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Neves C, Ribeiro B, Amaro R, Expósito J, Grimplet J, Fortes AM. Network of GRAS transcription factors in plant development, fruit ripening and stress responses. HORTICULTURE RESEARCH 2023; 10:uhad220. [PMID: 38077496 PMCID: PMC10699852 DOI: 10.1093/hr/uhad220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/20/2023] [Indexed: 06/23/2024]
Abstract
The plant-specific family of GRAS transcription factors has been wide implicated in the regulation of transcriptional reprogramming associated with a diversity of biological functions ranging from plant development processes to stress responses. Functional analyses of GRAS transcription factors supported by in silico structural and comparative analyses are emerging and clarifying the regulatory networks associated with their biological roles. In this review, a detailed analysis of GRAS proteins' structure and biochemical features as revealed by recent discoveries indicated how these characteristics may impact subcellular location, molecular mechanisms, and function. Nomenclature issues associated with GRAS classification into different subfamilies in diverse plant species even in the presence of robust genomic resources are discussed, in particular how it affects assumptions of biological function. Insights into the mechanisms driving evolution of this gene family and how genetic and epigenetic regulation of GRAS contributes to subfunctionalization are provided. Finally, this review debates challenges and future perspectives on the application of this complex but promising gene family for crop improvement to cope with challenges of environmental transition.
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Affiliation(s)
- Catarina Neves
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Beatriz Ribeiro
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Rute Amaro
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Jesús Expósito
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Jérôme Grimplet
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Gobierno de Aragón, Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón—IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet 177, 50013 Zaragoza, Spain
| | - Ana Margarida Fortes
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
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2
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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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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. PLANTA 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [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: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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4
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Gouthu S, Mandelli C, Eubanks BA, Deluc LG. Transgene-free genome editing and RNAi ectopic application in fruit trees: Potential and limitations. FRONTIERS IN PLANT SCIENCE 2022; 13:979742. [PMID: 36325537 PMCID: PMC9621297 DOI: 10.3389/fpls.2022.979742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
For the past fifteen years, significant research advances in sequencing technology have led to a substantial increase in fruit tree genomic resources and databases with a massive number of OMICS datasets (transcriptomic, proteomics, metabolomics), helping to find associations between gene(s) and performance traits. Meanwhile, new technology tools have emerged for gain- and loss-of-function studies, specifically in gene silencing and developing tractable plant models for genetic transformation. Additionally, innovative and adapted transformation protocols have optimized genetic engineering in most fruit trees. The recent explosion of new gene-editing tools allows for broadening opportunities for functional studies in fruit trees. Yet, the fruit tree research community has not fully embraced these new technologies to provide large-scale genome characterizations as in cereals and other staple food crops. Instead, recent research efforts in the fruit trees appear to focus on two primary translational tools: transgene-free gene editing via Ribonucleoprotein (RNP) delivery and the ectopic application of RNA-based products in the field for crop protection. The inherent nature of the propagation system and the long juvenile phase of most fruit trees are significant justifications for the first technology. The second approach might have the public favor regarding sustainability and an eco-friendlier environment for a crop production system that could potentially replace the use of chemicals. Regardless of their potential, both technologies still depend on the foundational knowledge of gene-to-trait relationships generated from basic genetic studies. Therefore, we will discuss the status of gene silencing and DNA-based gene editing techniques for functional studies in fruit trees followed by the potential and limitations of their translational tools (RNP delivery and RNA-based products) in the context of crop production.
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Affiliation(s)
- Satyanarayana Gouthu
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Christian Mandelli
- Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
| | - Britt A. Eubanks
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Laurent G. Deluc
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
- Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
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5
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Ding X, Yu L, Chen L, Li Y, Zhang J, Sheng H, Ren Z, Li Y, Yu X, Jin S, Cao J. Recent Progress and Future Prospect of CRISPR/Cas-Derived Transcription Activation (CRISPRa) System in Plants. Cells 2022; 11:3045. [PMID: 36231007 PMCID: PMC9564188 DOI: 10.3390/cells11193045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Genome editing technology has become one of the hottest research areas in recent years. Among diverse genome editing tools, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins system (CRISPR/Cas system) has exhibited the obvious advantages of specificity, simplicity, and flexibility over any previous genome editing system. In addition, the emergence of Cas9 mutants, such as dCas9 (dead Cas9), which lost its endonuclease activity but maintains DNA recognition activity with the guide RNA, provides powerful genetic manipulation tools. In particular, combining the dCas9 protein and transcriptional activator to achieve specific regulation of gene expression has made important contributions to biotechnology in medical research as well as agriculture. CRISPR/dCas9 activation (CRISPRa) can increase the transcription of endogenous genes. Overexpression of foreign genes by traditional transgenic technology in plant cells is the routine method to verify gene function by elevating genes transcription. One of the main limitations of the overexpression is the vector capacity constraint that makes it difficult to express multiple genes using the typical Ti plasmid vectors from Agrobacterium. The CRISPRa system can overcome these limitations of the traditional gene overexpression method and achieve multiple gene activation by simply designating several guide RNAs in one vector. This review summarizes the latest progress based on the development of CRISPRa systems, including SunTag, dCas9-VPR, dCas9-TV, scRNA, SAM, and CRISPR-Act and their applications in plants. Furthermore, limitations, challenges of current CRISPRa systems and future prospective applications are also discussed.
