (REQUIMTE) Laboratório Associado para a Química Verde (LAQV), Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Krzysztof Michalski
- Plant Breeding and Acclimatization Institute, National Research Institute, Błonie, Poland
| | - Musa Kavas
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Alessandro Nicolia
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Justyna Nowakowska
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Laszlo Sági
- Centre for Agricultural Research, Loránd Eötvös Research Network, Martonvásár, Hungary
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Milica Zlatković
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Goetz Hensel
- Heinrich-Heine-University, Institute of Plant Biochemistry, Centre for Plant Genome Engineering, Düsseldorf, Germany; Division of Molecular Biology, Centre of the Region Hana for Biotechnological and Agriculture Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Katrijn Van Laere
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium.
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Dagne H, S VP, Palanivel H, Yeshitila A, Benor S, Abera S, Abdi A. Advanced modeling and optimizing for surface sterilization process of grape vine ( Vitis vinifera) root stock 3309C through response surface, artificial neural network, and genetic algorithm techniques. Heliyon 2023; 9:e18628. [PMID: 37554794 PMCID: PMC10404695 DOI: 10.1016/j.heliyon.2023.e18628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/10/2023] Open
Abstract
In vitro, sterilization is one of the key components for proceeding with plant tissue cultures. Since the effectiveness of sterilization has a direct impact on the culture's final outcomes, there is a crucial need for optimization of the sterilization process. However, compared with traditional optimizing methods, the use of computational approaches through artificial intelligence-based process modeling and optimization algorithms provides a precise optimal condition for in vitro culturing. This study aimed to optimise in vitro sterilization of grape rootstock 3309C using RSM, ANN, and genetic algorithm (GA) techniques. In this context, two output responses, namely, Clean Culture and Explant Viability, were optimised using the models developed by RSM and ANN, followed by a GA, to obtain a globally optimal solution. The most influential independent factors, such as HgCl2, NaOCl, AgNO3, and immersion time, were considered input variables. The significance of the developed models was investigated with statistical and non-statistical techniques and was optimised to determine the significance of selected inputs. The optimal clean culture of 91%, and the explant viability of 89% can be obtained from 1.62% NaOCl at a 13.96 min immersion time, according to MLP-NSGAII. Sensitivity analysis revealed that the clean culture and explant viability were less sensitive to AgNO3 and more sensitive to immersion time. Results showed that the differences between the GA predicted and validation data were significant after the performance validation of predicted and optimised sterilising agents with immersion time combinations were tested. In general, GA, a potent methodology, may open the door to the development of new computational methods in plant tissue culture.
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Affiliation(s)
- Habtamu Dagne
- Department of Biotechnology, Centre of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Venkatesa Prabhu S
- Department of Chemical Engineering, Centre of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Hemalatha Palanivel
- Department of Biotechnology, Centre of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Alazar Yeshitila
- Department of Biotechnology, Centre of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Solomon Benor
- Department of Plant Biology and Biodiversity Management, College of Natural and Computational Sciences, Addis Ababa University, Ethiopia
| | - Solomon Abera
- Department of Biotechnology, Centre of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Adugna Abdi
- Department of Biotechnology, Centre of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
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Murthy HN, Joseph KS, Hahn JE, Lee HS, Paek KY, Park SY. Suspension culture of somatic embryos for the production of high-value secondary metabolites. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1153-1177. [PMID: 37829704 PMCID: PMC10564700 DOI: 10.1007/s12298-023-01365-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Secondary metabolites from plants are ubiquitous and have applications in medicines, food additives, scents, colorants, and natural pesticides. Biotechnological production of secondary metabolites that have economic benefits is an attractive alternative to conventional methods. Cell, adventitious, and hairy root suspension cultures are typically used to produce secondary metabolites. According to recent studies, somatic embryos in suspension culture are useful tools for the generation of secondary metabolites. Somatic embryogenesis is a mode of regeneration in several plant species. This review provides an update on the use of somatic embryogenesis in the production of valuable secondary metabolites. The factors influencing the generation of secondary metabolites using somatic embryos in suspension cultures, elicitation methods, and prospective applications are also discussed in this review. Graphical abstract
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Affiliation(s)
- Hosakatte Niranjana Murthy
- Department of Botany, Karnatak University, Dharwad, 580003 India
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | | | - Jong-Eun Hahn
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Han-Sol Lee
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Kee Yoeup Paek
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - So Young Park
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
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8
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Ingvardsen CR, Brinch-Pedersen H. Challenges and potentials of new breeding techniques in Cannabis sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1154332. [PMID: 37360738 PMCID: PMC10285108 DOI: 10.3389/fpls.2023.1154332] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023]
Abstract
Cannabis sativa L. is an ancient crop used for fiber and seed production and not least for its content of cannabinoids used for medicine and as an intoxicant drug. Due to the psychedelic effect of one of the compounds, tetrahydrocannabinol (THC), many countries had regulations or bands on Cannabis growing, also as fiber or seed crop. Recently, as many of these regulations are getting less tight, the interest for the many uses of this crop is increasing. Cannabis is dioecious and highly heterogenic, making traditional breeding costly and time consuming. Further, it might be difficult to introduce new traits without changing the cannabinoid profile. Genome editing using new breeding techniques might solve these problems. The successful use of genome editing requires sequence information on suitable target genes, a genome editing tool to be introduced into plant tissue and the ability to regenerate plants from transformed cells. This review summarizes the current status of Cannabis breeding, uncovers potentials and challenges of Cannabis in an era of new breeding techniques and finally suggests future focus areas that may help to improve our overall understanding of Cannabis and realize the potentials of the plant.
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9
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Liu X, Zhu K, Xiao J. Recent advances in understanding of the epigenetic regulation of plant regeneration. ABIOTECH 2023; 4:31-46. [PMID: 37220541 PMCID: PMC10199984 DOI: 10.1007/s42994-022-00093-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/27/2022] [Indexed: 05/22/2023]
Abstract
Ever since the concept of "plant cell totipotency" was first proposed in the early twentieth century, plant regeneration has been a major focus of study. Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture. Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration. The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation. Here, we summarize how various aspects of epigenetic regulation, including histone modifications and variants, chromatin accessibility dynamics, DNA methylation, and microRNAs, modulate plant regeneration. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in boosting crop breeding, especially if coupled with emerging single-cell omics technologies.
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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, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kehui Zhu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
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10
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Lee K, Wang K. Strategies for genotype-flexible plant transformation. Curr Opin Biotechnol 2023; 79:102848. [PMID: 36463838 DOI: 10.1016/j.copbio.2022.102848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/23/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022]
Abstract
Recent advances in the genome-editing tools have demonstrated a great potential for accelerating functional genomics and crop trait improvements, but the low efficiency and genotype dependence in plant transformation hinder practical applications of such revolutionary tools. Morphogenic transcription factors (MTFs) such as Baby boom, Wuschel2, GROWTH-REGULATING FACTOR5, GROWTH-REGULATING FACTOR4 and its cofactor GRF-INTERACTING FACTOR1, and Wuschel-homeobox 5 related have been shown to greatly enhance plant transformation efficiency and expand the range of amenable species and genotypes. This review will summarize recent advancements in plant transformation technologies with an emphasis on the strategies developed for genotype-flexible transformation methods utilizing MTFs for both monocots and dicot plant species. We highlight several breakthrough studies that demonstrated a wide range of applicability.
