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Islam MR, Youngblood M, Kim HI, González-Gamboa I, Monroy-Borrego AG, Caparco AA, Lowry GV, Steinmetz NF, Giraldo JP. DNA Delivery by Virus-Like Nanocarriers in Plant Cells. NANO LETTERS 2024. [PMID: 38887996 DOI: 10.1021/acs.nanolett.3c04735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Tobacco mild green mosaic virus (TMGMV)-like nanocarriers were designed for gene delivery to plant cells. High aspect ratio TMGMVs were coated with a polycationic biopolymer, poly(allylamine) hydrochloride (PAH), to generate highly charged nanomaterials (TMGMV-PAH; 56.20 ± 4.7 mV) that efficiently load (1:6 TMGMV:DNA mass ratio) and deliver single-stranded and plasmid DNA to plant cells. The TMGMV-PAH were taken up through energy-independent mechanisms in Arabidopsis protoplasts. TMGMV-PAH delivered a plasmid DNA encoding a green fluorescent protein (GFP) to the protoplast nucleus (70% viability), as evidenced by GFP expression using confocal microscopy and Western blot analysis. TMGMV-PAH were inactivated (iTMGMV-PAH) using UV cross-linking to prevent systemic infection in intact plants. Inactivated iTMGMV-PAH-mediated pDNA delivery and gene expression of GFP in vivo was determined using confocal microscopy and RT-qPCR. Virus-like nanocarrier-mediated gene delivery can act as a facile and biocompatible tool for advancing genetic engineering in plants.
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Affiliation(s)
- Md Reyazul Islam
- Department of Botany and Plant Sciences, University of California, Riverside, California 92507, United States
| | - Marina Youngblood
- Department of Botany and Plant Sciences, University of California, Riverside, California 92507, United States
| | - Hye-In Kim
- Department of Botany and Plant Sciences, University of California, Riverside, California 92507, United States
| | - Ivonne González-Gamboa
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Adam A Caparco
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Gregory V Lowry
- Department of Civil and Environmental Engineering and Center for Environmental Implications of NanoTechnology (CEINT), Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, Department of Radiology, Center for Nano-Immuno Engineering, Shu and K.C. Chien and Peter Farrell Collaboratory, Institute for Materials Discovery and Design, Moores Cancer Center, and Center for Engineering in Cancer, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Juan Pablo Giraldo
- Department of Botany and Plant Sciences, University of California, Riverside, California 92507, United States
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2
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Nien YC, Vanek A, Axtell MJ. Trans-Species Mobility of RNA Interference between Plants and Associated Organisms. PLANT & CELL PHYSIOLOGY 2024; 65:694-703. [PMID: 38288670 DOI: 10.1093/pcp/pcae012] [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: 10/13/2023] [Revised: 01/09/2024] [Accepted: 01/24/2024] [Indexed: 05/31/2024]
Abstract
Trans-species RNA interference (RNAi) occurs naturally when small RNAs (sRNAs) silence genes in species different from their origin. This phenomenon has been observed between plants and various organisms including fungi, animals and other plant species. Understanding the mechanisms used in natural cases of trans-species RNAi, such as sRNA processing and movement, will enable more effective development of crop protection methods using host-induced gene silencing (HIGS). Recent progress has been made in understanding the mechanisms of cell-to-cell and long-distance movement of sRNAs within individual plants. This increased understanding of endogenous plant sRNA movement may be translatable to trans-species sRNA movement. Here, we review diverse cases of natural trans-species RNAi focusing on current theories regarding intercellular and long-distance sRNA movement. We also touch on trans-species sRNA evolution, highlighting its research potential and its role in improving the efficacy of HIGS.
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Affiliation(s)
- Ya-Chi Nien
- Plant Biology Intercollege Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Allison Vanek
- Bioinformatics and Genomics Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Plant Biology Intercollege Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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3
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Chen Y, Li Y, Luo G, Luo C, Xiao Z, Lu Y, Xiang Z, Hou Z, Xiao Q, Zhou Y, Tang Q. Gene identification, expression analysis, and molecular docking of SAT and OASTL in the metabolic pathway of selenium in Cardamine hupingshanensis. PLANT CELL REPORTS 2024; 43:148. [PMID: 38775862 PMCID: PMC11111505 DOI: 10.1007/s00299-024-03227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
KEY MESSAGE Identification of selenium stress-responsive expression and molecular docking of serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) in Cardamine hupingshanensis. A complex coupled with serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) is the key enzyme that catalyzes selenocysteine (Sec) synthesis in plants. The functions of SAT and OASTL genes were identified in some plants, but it is still unclear whether SAT and OASTL are involved in the selenium metabolic pathway in Cardamine hupingshanensis. In this study, genome-wide identification and comparative analysis of ChSATs and ChOASTLs were performed. The eight ChSAT genes were divided into three branches, and the thirteen ChOASTL genes were divided into four branches by phylogenetic analysis and sequence alignment, indicating the evolutionary conservation of the gene structure and its association with other plant species. qRT-PCR analysis showed that the ChSAT and ChOASTL genes were differentially expressed in different tissues under various selenium levels, suggesting their important roles in Sec synthesis. The ChSAT1;2 and ChOASTLA1;2 were silenced by the VIGS system to investigate their involvement in selenium metabolites in C. hupingshanensis. The findings contribute to understanding the gene functions of ChSATs and ChOASTLs in the selenium stress and provide a reference for further exploration of the selenium metabolic pathway in plants.
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Affiliation(s)
- Yushan Chen
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, 44500, China
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Yao Li
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Guoqiang Luo
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Cihang Luo
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Zhijing Xiao
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Yanke Lu
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Zhixin Xiang
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Zhi Hou
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Qiang Xiao
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, 44500, China
- College of Forestry and Horticulture, Hubei Minzu University, Enshi, 44500, China
| | - Yifeng Zhou
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, 44500, China.
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China.
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China.
| | - Qiaoyu Tang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, 44500, China.
- College of Forestry and Horticulture, Hubei Minzu University, Enshi, 44500, China.