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Affiliation(s)
- Xiao Ding
- Institute of Cotton, Shanxi Agricultural University, Yuncheng 044000, China
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Luo Chen
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yujie Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinlun Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanyan Sheng
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengwei Ren
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunlong Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohan Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinglin Cao
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
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6
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Rahman F, Mishra A, Gupta A, Sharma R. Spatiotemporal Regulation of CRISPR/Cas9 Enables Efficient, Precise, and Heritable Edits in Plant Genomes. Front Genome Ed 2022; 4:870108. [PMID: 35558825 PMCID: PMC9087570 DOI: 10.3389/fgeed.2022.870108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 12/04/2022] Open
Abstract
CRISPR/Cas-mediated editing has revolutionized crop engineering. Due to the broad scope and potential of this technology, many studies have been carried out in the past decade towards optimizing genome editing constructs. Clearly, the choice of the promoter used to drive gRNA and Cas9 expression is critical to achieving high editing efficiency, precision, and heritability. While some important considerations for choosing a promoter include the number and nature of targets, host organism, mode of transformation and goal of the experiment, spatiotemporal regulation of Cas9 expression using tissue-specific or inducible promoters enables higher heritability and efficiency of targeted mutagenesis with reduced off-target effects. In this review, we discuss specific studies that highlight the prospects and trade-offs associated with the choice of promoters on genome editing and emphasize the need for inductive exploration and discovery to further advance this area of research in crop plants.
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Affiliation(s)
- Farhanur Rahman
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
| | - Apurva Mishra
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Archit Gupta
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
- *Correspondence: Rita Sharma, ,
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7
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Ren C, Li H, Liu Y, Li S, Liang Z. Highly efficient activation of endogenous gene in grape using CRISPR/dCas9-based transcriptional activators. HORTICULTURE RESEARCH 2022; 9:uhab037. [PMID: 35039855 PMCID: PMC8807946 DOI: 10.1093/hr/uhab037] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/18/2022] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
Overexpression and knockout (or knockdown) of gene of interest are two commonly used strategies for gene functional study. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system-mediated gene knockout had been applied in most plant species, including grapevine. However, CRISPR/dCas9 (deactivated Cas9)-based transcriptional activation is still unreported in fruit crops, although a few studies had been documented in Arabidopsis and rice. Here, we tested two transcriptional activators VP64 and TV for transcriptional activation of endogenous genes in grape. Both the dCas9-VP64 and dCas9-TV systems are efficient enough for transcriptional activation of the UDP-glucose flavonoid glycosyltransferases (UFGT) gene in grape cells. The effectiveness of the dCas9-VP64 system in UFGT activation was about 1.6- to 5.6-fold, while the efficiency of the dCas9-TV system was around 5.7- to 7.2-fold. Moreover, in grapevine plants, highly efficient activation of the cold-responsive transcription factor gene CBF4 was achieved by using the dCas9-TV system. The expression of CBF4 was increased 3.7- to 42.3-fold in transgenic plants. Compared with the wild-type plants, the CBF4-activated plants exhibited lower electrolyte leakage after cold treatment. Our results demonstrate the effectiveness of the dCas9-VP64 and dCas9-TV system in gene activation in grape, which will facilitate application of transcriptional activation in this economically important species.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- University of Chinese Academy of Sciences,
19 Yuquan Rd, Beijing 100049, China
| | - Yanfei Liu
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- University of Chinese Academy of Sciences,
19 Yuquan Rd, Beijing 100049, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
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8
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Shah P, Magar ND, Barbadikar KM. Current technological interventions and applications of CRISPR/Cas for crop improvement. Mol Biol Rep 2021; 49:5751-5770. [PMID: 34807378 DOI: 10.1007/s11033-021-06926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
Efficient and innovative breeding strategies are immensely required to meet the global food demand, nutritional security and sustainable agriculture. Genome editing tools have emerged as an effective technology for site-directed genome modification causing the change in gene expression and protein function for the improvement of various important traits in particular the CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein). As the technology evolved with time, advances have been observed like prime editing, base editing, PAMless editing, Drosha based editing with multiple targets having the potential to fulfill the regulatory processes around the world. These recent interventions are highly proficient, cost-efficient, user-friendly, and holds promise for a major revolution in basic and applied plant biology research in the ever-evolving climatic conditions. In the review, we have discussed the most recent technologies and advances for CRISPR/Cas editing in plants.
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Affiliation(s)
- Priya Shah
- Tamil Nadu Agricultural University, Tamil Nadu, India
| | - Nakul D Magar
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State, 500030, India
| | - Kalyani M Barbadikar
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State, 500030, India.