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Affiliation(s)
- Keunsub Lee
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA.
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11
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Liang Y, Heyman J, Lu R, De Veylder L. Evolution of wound-activated regeneration pathways in the plant kingdom. Eur J Cell Biol 2023; 102:151291. [PMID: 36709604 DOI: 10.1016/j.ejcb.2023.151291] [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: 11/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Regeneration serves as a self-protective mechanism that allows a tissue or organ to recover its entire form and function after suffering damage. However, the regenerative capacity varies greatly within the plant kingdom. Primitive plants frequently display an amazing regenerative ability as they have developed a complex system and strategy for long-term survival under extreme stress conditions. The regenerative ability of dicot species is highly variable, but that of monocots often exhibits extreme recalcitrance to tissue replenishment. Recent studies have revealed key factors and signals that affect cell fate during plant regeneration, some of which are conserved among the plant lineage. Among these, several members of the ETHYLENE RESPONSE FACTOR (ERF) transcription factors have been implicated in wound signaling, playing crucial roles in the regenerative mechanisms after different types of wounding. An understanding of plant regeneration may ultimately lead to an increased regenerative potential of recalcitrant species, producing more high-yielding, multi-resistant and environmentally friendly crops and ensuring the long-term development of global agriculture.
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Affiliation(s)
- Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.
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12
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Jin C, Dong L, Wei C, Wani MA, Yang C, Li S, Li F. Creating novel ornamentals via new strategies in the era of genome editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1142866. [PMID: 37123857 PMCID: PMC10140431 DOI: 10.3389/fpls.2023.1142866] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Ornamental breeding has traditionally focused on improving novelty, yield, quality, and resistance to biotic or abiotic stress. However, achieving these goals has often required laborious crossbreeding, while precise breeding techniques have been underutilized. Fortunately, recent advancements in plant genome sequencing and editing technology have opened up exciting new frontiers for revolutionizing ornamental breeding. In this review, we provide an overview of the current state of ornamental transgenic breeding and propose four promising breeding strategies that have already proven successful in crop breeding and could be adapted for ornamental breeding with the help of genome editing. These strategies include recombination manipulation, haploid inducer creation, clonal seed production, and reverse breeding. We also discuss in detail the research progress, application status, and feasibility of each of these tactics.
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Affiliation(s)
- Chunlian Jin
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
| | - Liqing Dong
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Chang Wei
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Muneeb Ahmad Wani
- Department of Floriculture and Landscape Architecture, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Chunmei Yang
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
| | - Shenchong Li
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- *Correspondence: Fan Li, ; Shenchong Li,
| | - Fan Li
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- *Correspondence: Fan Li, ; Shenchong Li,
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13
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Aasim M, Katirci R, Baloch FS, Mustafa Z, Bakhsh A, Nadeem MA, Ali SA, Hatipoğlu R, Çiftçi V, Habyarimana E, Karaköy T, Chung YS. Innovation in the Breeding of Common Bean Through a Combined Approach of in vitro Regeneration and Machine Learning Algorithms. Front Genet 2022; 13:897696. [PMID: 36092939 PMCID: PMC9451102 DOI: 10.3389/fgene.2022.897696] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Common bean is considered a recalcitrant crop for in vitro regeneration and needs a repeatable and efficient in vitro regeneration protocol for its improvement through biotechnological approaches. In this study, the establishment of efficient and reproducible in vitro regeneration followed by predicting and optimizing through machine learning (ML) models, such as artificial neural network algorithms, was performed. Mature embryos of common bean were pretreated with 5, 10, and 20 mg/L benzylaminopurine (BAP) for 20 days followed by isolation of plumular apice for in vitro regeneration and cultured on a post-treatment medium containing 0.25, 0.50, 1.0, and 1.50 mg/L BAP for 8 weeks. Plumular apice explants pretreated with 20 mg/L BAP exerted a negative impact and resulted in minimum shoot regeneration frequency and shoot count, but produced longer shoots. All output variables (shoot regeneration frequency, shoot counts, and shoot length) increased significantly with the enhancement of BAP concentration in the post-treatment medium. Interaction of the pretreatment × post-treatment medium revealed the need for a specific combination for inducing a high shoot regeneration frequency. Higher shoot count and shoot length were achieved from the interaction of 5 mg/L BAP × 1.00 mg/L BAP followed by 10 mg/L BAP × 1.50 mg/L BAP and 20 mg/L BAP × 1.50 mg/L BAP. The evaluation of data through ML models revealed that R2 values ranged from 0.32 to 0.58 (regeneration), 0.01 to 0.22 (shoot counts), and 0.18 to 0.48 (shoot length). On the other hand, the mean squared error values ranged from 0.0596 to 0.0965 for shoot regeneration, 0.0327 to 0.0412 for shoot count, and 0.0258 to 0.0404 for shoot length from all ML models. Among the utilized models, the multilayer perceptron model provided a better prediction and optimization for all output variables, compared to other models. The achieved results can be employed for the prediction and optimization of plant tissue culture protocols used for biotechnological approaches in a breeding program of common beans.
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Affiliation(s)
- Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Ramazan Katirci
- Department of Metallurgical and Materials Engineering, Faculty of Engineering and Natural Sciences, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
- *Correspondence: Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Zemran Mustafa
- Department of Plant Production and Technologies, Faculty of Agricultural Science and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Allah Bakhsh
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Seyid Amjad Ali
- Department of Information Systems and Technologies, Bilkent University, Ankara, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
- *Correspondence: Faheem Shehzad Baloch, ; Yong Suk Chung,
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14
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Liang Y, Heyman J, Xiang Y, Vandendriessche W, Canher B, Goeminne G, De Veylder L. The wound-activated ERF15 transcription factor drives Marchantia polymorpha regeneration by activating an oxylipin biosynthesis feedback loop. SCIENCE ADVANCES 2022; 8:eabo7737. [PMID: 35960801 PMCID: PMC9374346 DOI: 10.1126/sciadv.abo7737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The regenerative potential in response to wounding varies widely among species. Within the plant lineage, the liverwort Marchantia polymorpha displays an extraordinary regeneration capacity. However, its molecular pathways controlling the initial regeneration response are unknown. Here, we demonstrate that the MpERF15 transcription factor gene is instantly activated after wounding and is essential for gemmaling regeneration following tissue incision. MpERF15 operates both upstream and downstream of the MpCOI1 oxylipin receptor by controlling the expression of oxylipin biosynthesis genes. The resulting rise in the oxylipin dinor-12-oxo-phytodienoic acid (dn-OPDA) levels results in an increase in gemma cell number and apical notch organogenesis, generating highly disorganized and compact thalli. Our data pinpoint MpERF15 as a key factor activating an oxylipin biosynthesis amplification loop after wounding, which eventually results in reactivation of cell division and regeneration. We suggest that the genetic networks controlling oxylipin biosynthesis in response to wounding might have been reshuffled over evolution.