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Lei S, Zhu Y, Jia W, Zhang J, Chi Y, Xu B. A protoplast-based transient gene expression assay for the identification of heat and oxidative stress-regulatory genes in perennial ryegrass. PLANT METHODS 2024; 20:67. [PMID: 38725058 PMCID: PMC11080139 DOI: 10.1186/s13007-024-01192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND With the accumulating omics data, an efficient and time-saving transient assay to express target genes is desired. Mesophyll protoplasts, maintaining most stress-physiological responses and cellular activities as intact plants, offer an alternative transient assay to study target genes' effects on heat and oxidative stress responses. RESULTS In this study, a perennial ryegrass (Lolium perenne L.) mesophyll protoplast-based assay was established to effectively over- or down-regulate target genes. The relative expression levels of the target genes could be quantified using RT-qPCR, and the effects of heat and H2O2-induced oxidative stress on protoplasts' viability could be quantitatively measured. The practicality of the assay was demonstrated by identifying the potential thermos-sensor genes LpTT3.1/LpTT3.2 in ryegrass that over-expressing these genes significantly altered protoplasts' viability rates after heat stress. CONCLUSION This protoplast-based rapid stress regulatory gene identification assay was briefed as 'PRIDA' that will complement the stable genetic transformation studies to rapidly identify candidate stress-regulatory genes in perennial ryegrass and other grass species.
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Affiliation(s)
- Shanshan Lei
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yaolong Zhu
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Weiyu Jia
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jing Zhang
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yingjun Chi
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Bin Xu
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Morey K, Khakhar A. Exploring the frontier of rapid prototyping technologies for plant synthetic biology and what could lie beyond. THE NEW PHYTOLOGIST 2024; 242:903-908. [PMID: 38426415 DOI: 10.1111/nph.19650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
Realizing the full potential of plant synthetic biology both to elucidate the relationship between genotype and phenotype and to apply these insights to engineer traits requires rapidly iterating through design-build-test cycles. However, the months-long process of transgenesis, the long generation times, and the size-based limitations on experimentation have stymied progress by limiting the speed and scale of these cycles. Herein, we review a representative sample of recent studies that demonstrate a variety of rapid prototyping technologies that overcome some of these bottlenecks and accelerate progress. However, each of them has caveats that limit their broad utility. Their complementary strengths and weaknesses point to the intriguing possibility that these strategies could be combined in the future to enable rapid and scalable deployment of synthetic biology in plants.
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Affiliation(s)
- Kevin Morey
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80525, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80525, USA
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6
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Becker A, Bachelier JB, Carrive L, Conde E Silva N, Damerval C, Del Rio C, Deveaux Y, Di Stilio VS, Gong Y, Jabbour F, Kramer EM, Nadot S, Pabón-Mora N, Wang W. A cornucopia of diversity-Ranunculales as a model lineage. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1800-1822. [PMID: 38109712 DOI: 10.1093/jxb/erad492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
The Ranunculales are a hyperdiverse lineage in many aspects of their phenotype, including growth habit, floral and leaf morphology, reproductive mode, and specialized metabolism. Many Ranunculales species, such as opium poppy and goldenseal, have a high medicinal value. In addition, the order includes a large number of commercially important ornamental plants, such as columbines and larkspurs. The phylogenetic position of the order with respect to monocots and core eudicots and the diversity within this lineage make the Ranunculales an excellent group for studying evolutionary processes by comparative studies. Lately, the phylogeny of Ranunculales was revised, and genetic and genomic resources were developed for many species, allowing comparative analyses at the molecular scale. Here, we review the literature on the resources for genetic manipulation and genome sequencing, the recent phylogeny reconstruction of this order, and its fossil record. Further, we explain their habitat range and delve into the diversity in their floral morphology, focusing on perianth organ identity, floral symmetry, occurrences of spurs and nectaries, sexual and pollination systems, and fruit and dehiscence types. The Ranunculales order offers a wealth of opportunities for scientific exploration across various disciplines and scales, to gain novel insights into plant biology for researchers and plant enthusiasts alike.
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Affiliation(s)
- Annette Becker
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Giessen, Germany
| | - Julien B Bachelier
- Institute of Biology/Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Laetitia Carrive
- Université de Rennes, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Natalia Conde E Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Cédric Del Rio
- CR2P - Centre de Recherche en Paléontologie - Paris, MNHN - Sorbonne Université - CNRS, 43 Rue Buffon, 75005 Paris, France
| | - Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | | | - Yan Gong
- Department of Organismic and Evolutionary Biology, Harvard University, MA, 02138, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, Paris, 75005, France
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, MA, 02138, USA
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie, Systématique et Evolution, Gif-sur-Yvette, France
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China and University of Chinese Academy of Sciences, Beijing, 100049China
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7
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Campa M, Miranda S, Licciardello C, Lashbrooke JG, Dalla Costa L, Guan Q, Spök A, Malnoy M. Application of new breeding techniques in fruit trees. PLANT PHYSIOLOGY 2024; 194:1304-1322. [PMID: 37394947 DOI: 10.1093/plphys/kiad374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
Climate change and rapid adaption of invasive pathogens pose a constant pressure on the fruit industry to develop improved varieties. Aiming to accelerate the development of better-adapted cultivars, new breeding techniques have emerged as a promising alternative to meet the demand of a growing global population. Accelerated breeding, cisgenesis, and CRISPR/Cas genome editing hold significant potential for crop trait improvement and have proven to be useful in several plant species. This review focuses on the successful application of these technologies in fruit trees to confer pathogen resistance and tolerance to abiotic stress and improve quality traits. In addition, we review the optimization and diversification of CRISPR/Cas genome editing tools applied to fruit trees, such as multiplexing, CRISPR/Cas-mediated base editing and site-specific recombination systems. Advances in protoplast regeneration and delivery techniques, including the use of nanoparticles and viral-derived replicons, are described for the obtention of exogenous DNA-free fruit tree species. The regulatory landscape and broader social acceptability for cisgenesis and CRISPR/Cas genome editing are also discussed. Altogether, this review provides an overview of the versatility of applications for fruit crop improvement, as well as current challenges that deserve attention for further optimization and potential implementation of new breeding techniques.