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9
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Cable J, Ronald PC, Voytas D, Zhang F, Levy AA, Takatsuka A, Arimura SI, Jacobsen SE, Toki S, Toda E, Gao C, Zhu JK, Boch J, Van Eck J, Mahfouz M, Andersson M, Fridman E, Weiss T, Wang K, Qi Y, Jores T, Adams T, Bagchi R. Plant genome engineering from lab to field-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:35-54. [PMID: 34435370 DOI: 10.1111/nyas.14675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022]
Abstract
Facing the challenges of the world's food sources posed by a growing global population and a warming climate will require improvements in plant breeding and technology. Enhancing crop resiliency and yield via genome engineering will undoubtedly be a key part of the solution. The advent of new tools, such as CRIPSR/Cas, has ushered in significant advances in plant genome engineering. However, several serious challenges remain in achieving this goal. Among them are efficient transformation and plant regeneration for most crop species, low frequency of some editing applications, and high attrition rates. On March 8 and 9, 2021, experts in plant genome engineering and breeding from academia and industry met virtually for the Keystone eSymposium "Plant Genome Engineering: From Lab to Field" to discuss advances in genome editing tools, plant transformation, plant breeding, and crop trait development, all vital for transferring the benefits of novel technologies to the field.
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Affiliation(s)
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, and the Joint BioEnergy Institute, Davis, California
| | - Daniel Voytas
- Department of Genetics, Cell Biology and Development; Center for Precision Plant Genomics; and Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota
| | - Feng Zhang
- College of Biological Sciences, University of Minnesota, St. Paul, Minnesota
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ayumu Takatsuka
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shin-Ichi Arimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Steven E Jacobsen
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; Department of Molecular, Cell and Developmental Biology; and Howard Hughes Medical Institute, University of California, Los Angeles, California
| | - Seiichi Toki
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Erika Toda
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, and College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, New York, and Plant Breeding and Genetics Section, Cornell University, Ithaca, New York
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eyal Fridman
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Trevor Weiss
- Department of Genetics, Cell Biology and Development; Center for Precision Plant Genomics; and Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, Iowa
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | | | - Rammyani Bagchi
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, North Carolina
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10
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Zhang Y, Zhou P, Bozorov TA, Zhang D. Application of CRISPR/Cas9 technology in wild apple (Malus sieverii) for paired sites gene editing. PLANT METHODS 2021; 17:79. [PMID: 34281579 PMCID: PMC8287690 DOI: 10.1186/s13007-021-00769-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/14/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Xinjiang wild apple is an important tree of the Tianshan Mountains, and in recent years, it has undergone destruction by many biotic and abiotic stress and human activities. It is necessary to use new technologies to research its genomic function and molecular improvement. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability varies depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. RESULTS In this study, we used 2 systems of vectors with paired sgRNAs targeting to MsPDS. As expected, we successfully induced the albino phenotype of calli and buds in both systems. CONCLUSIONS We conclude that CRISPR/Cas9 is a powerful system for editing the wild apple genome and expands the range of plants available for gene editing.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tohir A Bozorov
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- Xinjiang Key Laboratory of Stress Resistant Plant Conservation and Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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11
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Basso MF, Duarte KE, Santiago TR, de Souza WR, Garcia BDO, da Cunha BDB, Kobayashi AK, Molinari HBC. Efficient genome editing and gene knockout in Setaria viridis with CRISPR/Cas9 directed gene editing by the non-homologous end-joining pathway. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:227-238. [PMID: 34393601 PMCID: PMC8329270 DOI: 10.5511/plantbiotechnology.21.0407a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/07/2021] [Indexed: 05/05/2023]
Abstract
The CRISPR/Cas9 system has been used for genome editing in several organisms, including higher plants. This system induces site-specific mutations in the genome based on the nucleotide sequence of engineered guide RNAs. The complex genomes of C4 grasses makes genome editing a challenge in key grass crops like maize (Zea mays), sorghum (Sorghum bicolor), Brachiaria spp., switchgrass (Panicum virgatum), and sugarcane (Saccharum spp.). Setaria viridis is a diploid C4 grass widely used as a model for these C4 crop plants. Here, an optimized CRISPR/Cas9 binary vector that exploits the non-homologous end joining (NHEJ) system was used to knockout a green fluorescent protein (gfp) transgene in S. viridis accession A10.1. Transformation of embryogenic callus by A. tumefaciens generated ten glufosinate-ammonium resistant transgenic events. In the T0 generation, 60% of the events were biallelic mutants in the gfp transgene with no detectable accumulation of GFP protein and without insertions or deletions in predicted off-target sites. The gfp mutations generated by CRISPR/Cas9 were stable and displayed Mendelian segregation in the T1 generation. Altogether, the system described here is a highly efficient genome editing system for S. viridis, an important model plant for functional genomics studies in C4 grasses. Also, this system is a potential tool for improvement of agronomic traits in C4 crop plants with complex genomes.