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Affiliation(s)
- Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Yanli Xiang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Wiske Vandendriessche
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Balkan Canher
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
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15
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Yang S, de Haan M, Mayer J, Janacek DP, Hammes UZ, Poppenberger B, Sieberer T. A novel chemical inhibitor of polar auxin transport promotes shoot regeneration by local enhancement of HD-ZIP III transcription. THE NEW PHYTOLOGIST 2022; 235:1111-1128. [PMID: 35491431 DOI: 10.1111/nph.18196] [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: 11/18/2021] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
De novo shoot organogenesis is a prerequisite for numerous applications in plant research and breeding but is often a limiting factor, for example, in genome editing approaches. Class III homeodomain-leucine zipper (HD-ZIP III) transcription factors have been characterized as crucial regulators of shoot specification, however up-stream components controlling their activity during shoot regeneration are only partially identified. In a chemical genetic screen, we isolated ZIC2, a novel activator of HD-ZIP III activity. Using molecular, physiological and hormone transport analyses in Arabidopsis and sunflower (Helianthus annuus), we examined the molecular mechanism by which the drug promotes HD-ZIP III expression. ZIC2-dependent upregulation of HD-ZIP III transcription promotes shoot regeneration in Arabidopsis and is accompanied by the induction of shoot specifying factors WUS and RAP2.6L and a subset of cytokinin biosynthesis enzymes. ZIC2's effect on HD-ZIP III expression and regeneration is based on its ability to limit polar auxin transport. We further provide evidence that chemical modulation of auxin efflux can enhance de novo shoot formation in the regeneration recalcitrant species sunflower. Activation of HD-ZIP III transcription during shoot regeneration depends on the local distribution of auxin and chemical modulation of auxin transport can be used to overcome poor shoot organogenesis in tissue culture.
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Affiliation(s)
- Saiqi Yang
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Marjolein de Haan
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Julius Mayer
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Dorina P Janacek
- Plant Systems Biology, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Ulrich Z Hammes
- Plant Systems Biology, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Tobias Sieberer
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
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16
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Gammoudi N, Nagaz K, Ferchichi A. Establishment of optimized in vitro disinfection protocol of Pistacia vera L. explants mediated a computational approach: multilayer perceptron-multi-objective genetic algorithm. BMC PLANT BIOLOGY 2022; 22:324. [PMID: 35790933 PMCID: PMC9254583 DOI: 10.1186/s12870-022-03674-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/31/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND Contamination-free culture is a prerequisite for the success of in vitro - based plant biotechnology. Aseptic initiation is an extremely strenuous stride, particularly in woody species. Meanwhile, over-sterilization is potentially detrimental to plant tissue. The recent rise of machine learning algorithms in plant tissue culture proposes an advanced interpretive tool for the combinational effect of influential factors for such in vitro - based steps. RESULTS A multilayer perceptron (MLP) model of artificial neural network (ANN) was implemented with four inputs, three sterilizing chemicals at various concentrations and the immersion time, and two outputs, disinfection efficiency (DE) and negative disinfection effect (NDE), intending to assess twenty-seven disinfection procedures of Pistacia vera L. seeds. Mercury chloride (HgCl2; 0.05-0.2%; 5-15 min) appears the most effective with 100% DE, then hydrogen peroxide (H2O2; 5.25-12.25%; 10-30 min) with 66-100% DE, followed by 27-77% DE for sodium hypochlorite (NaOCl; 0.54-1.26% w/v; 10-30 min). Concurrently, NDE was detected, including chlorosis, hard embryo germination, embryo deformation, and browning tissue, namely, a low repercussion with NaOCl (0-14%), a moderate impact with H2O2 (6-46%), and pronounced damage with HgCl2 (22-100%). Developed ANN showed R values of 0.9658, 0.9653, 0.8937, and 0.9454 for training, validation, testing, and all sets, respectively, which revealed the uprightness of the model. Subsequently, the model was linked to multi-objective genetic algorithm (MOGA) which proposed an optimized combination of 0.56% NaOCl, 12.23% H2O2, and 0.068% HgCl2 for 5.022 min. The validation assay reflects the high utility and accuracy of the model with maximum DE (100%) and lower phytotoxicity (7.1%). CONCLUSION In one more case, machine learning algorithms emphasized their ability to resolve commonly encountered problems. The current successful implementation of MLP-MOGA inspires its application for more complicated plant tissue culture processes.
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Affiliation(s)
- Najet Gammoudi
- Arid and Oases Cropping Laboratory, Arid Lands Institute (IRA), 4119, Medenine, Tunisia.
| | - Kamel Nagaz
- Arid and Oases Cropping Laboratory, Arid Lands Institute (IRA), 4119, Medenine, Tunisia
| | - Ali Ferchichi
- National Institute of Agronomy of Tunis, 43 Charles Nicolle, 1082, Tunis, Tunisia
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17
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Long Y, Yang Y, Pan G, Shen Y. New Insights Into Tissue Culture Plant-Regeneration Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:926752. [PMID: 35845646 PMCID: PMC9280033 DOI: 10.3389/fpls.2022.926752] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/31/2022] [Indexed: 05/08/2023]
Abstract
Plant regeneration occurs when plants repair or replace damaged structures based on the totipotency and pluripotency of their cells. Tissue culture is one of the most widely used regenerative technologies. Recently, a series of breakthroughs were made in the study of plant regeneration. This review summarizes two regenerative pathways in tissue culture: somatic embryogenesis and de novo organogenesis. Furthermore, we review the environmental factors influencing plant regeneration from explant sources, basal culture medium, plant growth regulators, and light/dark treatment. Additionally, we analyse the molecular mechanisms underlying two pathways. This knowledge will promote an understanding of the fundamental principles of plant regeneration from precursor cells and lay a solid foundation for applying plant micropropagation and genetic modification.
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Affiliation(s)
- Yun Long
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Yun Yang
- Nanchong Academy of Agricultural Sciences, Nanchong, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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18
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Yuan J, Kaur D, Zhou Z, Nagle M, Kiddle NG, Doshi NA, Behnoudfar A, Peremyslova E, Ma C, Strauss SH, Li F. Robust High-Throughput Phenotyping with Deep Segmentation Enabled by a Web-Based Annotator. PLANT PHENOMICS 2022; 2022:9893639. [PMID: 36059601 PMCID: PMC9394117 DOI: 10.34133/2022/9893639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/17/2022] [Indexed: 11/24/2022]
Abstract
The abilities of plant biologists and breeders to characterize the genetic basis of physiological traits are limited by their abilities to obtain quantitative data representing precise details of trait variation, and particularly to collect this data at a high-throughput scale with low cost. Although deep learning methods have demonstrated unprecedented potential to automate plant phenotyping, these methods commonly rely on large training sets that can be time-consuming to generate. Intelligent algorithms have therefore been proposed to enhance the productivity of these annotations and reduce human efforts. We propose a high-throughput phenotyping system which features a Graphical User Interface (GUI) and a novel interactive segmentation algorithm: Semantic-Guided Interactive Object Segmentation (SGIOS). By providing a user-friendly interface and intelligent assistance with annotation, this system offers potential to streamline and accelerate the generation of training sets, reducing the effort required by the user. Our evaluation shows that our proposed SGIOS model requires fewer user inputs compared to the state-of-art models for interactive segmentation. As a case study of the use of the GUI applied for genetic discovery in plants, we present an example of results from a preliminary genome-wide association study (GWAS) of in planta regeneration in Populus trichocarpa (poplar). We further demonstrate that the inclusion of a semantic prior map with SGIOS can accelerate the training process for future GWAS, using a sample of a dataset extracted from a poplar GWAS of in vitro regeneration. The capabilities of our phenotyping system surpass those of unassisted humans to rapidly and precisely phenotype our traits of interest. The scalability of this system enables large-scale phenomic screens that would otherwise be time-prohibitive, thereby providing increased power for GWAS, mutant screens, and other studies relying on large sample sizes to characterize the genetic basis of trait variation. Our user-friendly system can be used by researchers lacking a computational background, thus helping to democratize the use of deep segmentation as a tool for plant phenotyping.