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Affiliation(s)
- Manuela Campa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Simón Miranda
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Concetta Licciardello
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
| | | | - Lorenza Dalla Costa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Armin Spök
- Science, Technology and Society Unit, Graz University of Technology, Graz, Austria
| | - Mickael Malnoy
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
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Larriba E, Yaroshko O, Pérez-Pérez JM. Recent Advances in Tomato Gene Editing. Int J Mol Sci 2024; 25:2606. [PMID: 38473859 DOI: 10.3390/ijms25052606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The use of gene-editing tools, such as zinc finger nucleases, TALEN, and CRISPR/Cas, allows for the modification of physiological, morphological, and other characteristics in a wide range of crops to mitigate the negative effects of stress caused by anthropogenic climate change or biotic stresses. Importantly, these tools have the potential to improve crop resilience and increase yields in response to challenging environmental conditions. This review provides an overview of gene-editing techniques used in plants, focusing on the cultivated tomatoes. Several dozen genes that have been successfully edited with the CRISPR/Cas system were selected for inclusion to illustrate the possibilities of this technology in improving fruit yield and quality, tolerance to pathogens, or responses to drought and soil salinity, among other factors. Examples are also given of how the domestication of wild species can be accelerated using CRISPR/Cas to generate new crops that are better adapted to the new climatic situation or suited to use in indoor agriculture.
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Affiliation(s)
- Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Olha Yaroshko
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
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9
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Geng S, Gao W, Li S, Chen Q, Jiao Y, Zhao J, Wang Y, Wang T, Qu Y, Chen Q. Rapidly mining candidate cotton drought resistance genes based on key indicators of drought resistance. BMC PLANT BIOLOGY 2024; 24:129. [PMID: 38383284 PMCID: PMC10880307 DOI: 10.1186/s12870-024-04801-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Focusing on key indicators of drought resistance is highly important for quickly mining candidate genes related to drought resistance in cotton. RESULTS In the present study, drought resistance was identified in drought resistance-related RIL populations during the flowering and boll stages, and multiple traits were evaluated; these traits included three key indicators: plant height (PH), single boll weight (SBW) and transpiration rate (Tr). Based on these three key indicators, three groups of extreme mixing pools were constructed for BSA-seq. Based on the mapping interval of each trait, a total of 6.27 Mb QTL intervals were selected on chromosomes A13 (3.2 Mb), A10 (2.45 Mb) and A07 (0.62 Mb) as the focus of this study. Based on the annotation information and qRT‒PCR analysis, three key genes that may be involved in the drought stress response of cotton were screened: GhF6'H1, Gh3AT1 and GhPER55. qRT‒PCR analysis of parental and extreme germplasm materials revealed that the expression of these genes changed significantly under drought stress. Cotton VIGS experiments verified the important impact of key genes on cotton drought resistance. CONCLUSIONS This study focused on the key indicators of drought resistance, laying the foundation for the rapid mining of drought-resistant candidate genes in cotton and providing genetic resources for directed molecular breeding of drought resistance in cotton.
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Affiliation(s)
- Shiwei Geng
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Wenju Gao
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Shengmei Li
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Qin Chen
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yang Jiao
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Jieyin Zhao
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yuxiang Wang
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - TingWei Wang
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yanying Qu
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Quanjia Chen
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China.
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10
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Panwar V, Bakkeren G. Editorial: Plant genomics and pathogenomics: from technology to application in improving crop disease resistance. FRONTIERS IN PLANT SCIENCE 2024; 15:1349113. [PMID: 38410730 PMCID: PMC10895055 DOI: 10.3389/fpls.2024.1349113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/15/2024] [Indexed: 02/28/2024]
Affiliation(s)
- Vinay Panwar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland, BC, Canada
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11
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Liu Y, Lyu R, Singleton JJ, Patra B, Pattanaik S, Yuan L. A Cotyledon-based Virus-Induced Gene Silencing (Cotyledon-VIGS) approach to study specialized metabolism in medicinal plants. PLANT METHODS 2024; 20:26. [PMID: 38347628 PMCID: PMC10860238 DOI: 10.1186/s13007-024-01154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Virus-induced gene silencing (VIGS) is widely used in plant functional genomics. However, the efficiency of VIGS in young plantlets varies across plant species. Additionally, VIGS is not optimized for many plant species, especially medicinal plants that produce valuable specialized metabolites. RESULTS We evaluated the efficacy of five-day-old, etiolated seedlings of Catharanthus roseus (periwinkle) for VIGS. The seedlings were vacuum-infiltrated with Agrobacterium tumefaciens GV3101 cells carrying the tobacco rattle virus (TRV) vectors. The protoporphyrin IX magnesium chelatase subunit H (ChlH) gene, a key gene in chlorophyll biosynthesis, was used as the target for VIGS, and we observed yellow cotyledons 6 days after infiltration. As expected, the expression of CrChlH and the chlorophyll contents of the cotyledons were significantly decreased after VIGS. To validate the cotyledon based-VIGS method, we silenced the genes encoding several transcriptional regulators of the terpenoid indole alkaloid (TIA) biosynthesis in C. roseus, including two activators (CrGATA1 and CrMYC2) and two repressors (CrGBF1 and CrGBF2). Silencing CrGATA1 led to downregulation of the vindoline pathway genes (T3O, T3R, and DAT) and decreased vindoline contents in cotyledons. Silencing CrMYC2, followed by elicitation with methyl jasmonate (MeJA), resulted in the downregulation of ORCA2 and ORCA3. We also co-infiltrated C. roseus seedlings with TRV vectors that silence both CrGBF1 and CrGBF2 and overexpress CrMYC2, aiming to simultaneous silencing two repressors while overexpressing an activator. The simultaneous manipulation of repressors and activator resulted in significant upregulation of the TIA pathway genes. To demonstrate the broad application of the cotyledon-based VIGS method, we optimized the method for two other valuable medicinal plants, Glycyrrhiza inflata (licorice) and Artemisia annua (sweet wormwood). When TRV vectors carrying the fragments of the ChlH genes were infiltrated into the seedlings of these plants, we observed yellow cotyledons with decreased chlorophyll contents. CONCLUSIONS The widely applicable cotyledon-based VIGS method is faster, more efficient, and easily accessible to additional treatments than the traditional VIGS method. It can be combined with transient gene overexpression to achieve simultaneous up- and down-regulation of desired genes in non-model plants. This method provides a powerful tool for functional genomics of medicinal plants, facilitating the discovery and production of valuable therapeutic compounds.