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Affiliation(s)
- Marcos Fernando Basso
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- BIOMOL/BIOTEC Laboratory, Mato Grosso Cotton Institute (IMAmt), Rondonópolis, MT, 78740-970, Brazil
| | - Karoline Estefani Duarte
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- Center for Natural and Human Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, São Paulo, 09606-045, Brazil
| | - Thais Ribeiro Santiago
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- Departament of Phytopathology, Federal University of Brasília, Brasília (UNB), Distrito Federal, 70910-900, Brazil
| | - Wagner Rodrigo de Souza
- Center for Natural and Human Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, São Paulo, 09606-045, Brazil
| | - Bruno de Oliveira Garcia
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Bárbara Dias Brito da Cunha
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Adilson Kenji Kobayashi
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Hugo Bruno Correa Molinari
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- E-mail: Tel: +55-61-3448-2307, Fax: +55-61-34481598
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12
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Mushtaq M, Ahmad Dar A, Skalicky M, Tyagi A, Bhagat N, Basu U, Bhat BA, Zaid A, Ali S, Dar TUH, Rai GK, Wani SH, Habib-Ur-Rahman M, Hejnak V, Vachova P, Brestic M, Çığ A, Çığ F, Erman M, EL Sabagh A. CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges. Genes (Basel) 2021; 12:797. [PMID: 34073848 PMCID: PMC8225059 DOI: 10.3390/genes12060797] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Nancy Bhagat
- School of Biotechnology, University of Jammu, Jammu 180006, India;
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India;
| | | | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany Aligarh Muslim University, Aigarh 202002, India;
| | - Sajad Ali
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India;
| | | | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu 192101, India
| | - Muhammad Habib-Ur-Rahman
- Department of Crop Science, Institute of Crop Science and Resource Conservation (INRES), University Bonn, 53115 Bonn, Germany;
| | - Vaclav Hejnak
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia
| | - Arzu Çığ
- Department of Horticulture, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey;
| | - Fatih Çığ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Murat Erman
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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13
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Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
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Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
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14
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Vu TV, Sivankalyani V, Kim E, Doan DTH, Tran MT, Kim J, Sung YW, Park M, Kang YJ, Kim J. Highly efficient homology-directed repair using CRISPR/Cpf1-geminiviral replicon in tomato. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2133-2143. [PMID: 32176419 PMCID: PMC7540044 DOI: 10.1111/pbi.13373] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/08/2020] [Accepted: 02/23/2020] [Indexed: 05/04/2023]
Abstract
Genome editing via the homology-directed repair (HDR) pathway in somatic plant cells is very inefficient compared with error-prone repair by nonhomologous end joining (NHEJ). Here, we increased HDR-based genome editing efficiency approximately threefold compared with a Cas9-based single-replicon system via the use of de novo multi-replicon systems equipped with CRISPR/LbCpf1 in tomato and obtained replicon-free but stable HDR alleles. The efficiency of CRISPR/LbCpf1-based HDR was significantly modulated by physical culture conditions such as temperature and light. Ten days of incubation at 31 °C under a light/dark cycle after Agrobacterium-mediated transformation resulted in the best performance among the tested conditions. Furthermore, we developed our single-replicon system into a multi-replicon system that effectively increased HDR efficiency. Although this approach is still challenging, we showed the feasibility of HDR-based genome editing of a salt-tolerant SlHKT1;2 allele without genomic integration of antibiotic markers or any phenotypic selection. Self-pollinated offspring plants carrying the HKT1;2 HDR allele showed stable inheritance and germination tolerance in the presence of 100 mm NaCl. Our work may pave the way for transgene-free editing of alleles of interest in asexually and sexually reproducing plants.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteBac Tu LiemVietnam
| | - Velu Sivankalyani
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Eun‐Jung Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | | | - Yang Jae Kang
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
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15
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Sandhya D, Jogam P, Allini VR, Abbagani S, Alok A. The present and potential future methods for delivering CRISPR/Cas9 components in plants. J Genet Eng Biotechnol 2020; 18:25. [PMID: 32638190 PMCID: PMC7340682 DOI: 10.1186/s43141-020-00036-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/04/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND CRISPR/Cas9 genome editing technology is a DNA manipulation tool for trait improvement. This technology has been demonstrated and successfully applied to edit the genome in various species of plants. The delivery of CRISPR/Cas9 components within rigid plant cells is very crucial for high editing efficiency. Here, we insight the strengths and weaknesses of each method of delivery. MAIN TEXT The mutation efficiency of genome editing may vary and affected by different factors. Out of various factors, the delivery of CRISPR/Cas9 components into cells and genome is vital. The way of delivery defines whether the edited plant is transgenic or transgene-free. In many countries, the transgenic approach of improvement is a significant limitation in the regulatory approval of genetically modified crops. Gene editing provides an opportunity for generating transgene-free edited genome of the plant. Nevertheless, the mode of delivery of the CRISPR/Cas9 component is of crucial importance for genome modification in plants. Different delivery methods such as Agrobacterium-mediated, bombardment or biolistic method, floral-dip, and PEG-mediated protoplast are frequently applied to crops for efficient genome editing. CONCLUSION We have reviewed different delivery methods with prons and cons for genome editing in plants. A novel nanoparticle and pollen magnetofection-mediated delivery systems which would be very useful in the near future. Further, the factors affecting editing efficiency, such as the promoter, transformation method, and selection pressure, are discussed in the present review.