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Affiliation(s)
| | | | - Zheng Zhou
- Oregon State University, Corvallis, OR, USA
| | | | | | | | | | | | | | | | - Fuxin Li
- Oregon State University, Corvallis, OR, USA
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19
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Bull T, Michelmore R. Molecular Determinants of in vitro Plant Regeneration: Prospects for Enhanced Manipulation of Lettuce ( Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:888425. [PMID: 35615120 PMCID: PMC9125155 DOI: 10.3389/fpls.2022.888425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 05/12/2023]
Abstract
In vitro plant regeneration involves dedifferentiation and molecular reprogramming of cells in order to regenerate whole organs. Plant regeneration can occur via two pathways, de novo organogenesis and somatic embryogenesis. Both pathways involve intricate molecular mechanisms and crosstalk between auxin and cytokinin signaling. Molecular determinants of both pathways have been studied in detail in model species, but little is known about the molecular mechanisms controlling de novo shoot organogenesis in lettuce. This review provides a synopsis of our current knowledge on molecular determinants of de novo organogenesis and somatic embryogenesis with an emphasis on the former as well as provides insights into applying this information for enhanced in vitro regeneration in non-model species such as lettuce (Lactuca sativa L.).
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Affiliation(s)
- Tawni Bull
- The Genome Center, University of California, Davis, Davis, CA, United States
- Graduate Group in Horticulture and Agronomy, University of California, Davis, Davis, CA, United States
| | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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20
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Yao SC, Jiang YY, Ni S, Wang L, Feng J, Yang RW, Yang LX, Len QY, Zhang L. Development of a highly efficient virus-free regeneration system of Salvia miltiorrhiza from Sichuan using apical meristem as explants. PLANT METHODS 2022; 18:50. [PMID: 35436933 PMCID: PMC9014595 DOI: 10.1186/s13007-022-00872-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
BCAKGROUND The dry root and rhizome of Salvia miltiorrhiza are used to treat cardiovascular diseases, chronic pain, and thoracic obstruction over 2000 years in Asian countries. For high quality, Sichuan Zhongjiang is regarded as the genuine producing area of S. miltiorrhiza. Given its abnormal pollen development, S. miltiorrhiza from Sichuan (S.m.-SC) relies on root reproduction and zymad accumulation; part of diseased plants present typical viral disease symptoms and seed quality degeneration. This study aim to detected unknown viruses from mosaic-diseased plants and establish a highly efficient virus-free regeneration system to recover germplasm properties. RESULTS Tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV) were detected from mosaic-diseased plants. Primary apical meristem with two phyllo podium in 0.15-0.5 mm peeled from diseased plants were achieved 73.33% virus-free rate. The results showed that the medium containing MS, 0.5 mg/L 6-BA, 0.1 mg/L NAA, 0.1 mg/L GA3, 30 g/L sucrose and 7.5 g/L agar can achieve embryonic-tissue (apical meristem, petiole and leaf callus) high efficient organogenesis. For callus induction, the optimal condition was detected on the medium containing MS, 2 mg/L TDZ, 0.1 mg/L NAA by using secondary petiole of virus-free plants under 24 h dark/d condition for 21 d. The optimal system for root induction was the nutrient solution with 1/2 MS supplemented with 1 mg/L NAA. After transplant, the detection of agronomic metric and salvianolic acid B content confirmed the great germplasm properties of S.m.-SC virus-free plants. CONCLUSIONS A highly efficient virus-free regeneration system of S.m.-SC was established based on the detected viruses to recover superior seed quality. The proposed system laid support to control disease spread, recover good germplasm properties in S.m.-SC.
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Affiliation(s)
- Si Cheng Yao
- College of Science, Sichuan Agricultural University, Ya'an, 625000, China
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China
| | - Yuan Yuan Jiang
- College of Science, Sichuan Agricultural University, Ya'an, 625000, China
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China
| | - Su Ni
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China
- College of Agriculture, Sichuan Agricultural University, Chengdu, 610000, China
| | - Long Wang
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China
| | - Jun Feng
- College of Science, Sichuan Agricultural University, Ya'an, 625000, China
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China
| | - Rui Wu Yang
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China
| | - Li Xia Yang
- College of Science, Sichuan Agricultural University, Ya'an, 625000, China
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China
| | - Qiu Yan Len
- College of Science, Sichuan Agricultural University, Ya'an, 625000, China
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China
| | - Li Zhang
- College of Science, Sichuan Agricultural University, Ya'an, 625000, China.
- Featured Medicinal Plants Sharing and Service Plantform of Sichuan Province, Ya'an, 625000, China.
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21
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Lin CS, Hsu CT, Yuan YH, Zheng PX, Wu FH, Cheng QW, Wu YL, Wu TL, Lin S, Yue JJ, Cheng YH, Lin SI, Shih MC, Sheen J, Lin YC. DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration. PLANT PHYSIOLOGY 2022; 188:1917-1930. [PMID: 35088855 PMCID: PMC8968427 DOI: 10.1093/plphys/kiac022] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 05/24/2023]
Abstract
Wild tomatoes (Solanum peruvianum) are important genomic resources for tomato research and breeding. Development of a foreign DNA-free clustered regularly interspaced short palindromic repeat (CRISPR)-Cas delivery system has potential to mitigate public concern about genetically modified organisms. Here, we established a DNA-free CRISPR-Cas9 genome editing system based on an optimized protoplast regeneration protocol of S. peruvianum, an important resource for tomato introgression breeding. We generated mutants for genes involved in small interfering RNAs biogenesis, RNA-DEPENDENT RNA POLYMERASE 6 (SpRDR6), and SUPPRESSOR OF GENE SILENCING 3 (SpSGS3); pathogen-related peptide precursors, PATHOGENESIS-RELATED PROTEIN-1 (SpPR-1) and PROSYSTEMIN (SpProSys); and fungal resistance (MILDEW RESISTANT LOCUS O, SpMlo1) using diploid or tetraploid protoplasts derived from in vitro-grown shoots. The ploidy level of these regenerants was not affected by PEG-Ca2+-mediated transfection, CRISPR reagents, or the target genes. By karyotyping and whole genome sequencing analysis, we confirmed that CRISPR-Cas9 editing did not introduce chromosomal changes or unintended genome editing sites. All mutated genes in both diploid and tetraploid regenerants were heritable in the next generation. spsgs3 null T0 regenerants and sprdr6 null T1 progeny had wiry, sterile phenotypes in both diploid and tetraploid lines. The sterility of the spsgs3 null mutant was partially rescued, and fruits were obtained by grafting to wild-type (WT) stock and pollination with WT pollen. The resulting seeds contained the mutated alleles. Tomato yellow leaf curl virus proliferated at higher levels in spsgs3 and sprdr6 mutants than in the WT. Therefore, this protoplast regeneration technique should greatly facilitate tomato polyploidization and enable the use of CRISPR-Cas for S. peruvianum domestication and tomato breeding.