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Affiliation(s)
- Yongliang Liu
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Ruiqing Lyu
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Joshua J Singleton
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Barunava Patra
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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12
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Nagalakshmi U, Meier N, Dinesh-Kumar SP. Virus-Induced Heritable Gene Editing in Plants. Methods Mol Biol 2024; 2724:273-288. [PMID: 37987913 DOI: 10.1007/978-1-0716-3485-1_20] [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: 11/22/2023]
Abstract
Gene editing using clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) nuclease is an excellent tool for assessing gene function in plants. However, delivery of CRISPR/Cas-editing components into plant cells is still a major bottleneck and requires tissue culture-based approaches and regeneration of plants. To overcome this limitation, several plant viral vectors have recently been engineered to deliver single-guide RNA (sgRNA) targets into SpCas9-expressing plants. Here, we describe an optimized, step-by-step protocol based on the tobacco rattle virus (TRV)-based vector system to deliver sgRNAs fused to mobile tRNA sequences for efficient heritable editing in Nicotiana benthamiana and Arabidopsis thaliana model systems. The protocol described here could be adopted to study the function of any gene of interest.
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Affiliation(s)
- Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA.
| | - Nathan Meier
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA.
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13
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Bellinazzo F. Advances in virus-induced flowering in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1-4. [PMID: 38128901 PMCID: PMC10735631 DOI: 10.1093/jxb/erad407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This article comments on:Deng Y, Yarur-Thys A, Baulcombe DC. 2024. Virus-induced overexpression of heterologous FLOWERING LOCUS T for efficient speed breeding in tomato. Journal of Experimental Botany 75, 36–44.
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Affiliation(s)
- Francesca Bellinazzo
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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14
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Yao L, Wu X, Jiang X, Shan M, Zhang Z, Li Y, Yang A, Li Y, Yang C. Subcellular compartmentalization in the biosynthesis and engineering of plant natural products. Biotechnol Adv 2023; 69:108258. [PMID: 37722606 DOI: 10.1016/j.biotechadv.2023.108258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.
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Affiliation(s)
- Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xun Jiang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Zhuoxiang Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yiting Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Changqing Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China.
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15
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Li J, Wang L, Ackah M, Amoako FK, Jiang Z, Shi Y, Li H, Zhao W. The Competing Endogenous RNAs Regulatory Genes Network Mediates Leaf Shape Variation and Main Effector Gene Function in Mulberry Plant ( Morus alba). Int J Mol Sci 2023; 24:16860. [PMID: 38069181 PMCID: PMC10706577 DOI: 10.3390/ijms242316860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Mulberry plants (Morus alba) have leaf shapes, ranging from unlobed to lobed, which are crucial for yield, growth, and adaptability, indicating their ability to adapt to their environment. Competing endogenous RNAs (ceRNAs) constitute a web of RNAs within the organism's transcriptional regulatory system, including protein-coding genes (mRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and others. In this study, samples for ceRNA sequencing were categorized into two groups: whole leaves and lobed leaves, each group with three replicates. In addition, we isolated, cloned, and characterized the precursor miRNA (miR156x) from the leaves of M. alba. miR156x precursor had a length of 107 base pairs and a minimum folding free energy of 50.27 kcal/mol. We constructed a pCAMBIA-35S-GUS-miR156x dual overexpression vector and established a transient transformation system for mulberry. At an optimal transformation solution (OD600 = 0.7), the GUS gene showed a higher expression in the leaves of transiently transformed mulberry with miR156x overexpression, four days after transformation, while the target genes of miR156x had decreased expression in the same leaves. Investigations into the transgenic mulberry plants uncovered various modifications to physio-chemical parameters including POD, SOD, PRO, MDA, soluble proteins and sugars, and chlorophyl content. miRNAs in the plants were found to act as negative regulators of gene expression in response to changes in leaf shape regulation, which was confirmed in vitro using dual-luciferase reporter assays. Subsequently, we cloned Maspl3 in vitro and conducted GST-Pull down assays, obtaining multiple proteins that interacted with the Maspl3 gene. This indicates that the miR156x/Maspl3/MSTRG.25812.1 regulatory module contributes to the differences in mulberry leaf shape.
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Affiliation(s)
- Jianbin Li
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (J.L.); (Z.J.); (Y.S.); (H.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Lei Wang
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (J.L.); (Z.J.); (Y.S.); (H.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Michael Ackah
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (J.L.); (Z.J.); (Y.S.); (H.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Frank Kwarteng Amoako
- Institute of Plant Nutrition and Soil Science, Kiel University, Hermann-Rodewald-Straße 2, 24118 Kiel, Germany;
| | - Zijie Jiang
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (J.L.); (Z.J.); (Y.S.); (H.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Yisu Shi
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (J.L.); (Z.J.); (Y.S.); (H.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Haonan Li
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (J.L.); (Z.J.); (Y.S.); (H.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (J.L.); (Z.J.); (Y.S.); (H.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
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16
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Li J, Liu X, Ahmad N, Wang Y, Ge H, Wang Y, Liu W, Li X, Wang N, Wang F, Dong Y. CePP2C19 confers tolerance to drought by regulating the ABA sensitivity in Cyperus esculentus. BMC PLANT BIOLOGY 2023; 23:524. [PMID: 37898801 PMCID: PMC10612301 DOI: 10.1186/s12870-023-04522-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023]
Abstract
BACKGROUND Tiger nut (Cyperus esculentus) is widely known as an additional source of food, oil and feed worldwide. The agricultural production of tiger nut has been greatly hindered by drought stress, reducing both yield and quality. Protein phosphatase 2 C (PP2Cs) plays an important role in plant responses to drought stress however, the molecular mechanism of PP2Cs in tiger nuts still unclear. RESULTS In this study, we identified a putative group A PP2C-encoding gene (CePP2C19) from tiger nut using transcriptome analysis, which is highly induced by drought stress. The transient expression assay suggested that CePP2C19 was localized to nucleus. Furthermore, the interaction between CePP2C19 and CePYR1, a coreceptor for ABA signaling, was first detected using a yeast two-hybrid assay and then verified using a bimolecular fluorescence complementation (BiFC) analysis. In addition, the transgenic Arabidopsis lines overexpressing CePP2C19 exhibited extreme tolerance to ABA and mannitol stresses during seed germination and root growth. At the mature stage, overexpression of CePP2C19 resulted in a higher tolerance to drought stress in transgenic Arabidopsis, as confirmed by a visible phenotype and several physiological parameters. Noticeably, the silencing of CePP2C19 by virus-induced gene silencing (VIGS) showed obvious reduction in drought tolerance in tiger nut plants. CONCLUSIONS The CePP2C19 emerges as a pivotal gene involved in the ABA signaling pathway, which likely reduce ABA sensitivity and thus enhances drought tolerance in Cyperus esculentus.