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Affiliation(s)
- Dulam Sandhya
- Department of Biotechnology, Kakatiya University, Warangal, Telangana India
| | - Phanikanth Jogam
- Department of Biotechnology, Kakatiya University, Warangal, Telangana India
| | | | | | - Anshu Alok
- Department of Biotechnology, UIET, Panjab University, Chandigarh, India
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16
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Zheng X, Qi C, Yang L, Quan Q, Liu B, Zhong Z, Tang X, Fan T, Zhou J, Zhang Y. The Improvement of CRISPR-Cas9 System With Ubiquitin-Associated Domain Fusion for Efficient Plant Genome Editing. FRONTIERS IN PLANT SCIENCE 2020; 11:621. [PMID: 32508867 PMCID: PMC7253670 DOI: 10.3389/fpls.2020.00621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/22/2020] [Indexed: 05/05/2023]
Abstract
Genome editing technology represented by CRISPR-Cas9 had been widely used in many biological fields such as gene function analysis, gene therapy, and crop improvement. However, in the face of the complexity of the eukaryotic genome, the CRISPR-Cas9 genome editing tools have shown an unstable editing efficiency with large variability at different target sites. It was important to further improve the editing efficiency of the CRISPR-Cas9 system among the whole genome. In this study, based on the previous single transcription unit genome editing system (STU-SpCas9), using the ubiquitin-associated domain (UBA) to enhance the stability of Cas9 protein, we constructed three Cas9-UBA fusion systems (SpCas9-SD01, SpCas9-SD02, and SpCas9-SD03). Four different target sites of rice OsPDS, OsDEP1 and OsROC5 genes were chosen to evaluate the genome editing efficiency in rice protoplasts and stable transformed rice plants. The results showed that the fusion of UBA domains did not affect the cleavage mode of Cas9 protein, and effectively increase the editing efficiency of STU-SpCas9 at the target sites. This new CRISPR-Cas9-UBA system provided a new strategy and tool for improving the genome editing efficiency of CRISPR-Cas9 in plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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17
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Efficient expression of multiple guide RNAs for CRISPR/Cas genome editing. ABIOTECH 2020; 1:123-134. [PMID: 36304720 PMCID: PMC9590505 DOI: 10.1007/s42994-019-00014-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/21/2019] [Indexed: 01/16/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein system (CRISPR/Cas) has recently become the most powerful tool available for genome engineering in various organisms. With efficient and proper expression of multiple guide RNAs (gRNAs), the CRISPR/Cas system is particularly suitable for multiplex genome editing. During the past several years, different CRISPR/Cas expression strategies, such as two-component transcriptional unit, single transcriptional unit, and bidirectional promoter systems, have been developed to efficiently express gRNAs as well as Cas nucleases. Significant progress has been made to optimize gRNA production using different types of promoters and RNA processing strategies such as ribozymes, endogenous RNases, and exogenous endoribonuclease (Csy4). Besides being constitutively and ubiquitously expressed, inducible and spatiotemporal regulations of gRNA expression have been demonstrated using inducible, tissue-specific, and/or synthetic promoters for specific research purposes. Most recently, the emergence of CRISPR/Cas ribonucleoprotein delivery methods, such as engineered nanoparticles, further revolutionized transgene-free and multiplex genome editing. In this review, we discuss current strategies and future perspectives for efficient expression and engineering of gRNAs with a goal to facilitate CRISPR/Cas-based multiplex genome editing.
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18
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Liu X, Zhou X, Li K, Wang D, Ding Y, Liu X, Luo J, Fang C. A simple and efficient cloning system for CRISPR/Cas9-mediated genome editing in rice. PeerJ 2020; 8:e8491. [PMID: 32030327 PMCID: PMC6995270 DOI: 10.7717/peerj.8491] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/30/2019] [Indexed: 11/20/2022] Open
Abstract
Rapidly growing genetics and bioinformatics studies provide us with an opportunity to obtain a global view of the genetic basis of traits, but also give a challenge to the function validation of candidate genes. CRISPR/Cas9 is an emerging and efficient tool for genome editing. To construct expression clones for the CRISPR/Cas9, most current methods depend on traditional cloning using Gateway reaction or specific type IIS restriction enzymes and DNA ligation, based on multiple steps of PCR. We developed a system for introducing sgRNA expression cassette(s) directly into plant binary vectors in one step. In this system, one sgRNA expression cassette(s) is generated by an optimized multiplex PCR, in which an overlapping PCR took place. Whilst, two sgRNA expression cassettes were amplified in a single round of PCR. Subsequently, an LR or Golden gate reaction was set up with unpurified PCR product and befitting destination vector. We are able to construct expression clones within 36 h, which greatly improves efficiency and saves cost. Furthermore, the efficiency of this system was verified by an agrobacterium-mediated genetic transformation in rice. The system reported here provides a much more efficient and simpler procedure to construct expression clones for CRISPR/Cas9-mediated genome editing.
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Affiliation(s)
- Xiaoli Liu
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Xiujuan Zhou
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Kang Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dehong Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanhao Ding
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, Hainan, China.,National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chuanying Fang
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
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19
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Manipulating gene translation in plants by CRISPR-Cas9-mediated genome editing of upstream open reading frames. Nat Protoc 2020; 15:338-363. [PMID: 31915386 DOI: 10.1038/s41596-019-0238-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/27/2019] [Indexed: 12/27/2022]
Abstract
Gene expression is regulated by multiple processes, and the translation of mRNAs into proteins is an especially critical step. Upstream open reading frames (uORFs) are widespread cis-elements in eukaryotic genes that usually suppress the translation of downstream primary ORFs (pORFs). Here, we describe a protocol for fine-tuning gene translation in plants by editing endogenous uORFs with the CRISPR-Cas9 system. The method we present readily yields transgene-free uorf mutant offspring. We provide detailed protocols for predicting uORFs and testing their effects on downstream pORFs using a dual-luciferase reporter system, designing and constructing single guide RNA (sgRNA)-Cas9 vectors, identifying transgene-free uorf mutants, and finally comparing the mRNA, protein and phenotypic levels of target genes in uorf mutants and controls. Predicting uORFs and confirming their effects in protoplasts takes only 2-3 weeks, and transgene-free mutants with edited target uORFs controlling different levels of pORF translation can be obtained within 4 months. Unlike previous methods, our strategy achieves fine-tuning of gene translation in transgene-free derivatives, which accelerates the analysis of gene function and the improvement of crop traits.