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Affiliation(s)
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Hsuan Yuan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Xing Zheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Qiao-Wei Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Lin Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ting-Li Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Steven Lin
- Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan
| | - Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311, China
| | - Ying-Huey Cheng
- Plant Pathology Division, Taiwan Agricultural Research Institute, Taichung 413, Taiwan
| | - Shu-I Lin
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 106, Taiwan
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22
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Monja-Mio KM, Rescalvo-Morales A, Robert ML. Use of Thin Cell Layer Technique for Induction of Somatic Embryogenesis of Agave fourcroydes. Methods Mol Biol 2022; 2527:59-67. [PMID: 35951183 DOI: 10.1007/978-1-0716-2485-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Agave fourcroydes (henequén) is a plant used for the extraction of hard fiber from its leaves. Due to its long-life cycle, it is very difficult to genetically improve. Somatic embryogenesis (SE) is a very useful micropropagation technique, that can be used for genetic improvement programs and increase the micropropagation of this species. SE is a morphogenic process by which somatic embryos are generated from somatic cells reprogramming. To initiate the regeneration program, the loss of cell-cell communication is suggested to be important. The Thin Cell Layer (TCL) technique allows for the isolation of specific cell or tissue layers, and in conjunction with strictly controlled growth conditions, may lead to the in vitro induction of specific morphogenic programs. Here, we describe a new protocol for the induction of somatic embryogenesis through TCL culture technique, from stem of elite clonal A. fourcroydes vitroplants previously generated through micropropagation of adventitious shoots.
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Affiliation(s)
- Kelly M Monja-Mio
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Mérida, Yucatán, Mexico.
| | | | - Manuel L Robert
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Mérida, Yucatán, Mexico
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23
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Yuan G, Lu H, Weston DJ, Jawdy S, Tschaplinski TJ, Tuskan GA, Yang X. Reporter genes confer new-to-nature ornamental traits in plants. HORTICULTURE RESEARCH 2022; 9:uhac077. [PMID: 35669710 PMCID: PMC9160727 DOI: 10.1093/hr/uhac077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/17/2022] [Indexed: 05/14/2023]
Abstract
This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).
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Affiliation(s)
- Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Corresponding author: ;
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Corresponding author: ;
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24
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Liu S, Wang X, Ding N, Liu Y, Li N, Ma Y, Zhao J, Wang Z, Li X, Fu X, Li L. Nucleotide Sequence Variation in Long-Term Tissue Cultures of Chinese Ginseng ( Panax ginseng C. A. Mey.). PLANTS (BASEL, SWITZERLAND) 2021; 11:79. [PMID: 35009083 PMCID: PMC8747682 DOI: 10.3390/plants11010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022]
Abstract
Plants have the salient biological property of totipotency, i.e., the capacity to regenerate a whole plant from virtually any kind of fully differentiated somatic cells after a process of dedifferentiation. This property has been well-documented by successful plant regeneration from tissue cultures of diverse plant species. However, the accumulation of somaclonal variation, especially karyotype alteration, during the tissue culture process compromises cell totipotency. In this respect, Chinese ginseng (Panax ginseng C. A. Mey.) is an exception in that it shows little decline in cell totipotency accompanied by remarkable chromosomal stability even after prolonged tissue cultures. However, it remains unclear whether chromosomal level stability necessarily couples with molecular genetic stability at the nucleotide sequence level, given that the two types of stabilities are generated by largely distinct mechanisms. Here, we addressed this issue by genome-wide comparisons at the single-base resolution of long-term tissue culture-regenerated P. ginseng plants. We identified abundant single nucleotide polymorphisms (SNPs) that have accumulated in cultured ginseng callus and are retained in the process of plant regeneration. These SNPs did not occur at random but showed differences among chromosomes and biased regional aggregation along a given chromosome. In addition, our results demonstrate that, compared with the overall genes, genes related to processes of cell totipotency and chromosomal stability possess lower mutation rates at both coding and flanking regions. In addition, collectively, the mutated genes exhibited higher expression levels than non-mutated genes and are significantly enriched in fundamental biological processes, including cellular component organization, development, and reproduction. These attributes suggest that the precipitated molecular level genetic variations during the process of regeneration in P. ginseng are likely under selection to fortify normal development. As such, they likely did not undermine chromosomal stability and totipotency of the long-term ginseng cultures.
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Affiliation(s)
- Sitong Liu
- School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Xinfeng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.W.); (N.D.)
| | - Ning Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.W.); (N.D.)
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.L.); (N.L.); (J.Z.); (X.L.)
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.L.); (N.L.); (J.Z.); (X.L.)
| | - Yiqiao Ma
- Jilin Academy of Vegetable and Flower Sciences, Changchun 130033, China;
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.L.); (N.L.); (J.Z.); (X.L.)
| | - Zhenhui Wang
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China;
| | - Xiaomeng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.L.); (N.L.); (J.Z.); (X.L.)
| | - Xueqi Fu
- School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.W.); (N.D.)
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25
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Integrating the Roles for Cytokinin and Auxin in De Novo Shoot Organogenesis: From Hormone Uptake to Signaling Outputs. Int J Mol Sci 2021; 22:ijms22168554. [PMID: 34445260 PMCID: PMC8395325 DOI: 10.3390/ijms22168554] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 12/01/2022] Open
Abstract
De novo shoot organogenesis (DNSO) is a procedure commonly used for the in vitro regeneration of shoots from a variety of plant tissues. Shoot regeneration occurs on nutrient media supplemented with the plant hormones cytokinin (CK) and auxin, which play essential roles in this process, and genes involved in their signaling cascades act as master regulators of the different phases of shoot regeneration. In the last 20 years, the genetic regulation of DNSO has been characterized in detail. However, as of today, the CK and auxin signaling events associated with shoot regeneration are often interpreted as a consequence of these hormones simply being present in the regeneration media, whereas the roles for their prior uptake and transport into the cultivated plant tissues are generally overlooked. Additionally, sucrose, commonly added to the regeneration media as a carbon source, plays a signaling role and has been recently shown to interact with CK and auxin and to affect the efficiency of shoot regeneration. In this review, we provide an integrative interpretation of the roles for CK and auxin in the process of DNSO, adding emphasis on their uptake from the regeneration media and their interaction with sucrose present in the media to their complex signaling outputs that mediate shoot regeneration.
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26
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Giudice G, Moffa L, Varotto S, Cardone MF, Bergamini C, De Lorenzis G, Velasco R, Nerva L, Chitarra W. Novel and emerging biotechnological crop protection approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1495-1510. [PMID: 33945200 PMCID: PMC8384607 DOI: 10.1111/pbi.13605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 05/05/2023]
Abstract
Traditional breeding or genetically modified organisms (GMOs) have for a long time been the sole approaches to effectively cope with biotic and abiotic stresses and implement the quality traits of crops. However, emerging diseases as well as unpredictable climate changes affecting agriculture over the entire globe force scientists to find alternative solutions required to quickly overcome seasonal crises. In this review, we first focus on cisgenesis and genome editing as challenging biotechnological approaches for breeding crops more tolerant to biotic and abiotic stresses. In addition, we take into consideration a toolbox of new techniques based on applications of RNA interference and epigenome modifications, which can be adopted for improving plant resilience. Recent advances in these biotechnological applications are mainly reported for non-model plants and woody crops in particular. Indeed, the characterization of RNAi machinery in plants is fundamental to transform available information into biologically or biotechnologically applicable knowledge. Finally, here we discuss how these innovative and environmentally friendly techniques combined with traditional breeding can sustain a modern agriculture and be of potential contribution to climate change mitigation.