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Affiliation(s)
- Jia Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Xinyi Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yifei Wang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Hengshuo Ge
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yijin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Weican Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Xiaowei Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Nan Wang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Fawei Wang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yuanyuan Dong
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
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17
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Cisneros AE, Martín-García T, Primc A, Kuziuta W, Sánchez-Vicente J, Aragonés V, Daròs JA, Carbonell A. Transgene-free, virus-based gene silencing in plants by artificial microRNAs derived from minimal precursors. Nucleic Acids Res 2023; 51:10719-10736. [PMID: 37713607 PMCID: PMC10602918 DOI: 10.1093/nar/gkad747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023] Open
Abstract
Artificial microRNAs (amiRNAs) are highly specific, 21-nucleotide (nt) small RNAs designed to silence target transcripts. In plants, their application as biotechnological tools for functional genomics or crop improvement is limited by the need of transgenically expressing long primary miRNA (pri-miRNA) precursors to produce the amiRNAs in vivo. Here, we analyzed the minimal structural and sequence requirements for producing effective amiRNAs from the widely used, 521-nt long AtMIR390a pri-miRNA from Arabidopsis thaliana. We functionally screened in Nicotiana benthamiana a large collection of constructs transiently expressing amiRNAs against endogenous genes and from artificially shortened MIR390-based precursors and concluded that highly effective and accurately processed amiRNAs can be produced from a chimeric precursor of only 89 nt. This minimal precursor was further validated in A. thaliana transgenic plants expressing amiRNAs against endogenous genes. Remarkably, minimal but not full-length precursors produce authentic amiRNAs and induce widespread gene silencing in N. benthamiana when expressed from an RNA virus, which can be applied into leaves by spraying infectious crude extracts. Our results reveal that the length of amiRNA precursors can be shortened without affecting silencing efficacy, and that viral vectors including minimal amiRNA precursors can be applied in a transgene-free manner to induce whole-plant gene silencing.
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Affiliation(s)
- Adriana E Cisneros
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Tamara Martín-García
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Anamarija Primc
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Wojtek Kuziuta
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Javier Sánchez-Vicente
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
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Gao W, Chen Q, Fu J, Jiang H, Sun F, Geng S, Wang Y, Zhao J, Xie Y, Zhou M, Qu Y, Chen Q. Using association mapping and local interval haplotype association analysis to improve the cotton drought stress response. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111813. [PMID: 37543225 DOI: 10.1016/j.plantsci.2023.111813] [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: 04/19/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/07/2023]
Abstract
Drought stress has a serious impact on the growth and development of cotton. To explore the relevant molecular mechanism of the drought stress response in cotton, gene mapping based on the QTL interval mapped by simplified genome BSA-seq of the drought-resistance-related RIL population was performed. A QTL region spanning 2.02 Mb on chromosome D07 was selected, and 201 resource materials were genotyped using 9 KASP markers in the interval. After local interval haplotype association analysis, the overlap of the 110 kb peak region confirmed the reliability of this region, and at the same time, the role of GhGF14-30, the only gene in the overlapping region, was modeled in the response of cotton to drought stress. qRTPCR analysis of the materials and population parents proved that this gene plays a role in the drought stress response in cotton. Virus-induced gene silencing proved the importance of this gene in drought-sensitive materials, and drought-resistance-related marker genes also proved that the GhGF14-30 gene may play an important role in the ABA and SOS signaling pathways. This study provides a basis for mining drought stress response functional genes in cotton and lays the foundation for the molecular mechanism of the GhGF14-30 gene in response to drought stress in cotton.
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Affiliation(s)
- Wenju Gao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Qin Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Jincheng Fu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Hui Jiang
- Join Hope Seeds Co., Ltd. Room 1, 1st Layer, Block No. 27, Railway Station, Sangong Town, Changji City, Xinjiang Province 831100, China
| | - Fenglei Sun
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Shiwei Geng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yuting Xie
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Man Zhou
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China.
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Zhang L, Wang S, Ruan S, Nzabanita C, Wang Y, Guo L. A Mycovirus VIGS Vector Confers Hypovirulence to a Plant Pathogenic Fungus to Control Wheat FHB. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302606. [PMID: 37587761 PMCID: PMC10582431 DOI: 10.1002/advs.202302606] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/01/2023] [Indexed: 08/18/2023]
Abstract
Mycovirus-mediated hypovirulence has the potential to control fungal diseases. However, the availability of hypovirulence-conferring mycoviruses for plant fungal disease control is limited as most fungal viruses are asymptomatic. In this study, the virus-induced gene silencing (VIGS) vector p26-D4 of Fusarium graminearum gemytripvirus 1 (FgGMTV1), a tripartite circular single-stranded DNA mycovirus, is successfully constructed to convert the causal fungus of cereal Fusarium head blight (FHB) into a hypovirulent strain. p26-D4, with an insert of a 75-150 bp fragment of the target reporter transgene transcript in both sense and antisense orientations, efficiently triggered gene silencing in Fusarium graminearum. Notably, the two hypovirulent strains, p26-D4-Tri101, and p26-D4-FgPP1, obtained by silencing the virulence-related genes Tri101 and FgPP1 with p26-D4, can be used as biocontrol agents to protect wheat from a fungal disease FHB and mycotoxin contamination at the field level. This study not only describes the first mycovirus-derived VIGS system but also proves that the VIGS vector can be used to establish multiple hypovirulent strains to control pathogenic fungi.