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20
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Moradpour M, Abdulah SNA. CRISPR/dCas9 platforms in plants: strategies and applications beyond genome editing. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:32-44. [PMID: 31392820 PMCID: PMC6920162 DOI: 10.1111/pbi.13232] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 05/19/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) and Cas9-associated protein systems provide a powerful genetic manipulation tool that can drive plant research forward. Nuclease-dead Cas9 (dCas9) is an enzymatically inactive mutant of Cas9 in which its endonuclease activity is non-functional. The applications of CRISPR/dCas9 have expanded and diversified in recent years. Originally, dCas9 was used as a CRISPR/Cas9 re-engineering tool that enables targeted expression of any gene or multiple genes through recruitment of transcriptional effector domains without introducing irreversible DNA-damaging mutations. Subsequent applications have made use of its ability to recruit modifying enzymes and reporter proteins to DNA target sites. In this paper, the most recent progress in the applications of CRISPR/dCas9 in plants, which include gene activation and repression, epigenome editing, modulation of chromatin topology, live-cell chromatin imaging and DNA-free genetic modification, will be reviewed. The associated strategies for exploiting the CRISPR/dCas9 system for crop improvement with a dimer of the future of the CRISPR/dCas9 system in the functional genomics of crops and the development of traits will be briefly discussed.
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Affiliation(s)
- Mahdi Moradpour
- Laboratory of Science and TechnologyInstitute of Plantation StudiesUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Siti Nor Akmar Abdulah
- Laboratory of Science and TechnologyInstitute of Plantation StudiesUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Department of Agricultural TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangSelangorMalaysia
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21
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Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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22
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Zhang Y, Malzahn AA, Sretenovic S, Qi Y. The emerging and uncultivated potential of CRISPR technology in plant science. NATURE PLANTS 2019; 5:778-794. [PMID: 31308503 DOI: 10.1038/s41477-019-0461-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/24/2019] [Indexed: 05/18/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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Tang X, Ren Q, Yang L, Bao Y, Zhong Z, He Y, Liu S, Qi C, Liu B, Wang Y, Sretenovic S, Zhang Y, Zheng X, Zhang T, Qi Y, Zhang Y. Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1431-1445. [PMID: 30582653 PMCID: PMC6576101 DOI: 10.1111/pbi.13068] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 05/03/2023]
Abstract
CRISPR-Cas9 and Cas12a are two powerful genome editing systems. Expression of CRISPR in plants is typically achieved with a mixed dual promoter system, in which Cas protein is expressed by a Pol II promoter and a guide RNA is expressed by a species-specific Pol III promoter such as U6 or U3. To achieve coordinated expression and compact vector packaging, it is desirable to express both CRISPR components under a single Pol II promoter. Previously, we demonstrated a first-generation single transcript unit (STU)-Cas9 system, STU-Cas9-RZ, which is based on hammerhead ribozyme for processing single guide RNAs (sgRNAs). In this study, we developed two new STU-Cas9 systems and one STU-Cas12a system for applications in plants, collectively called the STU CRISPR 2.0 systems. We demonstrated these systems for genome editing in rice with both transient expression and stable transgenesis. The two STU-Cas9 2.0 systems process the sgRNAs with Csy4 ribonuclease and endogenous tRNA processing system respectively. Both STU-Cas9-Csy4 and STU-Cas9-tRNA systems showed more robust genome editing efficiencies than our first-generation STU-Cas9-RZ system and the conventional mixed dual promoter system. We further applied the STU-Cas9-tRNA system to compare two C to T base editing systems based on rAPOBEC1 and PmCDA1 cytidine deaminases. The results suggest STU-based PmCDA1 base editor system is highly efficient in rice. The STU-Cas12a system, based on Cas12a' self-processing of a CRISPR RNA (crRNA) array, was also developed and demonstrated for expression of a single crRNA and four crRNAs. Altogether, our STU CRISPR 2.0 systems further expanded the CRISPR toolbox for plant genome editing and other applications.