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Affiliation(s)
- Gaetano Giudice
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Department of Agricultural and Environmental Sciences ‐ Production, Landscape, Agroenergy (DiSAA)University of MilanoMilanoItaly
| | - Loredana Moffa
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A)University of UdineUdineItaly
| | - Serena Varotto
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE)University of PadovaLegnaroPDItaly
| | - Maria Francesca Cardone
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)TuriBAItaly
| | - Carlo Bergamini
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)TuriBAItaly
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences ‐ Production, Landscape, Agroenergy (DiSAA)University of MilanoMilanoItaly
| | - Riccardo Velasco
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)TorinoItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)TorinoItaly
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27
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Xu M, Du Q, Tian C, Wang Y, Jiao Y. Stochastic gene expression drives mesophyll protoplast regeneration. SCIENCE ADVANCES 2021; 7:eabg8466. [PMID: 34380624 PMCID: PMC8357238 DOI: 10.1126/sciadv.abg8466] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/22/2021] [Indexed: 05/06/2023]
Abstract
Cell pluripotency is fundamental to biology. It has long been known that differentiated somatic plant cells may reacquire pluripotency, but the underlying mechanism remains elusive. In many plant species, a single isolated mesophyll protoplast may regenerate into an entire plant, which is widely used in gene transformation. Here, we identified two transcription factors whose ectopic activation promotes protoplast regeneration. Furthermore, we found that their expression was induced by protoplast isolation but at a very low frequency. Using live imaging and single-cell transcriptomics, we show that isolating protoplasts induces enhanced expression variation at the genome level. Isolating protoplasts also leads to genome-wide increases in chromatin accessibility, which promotes stochastic activation of gene expression and enhances protoplast regeneration. We propose that transcriptome chaos with increased expression variability among cells creates a cellular-level evolutionary driver selecting for regenerating cells.
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Affiliation(s)
- Mengxue Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingwei Du
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caihuan Tian
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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28
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Histone Deacetylase Inhibitors Increase the Embryogenic Potential and Alter the Expression of Embryogenesis-Related and HDAC-Encoding Genes in Grapevine ( Vitis vinifera L., cv. Mencía). PLANTS 2021; 10:plants10061164. [PMID: 34201224 PMCID: PMC8228518 DOI: 10.3390/plants10061164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/08/2023]
Abstract
The low induction rates of somatic embryogenesis are one of the main limitations in its routine application in the grapevine (Vitis vinifera L.). The use of an induction medium containing histone deacetylase inhibitors (trichostatin A and, mainly, sodium butyrate) resulted in an improvement of the embryogenic responses in grapevine (cv. Mencía) cotyledonary and recently germinated somatic embryos. The relative expression of several grapevine genes related to embryogenic competence or encoding histone deacetylase enzymes was studied in cotyledonary somatic embryos that were cultured in the presence of 0.5 mM sodium butyrate. The results showed a significant overexpression of the BBM and VvSERK2 genes after 24 h of culture, whereas the VvWOX2 gene was underexpressed less in treated versus untreated explants. The results suggest that the inhibitor may trigger a molecular response related to an increase in embryogenic competence and changes in the expression of associated genes. The treatment with sodium butyrate also produced significant variations in the expression of several histone deacetylase enzyme-encoding genes. These results may enhance the possibility of obtaining somatic embryos, reducing the seasonal constraints associated with the use of floral explants in grapevines.
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29
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Luo G, Palmgren M. GRF-GIF Chimeras Boost Plant Regeneration. TRENDS IN PLANT SCIENCE 2021; 26:201-204. [PMID: 33349565 DOI: 10.1016/j.tplants.2020.12.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/20/2020] [Accepted: 12/02/2020] [Indexed: 05/15/2023]
Abstract
Low regeneration efficiency hampers plant transformation. Two independent studies demonstrate that GROWTH-REGULATING FACTORs (GRFs) alone or in chimeras with GRF-INTERACTING FACTOR (GIF) dramatically boost regeneration from tissue cultures from a broad range of species. GRF-GIF chimeras could be a game-changer in plant transformation and gene editing.
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Affiliation(s)
- Guangbin Luo
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Michael Palmgren
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Denmark.
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30
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Abstract
Isolated microspore culture systems have been designed in maize by several groups, mainly from the late 1980s to early 2000s. However, even with optimized protocols, microspore embryogenesis induction has remained very dependent on the genotype in maize, with elite germplasm generally displaying no response or very low response. Yet, these last few years, significant progress has been accomplished in understanding and controlling microspore embryogenesis induction in model dicot and monocot species. This knowledge may be transferred to maize, and isolated microspore culture may gain new interest in this crop, at least for embryogenesis research. The methods we hereby present in detail permit the purification of 3-12 × 105 viable microspores per maize tassel, at the favorable stage for microspore embryogenesis. When cultured in appropriate liquid media, microspores from responsive genotypes give rise to androgenic embryos, which can then be regenerated into fertile doubled haploid plants.
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Affiliation(s)
- Philippe Vergne
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
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31
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Recent Advances in Adventitious Root Formation in Chestnut. PLANTS 2020; 9:plants9111543. [PMID: 33187282 PMCID: PMC7698097 DOI: 10.3390/plants9111543] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/06/2020] [Accepted: 11/05/2020] [Indexed: 01/13/2023]
Abstract
The genus Castanea includes several tree species that are relevant because of their geographical extension and their multipurpose character, that includes nut and timber production. However, commercial exploitation of the trees is hindered by several factors, particularly by their limited regeneration ability. Regardless of recent advances, there exists a serious limitation for the propagation of elite genotypes of chestnut due to decline of rooting ability as the tree ages. In the present review, we summarize the research developed in this genus during the last three decades concerning the formation of adventitious roots (ARs). Focusing on cuttings and in vitro microshoots, we gather the information available on several species, particularly C. sativa, C. dentata and the hybrid C.sativa × C. crenata, and analyze the influence of several factors on the achievements of the applied protocols, including genotype, auxin treatment, light regime and rooting media. We also pay attention to the acclimation phase, as well as compile the information available about biochemical and molecular related aspects. Furthermore, we considerate promising biotechnological approaches that might enable the improvement of the current protocols.
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32
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Tian R, Paul P, Joshi S, Perry SE. Genetic activity during early plant embryogenesis. Biochem J 2020; 477:3743-3767. [PMID: 33045058 PMCID: PMC7557148 DOI: 10.1042/bcj20190161] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Seeds are essential for human civilization, so understanding the molecular events underpinning seed development and the zygotic embryo it contains is important. In addition, the approach of somatic embryogenesis is a critical propagation and regeneration strategy to increase desirable genotypes, to develop new genetically modified plants to meet agricultural challenges, and at a basic science level, to test gene function. We briefly review some of the transcription factors (TFs) involved in establishing primary and apical meristems during zygotic embryogenesis, as well as TFs necessary and/or sufficient to drive somatic embryo programs. We focus on the model plant Arabidopsis for which many tools are available, and review as well as speculate about comparisons and contrasts between zygotic and somatic embryo processes.