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Affiliation(s)
- Lihang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Shuangchao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Shaojian Ruan
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Clement Nzabanita
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Yanfei Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
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20
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Qi X, Mo Q, Li J, Zi Z, Xu M, Yue S, Zhao H, Zhu H, Wang G. Establishment of virus-induced gene silencing (VIGS) system in Luffa acutangula using Phytoene desaturase (PDS) and tendril synthesis related gene (TEN). PLANT METHODS 2023; 19:94. [PMID: 37653449 PMCID: PMC10470258 DOI: 10.1186/s13007-023-01064-4] [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: 12/30/2022] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Virus-induced gene silencing (VIGS) is a reverse genetics technology that can efficiently and rapidly identify plant gene functions. Although a variety of VIGS vectors have been successfully used in plants, only a few reports on VIGS technology in Luffa exist. RESULTS In the present study, a new cucumber green mottle mosaic virus (CGMMV)-based VIGS vector, pV190, was applied to establish the CGMMV-VIGS to investigate the feasibility of the silencing system for Luffa. Phytoene desaturase (PDS) gene was initially selected as a VIGS marker gene to construct a recombinant vector. Plants infected with Agrobacterium harboring pV190-PDS successfully induced effective silencing in Luffa, and an effective gene silencing phenotype with obvious photobleaching was observed. To further validate the efficiency, we selected TEN for gene-silencing, which encodes a CYC/TB1-like transcription factor and is involved in tendril development. Luffa plants inoculated with the pV190-TEN exhibited shorter tendril length and nodal positions where tendrils appear are higher compared to those of non-inoculated plants. RT-qPCR showed that the expression levels of PDS and TEN were significantly reduced in the CGMMV-VIGS plants. Moreover, we evaluated the CGMMV-VIGS efficiency in three cucurbits, including cucumber, ridge gourd, and bottle gourd. CONCLUSION We successfully established a CGMMV-based VIGS system on ridge gourd and used marker genes to identify the feasibility of the silencing system in Luffa leaves and stems.
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Affiliation(s)
- Xiaoyu Qi
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qiaoping Mo
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jing Li
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- College of Plant Science, Tibet Agricultural and Animal Husbandry University, Tibet, 860000, Nyingchi, China
| | - Zhibo Zi
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Mengyun Xu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Suju Yue
- College of Life Sciences, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Hongbo Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Haisheng Zhu
- Fujian Key Laboratory of Vegetable Genetics and Breeding/Crops Research Institute, Fujian Academy of Agricultural Sciences, Fujian, 350013, Fuzhou, China.
| | - Guoping Wang
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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21
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Yang J, Zhang H, Chen H, Sun Z, Ke H, Wang G, Meng C, Wu L, Zhang Y, Wang X, Ma Z. Genome-wide association study reveals novel SNPs and genes in Gossypium hirsutum underlying Aphis gossypii resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:171. [PMID: 37420143 DOI: 10.1007/s00122-023-04415-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
A. gossypii resistance showed great variability in G. hirsutum varieties. One hundred and seventy-six SNPs associated with A. gossypii resistance were identified using GWAS. Four candidate resistance genes were functionally validated. Aphis gossypii is an economically important sap-feeding pest and is widely distributed in the world's cotton-producing regions. Identification of cotton genotypes and developing cultivars with improved A. gossypii resistance (AGR) is essential and desirable for sustainable agriculture. In the present study, A. gossypii was offered no choice but to propagate on 200 Gossypium hirsutum accessions. A relative aphid reproduction index (RARI) was used to evaluate the AGR, which showed large variability in cotton accessions and was classified into 6 grades. A significantly positive correlation was found between AGR and Verticillium wilt resistance. A total of 176 SNPs significantly associated with the RARI were identified using GWAS. Of these, 21 SNPs could be repeatedly detected in three replicates. Cleaved amplified polymorphic sequence, a restriction digestion-based genotyping assay, was developed using SNP1 with the highest observed -log10(P-value). Four genes within the 650 kb region of SNP1 were further identified, including GhRem (remorin-like), GhLAF1 (long after far-red light 1), GhCFIm25 (pre-mRNA cleavage factor Im 25 kDa subunit) and GhPMEI (plant invertase/pectin methylesterase inhibitor superfamily protein). The aphid infection could induce their expression and showed a significant difference between resistant and susceptible cotton varieties. Silencing of GhRem, GhLAF1 or GhCFIm25 could significantly increase aphid reproduction on cotton seedlings. Silencing of GhRem significantly reduced callose deposition, which is reasonably believed to be the cause for the higher AGR. Our results provide insights into understanding the genetic regulation of AGR in cotton and suggest candidate germplasms, SNPs and genes for developing cultivars with improved AGR.
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Affiliation(s)
- Jun Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Huimin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Haonan Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, Hebei, China.
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22
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Beernink BM, Whitham SA. Foxtail mosaic virus: A tool for gene function analysis in maize and other monocots. MOLECULAR PLANT PATHOLOGY 2023; 24:811-822. [PMID: 37036421 PMCID: PMC10257046 DOI: 10.1111/mpp.13330] [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: 10/31/2022] [Revised: 02/20/2023] [Accepted: 03/08/2023] [Indexed: 06/11/2023]
Abstract
Many plant viruses have been engineered into vectors for use in functional genomics studies, expression of heterologous proteins, and, most recently, gene editing applications. The use of viral vectors overcomes bottlenecks associated with mutagenesis and transgenesis approaches often implemented for analysis of gene function. There are several engineered viruses that are demonstrated or suggested to be useful in maize through proof-of-concept studies. However, foxtail mosaic virus (FoMV), which has a relatively broad host range, is emerging as a particularly useful virus for gene function studies in maize and other monocot crop or weed species. A few clones of FoMV have been independently engineered, and they have different features and capabilities for virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX) of proteins. In addition, FoMV can be used to deliver functional guide RNAs in maize and other plants expressing the Cas9 protein, demonstrating its potential utility in virus-induced gene editing applications. There is a growing number of studies in which FoMV vectors are being applied for VIGS or VOX in maize and the vast majority of these are related to maize-microbe interactions. In this review, we highlight the biology and engineering of FoMV as well as its applications in maize-microbe interactions and more broadly in the context of the monocot functional genomics toolbox.