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Affiliation(s)
- Xu Tang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Qiurong Ren
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Lijia Yang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyJiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCollege of AgricultureYangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Zhaohui Zhong
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yao He
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Shishi Liu
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Caiyan Qi
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Binglin Liu
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yan Wang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Xuelian Zheng
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyJiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCollege of AgricultureYangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
| | - Yong Zhang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
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Zhou J, Xin X, He Y, Chen H, Li Q, Tang X, Zhong Z, Deng K, Zheng X, Akher SA, Cai G, Qi Y, Zhang Y. Multiplex QTL editing of grain-related genes improves yield in elite rice varieties. PLANT CELL REPORTS 2019; 38:475-485. [PMID: 30159598 DOI: 10.1007/s00299-00018-02340-00293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/24/2018] [Indexed: 05/19/2023]
Abstract
Significant yield increase has been achieved by simultaneous introduction of three trait-related QTLs in three rice varieties with multiplex editing by CRISPR-Cas9. Using traditional breeding approaches to develop new elite rice varieties with high yield and superior quality is challenging. It usually requires introduction of multiple trait-related quantitative trait loci (QTLs) into an elite background through multiple rounds of crossing and selection. CRISPR-Cas9-based multiplex editing of QTLs represents a new breeding strategy that is straightforward and cost effective. To test this approach, we simultaneously targeted three yield-related QTLs for editing in three elite rice varieties, namely J809, L237 and CNXJ. The chosen yield-related QTL genes are OsGS3, OsGW2 and OsGn1a, which have been identified to negatively regulate the grain size, width and weight, and number, respectively. Our approach rapidly generated all seven combinations of single, double and triple mutants for the target genes in elite backgrounds. Detailed analysis of these mutants revealed differential contributions of QTL mutations to yield performance such as grain length, width, number and 1000-grain weight. Overall, the contributions are additive, resulting in 68 and 30% yield per panicle increase in triple mutants of J809 and L237, respectively. Our data hence demonstrates a promising genome editing approach for rapid breeding of QTLs in elite crop varieties.
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Affiliation(s)
- Jianping Zhou
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuhui Xin
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Yao He
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Hongqiao Chen
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qian Li
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xu Tang
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Zhaohui Zhong
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Kejun Deng
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuelian Zheng
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Sayed Abdul Akher
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Guangze Cai
- Xichang University, Xichang, 615013, Sichuan, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.
| | - Yong Zhang
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China.
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25
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Zhou J, Xin X, He Y, Chen H, Li Q, Tang X, Zhong Z, Deng K, Zheng X, Akher SA, Cai G, Qi Y, Zhang Y. Multiplex QTL editing of grain-related genes improves yield in elite rice varieties. PLANT CELL REPORTS 2019; 38:475-485. [PMID: 30159598 DOI: 10.1007/s00299-018-2340-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/24/2018] [Indexed: 05/21/2023]
Abstract
Significant yield increase has been achieved by simultaneous introduction of three trait-related QTLs in three rice varieties with multiplex editing by CRISPR-Cas9. Using traditional breeding approaches to develop new elite rice varieties with high yield and superior quality is challenging. It usually requires introduction of multiple trait-related quantitative trait loci (QTLs) into an elite background through multiple rounds of crossing and selection. CRISPR-Cas9-based multiplex editing of QTLs represents a new breeding strategy that is straightforward and cost effective. To test this approach, we simultaneously targeted three yield-related QTLs for editing in three elite rice varieties, namely J809, L237 and CNXJ. The chosen yield-related QTL genes are OsGS3, OsGW2 and OsGn1a, which have been identified to negatively regulate the grain size, width and weight, and number, respectively. Our approach rapidly generated all seven combinations of single, double and triple mutants for the target genes in elite backgrounds. Detailed analysis of these mutants revealed differential contributions of QTL mutations to yield performance such as grain length, width, number and 1000-grain weight. Overall, the contributions are additive, resulting in 68 and 30% yield per panicle increase in triple mutants of J809 and L237, respectively. Our data hence demonstrates a promising genome editing approach for rapid breeding of QTLs in elite crop varieties.
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Affiliation(s)
- Jianping Zhou
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuhui Xin
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Yao He
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Hongqiao Chen
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qian Li
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xu Tang
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Zhaohui Zhong
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Kejun Deng
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuelian Zheng
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Sayed Abdul Akher
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Guangze Cai
- Xichang University, Xichang, 615013, Sichuan, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.
| | - Yong Zhang
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China.
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26
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Shah T, Andleeb T, Lateef S, Noor MA. Genome editing in plants: Advancing crop transformation and overview of tools. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:12-21. [PMID: 29754773 DOI: 10.1016/j.plaphy.2018.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 04/03/2018] [Accepted: 05/05/2018] [Indexed: 05/22/2023]
Abstract
Genome manipulation technology is one of emerging field which brings real revolution in genetic engineering and biotechnology. Targeted editing of genomes pave path to address a wide range of goals not only to improve quality and productivity of crops but also permit to investigate the fundamental roots of biological systems. These goals includes creation of plants with valued compositional properties and with characters that confer resistance to numerous biotic and abiotic stresses. Numerous novel genome editing systems have been introduced during the past few years; these comprise zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). Genome editing technique is consistent for improving average yield to achieve the growing demands of the world's existing food famine and to launch a feasible and environmentally safe agriculture scheme, to more specific, productive, cost-effective and eco-friendly. These exciting novel methods, concisely reviewed herein, have verified themselves as efficient and reliable tools for the genetic improvement of plants.
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Affiliation(s)
- Tariq Shah
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Wuhan, 430062, China.
| | - Tayyaba Andleeb
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-e-azam University, Islamabad, Pakistan
| | - Sadia Lateef
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-e-azam University, Islamabad, Pakistan
| | - Mehmood Ali Noor
- Instiute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, 100081, China
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27
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Soyars CL, Peterson BA, Burr CA, Nimchuk ZL. Cutting Edge Genetics: CRISPR/Cas9 Editing of Plant Genomes. PLANT & CELL PHYSIOLOGY 2018; 59:1608-1620. [PMID: 29912402 DOI: 10.1093/pcp/pcy079] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/11/2018] [Indexed: 05/22/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system is a genome editing technology transforming the field of plant biology by virtue of the system's efficiency and specificity. The system has quickly evolved for many diverse applications including multiplex gene mutation, gene replacement and transcriptional control. As CRISPR/Cas9 is increasingly applied to plants, it is becoming clear that each component of the system can be modified to improve editing results. This review aims to highlight common considerations and options when conducting CRISPR/Cas9 experiments.