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Affiliation(s)
- Ran Tian
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Priyanka Paul
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
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33
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Pasternak T, Lystvan K, Betekhtin A, Hasterok R. From Single Cell to Plants: Mesophyll Protoplasts as a Versatile System for Investigating Plant Cell Reprogramming. Int J Mol Sci 2020; 21:E4195. [PMID: 32545519 PMCID: PMC7348876 DOI: 10.3390/ijms21124195] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/24/2023] Open
Abstract
Plants are sessile organisms that have a remarkable developmental plasticity, which ensures their optimal adaptation to environmental stresses. Plant cell totipotency is an extreme example of such plasticity, whereby somatic cells have the potential to form plants via direct shoot organogenesis or somatic embryogenesis in response to various exogenous and/or endogenous signals. Protoplasts provide one of the most suitable systems for investigating molecular mechanisms of totipotency, because they are effectively single cell populations. In this review, we consider the current state of knowledge of the mechanisms that induce cell proliferation from individual, differentiated somatic plant cells. We highlight initial explant metabolic status, ploidy level and isolation procedure as determinants of successful cell reprogramming. We also discuss the importance of auxin signalling and its interaction with stress-regulated pathways in governing cell cycle induction and further stages of plant cell totipotency.
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Affiliation(s)
- Taras Pasternak
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, 79104 Freiburg, Germany
| | - Kateryna Lystvan
- Institute of Cell Biology and Genetic Engineering of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine;
| | - Alexander Betekhtin
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland;
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland;
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Wójcikowska B, Wójcik AM, Gaj MD. Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants. Int J Mol Sci 2020; 21:ijms21072307. [PMID: 32225116 PMCID: PMC7177879 DOI: 10.3390/ijms21072307] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 12/22/2022] Open
Abstract
Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.
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Matand K, Shoemake M, Li C. High frequency in vitro regeneration of adventitious shoots in daylilies (Hemerocallis sp) stem tissue using thidiazuron. BMC PLANT BIOLOGY 2020; 20:31. [PMID: 31959097 PMCID: PMC6971949 DOI: 10.1186/s12870-020-2243-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/08/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Daylilies are a lucrative crop used for its floral beauty, medicinal proprieties, landscaping, fire prevention, nutritional value, and research. Despite the importance, daylilies remain extremely challenging for multiplying in vitro. The response difficulty is exacerbated because a few good protocols for daylilies micropropagation are generally difficult to reproduce across genotypes. An efficient strategy, currently applied at Langston University, is to systematically explore individual tissues or organs for their potential to micropropagation. This article is a partial report of the investigation carried out under room environmental conditions and focuses on developing an efficient daylilies in vitro propagation protocol that uses the stem tissue as the principal explant. RESULTS In less than three months, using thidiazuron, the use of the stem tissue as the in vitro experimental explant was successful in inducing multiple shoots several folds greater than current daylilies shoot organogenesis protocols. The study showed that tissue culture can be conducted successfully under unrestricted room environmental conditions as well as under the controlled environment of a growth chamber. It also showed that splitting lengthwise stem explants formed multiple shoots several folds greater than cross-sectioned and inverted explants. Shoot conversion rate was mostly independent of the number of shoots formed per explants. The overall response was explant and genotype-dependent. Efficient responses were observed in all thidiazuron treatments. CONCLUSION An efficient protocol, which can be applied for mass multiple shoots formation using the daylilies stem tissue as the main explant, was successfully developed. This could lead to a broad and rapid propagation of the crop under an array of environmental conditions to meet the market demand and hasten exogenous gene transfer and breeding selection processes.
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Affiliation(s)
- Kanyand Matand
- Center for Biotechnology Research and Education, Langston, USA.
| | - Meordrick Shoemake
- Undergraduate Student in the Department of Agriculture and Natural Resources, School of Agriculture and Applied Sciences, Langston University, Langston, OK, 73050, USA
| | - Chenxin Li
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, 95616, USA
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Savina MS, Pasternak T, Omelyanchuk NA, Novikova DD, Palme K, Mironova VV, Lavrekha VV. Cell Dynamics in WOX5-Overexpressing Root Tips: The Impact of Local Auxin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:560169. [PMID: 33193486 PMCID: PMC7642516 DOI: 10.3389/fpls.2020.560169] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/16/2020] [Indexed: 05/18/2023]
Abstract
Root stem cell niche functioning requires the formation and maintenance of the specific "auxin-rich domain" governed by directional auxin transport and local auxin production. Auxin maximum co-localizes with the WOX5 expression domain in the quiescent center that separates mitotically active proximal and distal root meristems. Here we unravel the interconnected processes happening under WOX5 overexpression by combining in vivo experiments and mathematical modeling. We showed that WOX5-induced TAA1-mediated auxin biosynthesis is the cause, whereas auxin accumulation, PIN transporters relocation, and auxin redistribution between proximal and distal root meristems are its subsequent effects that influence the formation of the well-described phenotype with an enlarged root cap. These findings helped us to clarify the role of WOX5, which serves as a local QC-specific regulator that activates biosynthesis of non-cell-autonomous signal auxin to regulate the distal meristem functioning. The mathematical model with WOX5-mediated auxin biosynthesis and auxin-regulated cell growth, division, and detachment reproduces the columella cells dynamics in both wild type and under WOX5 dysregulation.
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Affiliation(s)
- Maria S. Savina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
| | - Taras Pasternak
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Freiburg, Germany
| | | | | | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Freiburg, Germany
| | - Victoria V. Mironova
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
- LCTEB, Novosibirsk State University, Novosibirsk, Russia
| | - Viktoriya V. Lavrekha
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
- LCTEB, Novosibirsk State University, Novosibirsk, Russia
- *Correspondence: Viktoriya V. Lavrekha,
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Ichihashi Y, Hakoyama T, Iwase A, Shirasu K, Sugimoto K, Hayashi M. Common Mechanisms of Developmental Reprogramming in Plants-Lessons From Regeneration, Symbiosis, and Parasitism. FRONTIERS IN PLANT SCIENCE 2020; 11:1084. [PMID: 32765565 PMCID: PMC7378864 DOI: 10.3389/fpls.2020.01084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/30/2020] [Indexed: 05/09/2023]
Abstract
Most plants are exquisitely sensitive to their environment and adapt by reprogramming post-embryonic development. The systematic understanding of molecular mechanisms regulating developmental reprogramming has been underexplored because abiotic and biotic stimuli that lead to reprogramming of post-embryonic development vary and the outcomes are highly species-specific. In this review, we discuss the diversity and similarities of developmental reprogramming processes by summarizing recent key findings in reprogrammed development: plant regeneration, nodule organogenesis in symbiosis, and haustorial formation in parasitism. We highlight the potentially shared molecular mechanisms across the different developmental programs, especially a core network module mediated by the AUXIN RESPONSIVE FACTOR (ARF) and the LATERAL ORGAN BOUNDARIES DOMAIN (LBD) family of transcription factors. This allows us to propose a new holistic concept that will provide insights into the nature of plant development, catalyzing the fusion of subdisciplines in plant developmental biology.