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Affiliation(s)
- Bliss M. Beernink
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
- Department of BiologyUniversity of ManitobaWinnipegManitobaCanada
| | - Steven A. Whitham
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
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23
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Zhang Y, Niu N, Li S, Liu Y, Xue C, Wang H, Liu M, Zhao J. Virus-Induced Gene Silencing (VIGS) in Chinese Jujube. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112115. [PMID: 37299093 DOI: 10.3390/plants12112115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
Virus-induced gene silencing (VIGS) is a fast and efficient method for assaying gene function in plants. At present, the VIGS system mediated by Tobacco rattle virus (TRV) has been successfully practiced in some species such as cotton and tomato. However, little research of VIGS systems has been reported in woody plants, nor in Chinese jujube. In this study, the TRV-VIGS system of jujube was firstly investigated. The jujube seedlings were grown in a greenhouse with a 16 h light/8 h dark cycle at 23 °C. After the cotyledon was fully unfolded, Agrobacterium mixture containing pTRV1 and pTRV2-ZjCLA with OD600 = 1.5 was injected into cotyledon. After 15 days, the new leaves of jujube seedlings showed obvious photo-bleaching symptoms and significantly decreased expression of ZjCLA, indicating that the TRV-VIGS system had successfully functioned on jujube. Moreover, it found that two injections on jujube cotyledon could induce higher silencing efficiency than once injection. A similar silencing effect was then also verified in another gene, ZjPDS. These results indicate that the TRV-VIGS system in Chinese jujube has been successfully established and can be applied to evaluate gene function, providing a breakthrough in gene function verification methods.
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Affiliation(s)
- Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Nazi Niu
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Shijia Li
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Yin Liu
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Huibin Wang
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
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24
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Becker A, Yamada Y, Sato F. California poppy ( Eschscholzia californica), the Papaveraceae golden girl model organism for evodevo and specialized metabolism. FRONTIERS IN PLANT SCIENCE 2023; 14:1084358. [PMID: 36938015 PMCID: PMC10017456 DOI: 10.3389/fpls.2023.1084358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
California poppy or golden poppy (Eschscholzia californica) is the iconic state flower of California, with native ranges from Northern California to Southwestern Mexico. It grows well as an ornamental plant in Mediterranean climates, but it might be invasive in many parts of the world. California poppy was also highly prized by Native Americans for its medicinal value, mainly due to its various specialized metabolites, especially benzylisoquinoline alkaloids (BIAs). As a member of the Ranunculales, the sister lineage of core eudicots it occupies an interesting phylogenetic position. California poppy has a short-lived life cycle but can be maintained as a perennial. It has a comparatively simple floral and vegetative morphology. Several genetic resources, including options for genetic manipulation and a draft genome sequence have been established already with many more to come. Efficient cell and tissue culture protocols are established to study secondary metabolite biosynthesis and its regulation. Here, we review the use of California poppy as a model organism for plant genetics, with particular emphasis on the evolution of development and BIA biosynthesis. In the future, California poppy may serve as a model organism to combine two formerly separated lines of research: the regulation of morphogenesis and the regulation of secondary metabolism. This can provide insights into how these two integral aspects of plant biology interact with each other.
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Affiliation(s)
- Annette Becker
- Plant Development Lab, Institute of Botany, Hustus-Liebig-University, Giessen, Germany
| | - Yasuyuki Yamada
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Kobe, Japan
| | - Fumihiko Sato
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Bioorganic Research Institute, Suntory Foundation for Life Science, Kyoto, Japan
- Graduate School of Science, Osaka Metropolitan University, Sakai, Japan
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25
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Shakir S, Zaidi SSEA, Hashemi FSG, Nyirakanani C, Vanderschuren H. Harnessing plant viruses in the metagenomics era: from the development of infectious clones to applications. TRENDS IN PLANT SCIENCE 2023; 28:297-311. [PMID: 36379846 DOI: 10.1016/j.tplants.2022.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Recent metagenomic studies which focused on virus characterization in the entire plant environment have revealed a remarkable viral diversity in plants. The exponential discovery of viruses also requires the concomitant implementation of high-throughput methods to perform their functional characterization. Despite several limitations, the development of viral infectious clones remains a method of choice to understand virus biology, their role in the phytobiome, and plant resilience. Here, we review the latest approaches for efficient characterization of plant viruses and technical advances built on high-throughput sequencing and synthetic biology to streamline assembly of viral infectious clones. We then discuss the applications of plant viral vectors in fundamental and applied plant research as well as their technical and regulatory limitations, and we propose strategies for their safer field applications.
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Affiliation(s)
- Sara Shakir
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
| | - Syed Shan-E-Ali Zaidi
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Farahnaz Sadat Golestan Hashemi
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Chantal Nyirakanani
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium; Department of Crop Science, School of Agriculture, University of Rwanda, Musanze, Rwanda
| | - Hervé Vanderschuren
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium; Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Biosystems Department, KU Leuven, Leuven, Belgium.
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26
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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27
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Lappe RR, Elmore MG, Lozier ZR, Jander G, Miller WA, Whitham SA. Metagenomic identification of novel viruses of maize and teosinte in North America. BMC Genomics 2022; 23:767. [DOI: 10.1186/s12864-022-09001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America.
Results
Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North American maize.
Conclusions
Metagenomic studies of crop and crop-related species such as this may be useful for the identification and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security.