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Affiliation(s)
- Yasunori Ichihashi
- RIKEN BioResource Research Center, Tsukuba, Japan
- *Correspondence: Yasunori Ichihashi,
| | - Tsuneo Hakoyama
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Makoto Hayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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Kong J, Martin-Ortigosa S, Finer J, Orchard N, Gunadi A, Batts LA, Thakare D, Rush B, Schmitz O, Stuiver M, Olhoft P, Pacheco-Villalobos D. Overexpression of the Transcription Factor GROWTH-REGULATING FACTOR5 Improves Transformation of Dicot and Monocot Species. FRONTIERS IN PLANT SCIENCE 2020; 11:572319. [PMID: 33154762 PMCID: PMC7585916 DOI: 10.3389/fpls.2020.572319] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/21/2020] [Indexed: 05/08/2023]
Abstract
Successful regeneration of genetically modified plants from cell culture is highly dependent on the species, genotype, and tissue-type being targeted for transformation. Studies in some plant species have shown that when expression is altered, some genes regulating developmental processes are capable of triggering plant regeneration in a variety of plant cells and tissue-types previously identified as being recalcitrant to regeneration. In the present research, we report that developmental genes encoding GROWTH-REGULATING FACTORS positively enhance regeneration and transformation in both monocot and dicot species. In sugar beet (Beta vulgaris ssp. vulgaris), ectopic expression of Arabidopsis GRF5 (AtGRF5) in callus cells accelerates shoot formation and dramatically increases transformation efficiency. More importantly, overexpression of AtGRF5 enables the production of stable transformants in recalcitrant sugar beet varieties. The introduction of AtGRF5 and GRF5 orthologs into canola (Brassica napus L.), soybean (Glycine max L.), and sunflower (Helianthus annuus L.) results in significant increases in genetic transformation of the explant tissue. A positive effect on proliferation of transgenic callus cells in canola was observed upon overexpression of GRF5 genes and AtGRF6 and AtGRF9. In soybean and sunflower, the overexpression of GRF5 genes seems to increase the proliferation of transformed cells, promoting transgenic shoot formation. In addition, the transformation of two putative AtGRF5 orthologs in maize (Zea mays L.) significantly boosts transformation efficiency and resulted in fully fertile transgenic plants. Overall, the results suggest that overexpression of GRF genes render cells and tissues more competent to regeneration across a wide variety of crop species and regeneration processes. This sets GRFs apart from other developmental regulators and, therefore, they can potentially be applied to improve transformation of monocot and dicot plant species.
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Affiliation(s)
- Jixiang Kong
- Plant Cell & Transformation Technologies, Research & Development, KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Susana Martin-Ortigosa
- Plant Cell & Transformation Technologies, Research & Development, KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - John Finer
- OSU Plant Transformation Laboratory, College of Food, Agricultural and Environmental Sciences, Department of Horticulture and Crop Science, The Ohio State University, OH, United States
| | - Nuananong Orchard
- OSU Plant Transformation Laboratory, College of Food, Agricultural and Environmental Sciences, Department of Horticulture and Crop Science, The Ohio State University, OH, United States
| | - Andika Gunadi
- OSU Plant Transformation Laboratory, College of Food, Agricultural and Environmental Sciences, Department of Horticulture and Crop Science, The Ohio State University, OH, United States
| | - Lou Ann Batts
- BASF Corporation, Research Triangle Park, NC, United States
| | | | - Bradford Rush
- BASF Corporation, Research Triangle Park, NC, United States
| | | | - Maarten Stuiver
- BASF Belgium Coordination Center—Business Belux (Branch), Gent Zwijnaarde, Belgium
| | - Paula Olhoft
- BASF Corporation, Research Triangle Park, NC, United States
- *Correspondence: Paula Olhoft, ; David Pacheco-Villalobos,
| | - David Pacheco-Villalobos
- Plant Cell & Transformation Technologies, Research & Development, KWS SAAT SE & Co. KGaA, Einbeck, Germany
- *Correspondence: Paula Olhoft, ; David Pacheco-Villalobos,
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Primed histone demethylation regulates shoot regenerative competency. Nat Commun 2019; 10:1786. [PMID: 30992430 PMCID: PMC6467990 DOI: 10.1038/s41467-019-09386-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 03/07/2019] [Indexed: 01/09/2023] Open
Abstract
Acquisition of pluripotency by somatic cells is a striking process that enables multicellular organisms to regenerate organs. This process includes silencing of genes to erase original tissue memory and priming of additional cell type specification genes, which are then poised for activation by external signal inputs. Here, through analysis of genome-wide histone modifications and gene expression profiles, we show that a gene priming mechanism involving LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3) specifically eliminates H3K4me2 during formation of the intermediate pluripotent cell mass known as callus derived from Arabidopsis root cells. While LDL3-mediated H3K4me2 removal does not immediately affect gene expression, it does facilitate the later activation of genes that act to form shoot progenitors when external cues lead to shoot induction. These results give insights into the role of H3K4 methylation in plants, and into the primed state that provides plant cells with high regenerative competency. Plant regeneration can occur via formation of a mass of pluripotent cells known as callus. Here, Ishihara et al. show that acquisition of regenerative capacity of callus-forming cells requires a lysine-specific demethylase that removes H3K4me2 to prime gene expression in response to regenerative cues.
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Roeder AH, Jill Harrison C. Editorial overview: Scaling development through the plant tree of life. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:A1-A4. [PMID: 30850085 DOI: 10.1016/j.pbi.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Adrienne Hk Roeder
- Weill Institute for Cell and Molecular Biology and Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
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Du X, Fang T, Liu Y, Huang L, Zang M, Wang G, Liu Y, Fu J. Transcriptome Profiling Predicts New Genes to Promote Maize Callus Formation and Transformation. FRONTIERS IN PLANT SCIENCE 2019; 10:1633. [PMID: 31921272 PMCID: PMC6934073 DOI: 10.3389/fpls.2019.01633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/20/2019] [Indexed: 05/17/2023]
Abstract
Maize transformation is highly based on the formation of embryonic callus, which is mainly derived from scutellum cells of the immature maize embryo. However, only a few genes involved in callus induction have been identified in maize. To reveal the potential genes involved in the callus induction of maize, we carried out a high-throughput RNA sequencing on embryos that were cultured for 0, 1, 2, 4, 6, and 8 days, respectively, on a medium containing or lacking 2,4-dichlorophenoxyacetic acid. In total, 7,525 genes were found to be induced by 2,4-dichlorophenoxyacetic acid and categorized into eight clusters, with clusters 2 and 3 showing an increasing trend related to signal transmission, signal transduction, iron ion binding, and heme binding. Among the induced genes, 659 transcription factors belong to 51 families. An AP2 transcription factors, ZmBBM2, was dramatically and rapidly induced by auxin and further characterization showed that overexpression of ZmBBM2 can promote callus induction and proliferation in three inbred maize lines. Therefore, our comprehensive analyses provide some insight into the early molecular regulations during callus induction and are useful for further identification of the regulators governing callus formation.
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Affiliation(s)
- Xuemei Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Fang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liying Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Maosen Zang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yunjun Liu, ; Junjie Fu,
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yunjun Liu, ; Junjie Fu,
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