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28
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Rustgi S, Naveed S, Windham J, Zhang H, Demirer GS. Plant biomacromolecule delivery methods in the 21st century. Front Genome Ed 2022; 4:1011934. [PMID: 36311974 PMCID: PMC9614364 DOI: 10.3389/fgeed.2022.1011934] [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: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
The 21st century witnessed a boom in plant genomics and gene characterization studies through RNA interference and site-directed mutagenesis. Specifically, the last 15 years marked a rapid increase in discovering and implementing different genome editing techniques. Methods to deliver gene editing reagents have also attempted to keep pace with the discovery and implementation of gene editing tools in plants. As a result, various transient/stable, quick/lengthy, expensive (requiring specialized equipment)/inexpensive, and versatile/specific (species, developmental stage, or tissue) methods were developed. A brief account of these methods with emphasis on recent developments is provided in this review article. Additionally, the strengths and limitations of each method are listed to allow the reader to select the most appropriate method for their specific studies. Finally, a perspective for future developments and needs in this research area is presented.
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Affiliation(s)
- Sachin Rustgi
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States,*Correspondence: Sachin Rustgi, ; Gözde S. Demirer,
| | - Salman Naveed
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States
| | - Jonathan Windham
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States
| | - Huan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Gözde S. Demirer
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA, United States,*Correspondence: Sachin Rustgi, ; Gözde S. Demirer,
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29
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Yue J, Wei Y, Sun Z, Chen Y, Wei X, Wang H, Pasin F, Zhao M. AlkB RNA demethylase homologues and N 6 -methyladenosine are involved in Potyvirus infection. MOLECULAR PLANT PATHOLOGY 2022; 23:1555-1564. [PMID: 35700092 PMCID: PMC9452765 DOI: 10.1111/mpp.13239] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 05/28/2023]
Abstract
Proteins of the alkylation B (AlkB) superfamily show RNA demethylase activity removing methyl adducts from N6 -methyladenosine (m6 A). m6 A is a reversible epigenetic mark of RNA that regulates human virus replication but has unclear roles in plant virus infection. We focused on Potyvirus-the largest genus of plant RNA viruses-and report here the identification of AlkB domains within P1 of endive necrotic mosaic virus (ENMV) and an additional virus of a putative novel species within Potyvirus. We show that Nicotiana benthamiana m6 A levels are reduced by infection of plum pox virus (PPV) and potato virus Y (PVY). The two potyviruses lack AlkB and the results suggest a general involvement of RNA methylation in potyvirus infection and evolution. Methylated RNA immunoprecipitation sequencing of virus-infected samples showed that m6 A peaks are enriched in plant transcript 3' untranslated regions and in discrete internal and 3' terminal regions of PPV and PVY genomes. Down-regulation of N. benthamiana AlkB homologues of the plant-specific ALKBH9 clade caused a significant decrease in PPV and PVY accumulation. In summary, our study provides evolutionary and experimental evidence that supports the m6 A implication and the proviral roles of AlkB homologues in Potyvirus infection.
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Affiliation(s)
- Jianying Yue
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Yao Wei
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Zhenqi Sun
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Yahan Chen
- College of Plant ProtectionGansu Agricultural UniversityLanzhouChina
| | - Xuefeng Wei
- Development of Fine ChemicalsGuizhou UniversityGuizhouChina
| | - Haijuan Wang
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas—Universitat Politècnica de València (CSIC‐UPV)ValenciaSpain
- School of ScienceUniversity of PaduaPaduaItaly
| | - Mingmin Zhao
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
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30
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Virus-Induced Gene Editing and Its Applications in Plants. Int J Mol Sci 2022; 23:ijms231810202. [PMID: 36142116 PMCID: PMC9499690 DOI: 10.3390/ijms231810202] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
CRISPR/Cas-based genome editing technologies, which allow the precise manipulation of plant genomes, have revolutionized plant science and enabled the creation of germplasms with beneficial traits. In order to apply these technologies, CRISPR/Cas reagents must be delivered into plant cells; however, this is limited by tissue culture challenges. Recently, viral vectors have been used to deliver CRISPR/Cas reagents into plant cells. Virus-induced genome editing (VIGE) has emerged as a powerful method with several advantages, including high editing efficiency and a simplified process for generating gene-edited DNA-free plants. Here, we briefly describe CRISPR/Cas-based genome editing. We then focus on VIGE systems and the types of viruses used currently for CRISPR/Cas9 cassette delivery and genome editing. We also highlight recent applications of and advances in VIGE in plants. Finally, we discuss the challenges and potential for VIGE in plants.
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31
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Schröpfer S, Lempe J, Emeriewen OF, Flachowsky H. Recent Developments and Strategies for the Application of Agrobacterium-Mediated Transformation of Apple Malus × domestica Borkh. FRONTIERS IN PLANT SCIENCE 2022; 13:928292. [PMID: 35845652 PMCID: PMC9280197 DOI: 10.3389/fpls.2022.928292] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/08/2022] [Indexed: 05/09/2023]
Abstract
Genetic transformation has become an important tool in plant genome research over the last three decades. This applies not only to model plants such as Arabidopsis thaliana but also increasingly to cultivated plants, where the establishment of transformation methods could still pose many problems. One of such plants is the apple (Malus spp.), the most important fruit of the temperate climate zone. Although the genetic transformation of apple using Agrobacterium tumefaciens has been possible since 1989, only a few research groups worldwide have successfully applied this technology, and efficiency remains poor. Nevertheless, there have been some developments, especially in recent years, which allowed for the expansion of the toolbox of breeders and breeding researchers. This review article attempts to summarize recent developments in the Agrobacterium-mediated transformation strategies of apple. In addition to the use of different tissues and media for transformation, agroinfiltration, as well as pre-transformation with a Baby boom transcription factor are notable successes that have improved transformation efficiency in apple. Further, we highlight targeted gene silencing applications. Besides the classical strategies of RNAi-based silencing by stable transformation with hairpin gene constructs, optimized protocols for virus-induced gene silencing (VIGS) and artificial micro RNAs (amiRNAs) have emerged as powerful technologies for silencing genes of interest. Success has also been achieved in establishing methods for targeted genome editing (GE). For example, it was recently possible for the first time to generate a homohistont GE line into which a biallelic mutation was specifically inserted in a target gene. In addition to these methods, which are primarily aimed at increasing transformation efficiency, improving the precision of genetic modification and reducing the time required, methods are also discussed in which genetically modified plants are used for breeding purposes. In particular, the current state of the rapid crop cycle breeding system and its applications will be presented.
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