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Affiliation(s)
- Cara L Soyars
- Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC, USA
| | - Brenda A Peterson
- Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC, USA
| | - Christian A Burr
- Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC, USA
| | - Zachary L Nimchuk
- Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC, USA
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28
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Li A, Jia S, Yobi A, Ge Z, Sato SJ, Zhang C, Angelovici R, Clemente TE, Holding DR. Editing of an Alpha-Kafirin Gene Family Increases, Digestibility and Protein Quality in Sorghum. PLANT PHYSIOLOGY 2018; 177:1425-1438. [PMID: 29925584 PMCID: PMC6084649 DOI: 10.1104/pp.18.00200] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/02/2018] [Indexed: 05/24/2023]
Abstract
Kafirins are the major storage proteins in sorghum (Sorghum bicolor) grains and form protein bodies with poor digestibility. Since kafirins are devoid of the essential amino acid lysine, they also impart poor protein quality to the kernel. The α-kafirins, which make up most of the total kafirins, are largely encoded by the k1C family of highly similar genes. We used a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing approach to target the k1C genes to create variants with reduced kafirin levels and improved protein quality and digestibility. A single guide RNA was designed to introduce mutations in a conserved region encoding the endoplasmic reticulum signal peptide of α-kafirins. Sequencing of kafirin PCR products revealed extensive edits in 25 of 26 events in one or multiple k1C family members. T1 and T2 seeds showed reduced α-kafirin levels, and selected T2 events showed significantly increased grain protein digestibility and lysine content. Thus, a single consensus single guide RNA carrying target sequence mismatches is sufficient for extensive editing of all k1C genes. The resulting quality improvements can be deployed rapidly for breeding and the generation of transgene-free, improved cultivars of sorghum, a major crop worldwide.
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Affiliation(s)
- Aixia Li
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Shangang Jia
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Abou Yobi
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65201
| | - Zhengxiang Ge
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska 68588
| | - Shirley J Sato
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska 68588
| | - Chi Zhang
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Ruthie Angelovici
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65201
| | - Thomas E Clemente
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - David R Holding
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
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29
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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30
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Wen S, Liu H, Li X, Chen X, Hong Y, Li H, Lu Q, Liang X. TALEN-mediated targeted mutagenesis of fatty acid desaturase 2 (FAD2) in peanut (Arachis hypogaea L.) promotes the accumulation of oleic acid. PLANT MOLECULAR BIOLOGY 2018; 97:177-185. [PMID: 29700675 DOI: 10.1007/s11103-018-0731-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
A first creation of high oleic acid peanut varieties by using transcription activator-like effecter nucleases (TALENs) mediated targeted mutagenesis of Fatty Acid Desaturase 2 (FAD2). Transcription activator like effector nucleases (TALENs), which allow the precise editing of DNA, have already been developed and applied for genome engineering in diverse organisms. However, they are scarcely used in higher plant study and crop improvement, especially in allopolyploid plants. In the present study, we aimed to create targeted mutagenesis by TALENs in peanut. Targeted mutations in the conserved coding sequence of Arachis hypogaea fatty acid desaturase 2 (AhFAD2) were created by TALENs. Genetic stability of AhFAD2 mutations was identified by DNA sequencing in up to 9.52 and 4.11% of the regeneration plants at two different targeted sites, respectively. Mutation frequencies among AhFAD2 mutant lines were significantly correlated to oleic acid accumulation. Genetically, stable individuals of positive mutant lines displayed a 0.5-2 fold increase in the oleic acid content compared with non-transgenic controls. This finding suggested that TALEN-mediated targeted mutagenesis could increase the oleic acid content in edible peanut oil. Furthermore, this was the first report on peanut genome editing event, and the obtained high oleic mutants could serve for peanut breeding project.
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Affiliation(s)
- Shijie Wen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xingyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China.
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31
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Lowder LG, Zhou J, Zhang Y, Malzahn A, Zhong Z, Hsieh TF, Voytas DF, Zhang Y, Qi Y. Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems. MOLECULAR PLANT 2018; 11:245-256. [PMID: 29197638 DOI: 10.1016/j.molp.2017.11.010] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 05/22/2023]
Abstract
User-friendly tools for robust transcriptional activation of endogenous genes are highly demanded in plants. We previously showed that a dCas9-VP64 system consisting of the deactivated CRISPR-associated protein 9 (dCas9) fused with four tandem repeats of the transcriptional activator VP16 (VP64) could be used for transcriptional activation of endogenous genes in plants. In this study, we developed a second generation of vector systems for enhanced transcriptional activation in plants. We tested multiple strategies for dCas9-based transcriptional activation, and found that simultaneous recruitment of VP64 by dCas9 and a modified guide RNA scaffold gRNA2.0 (designated CRISPR-Act2.0) yielded stronger transcriptional activation than the dCas9-VP64 system. Moreover, we developed a multiplex transcription activator-like effector activation (mTALE-Act) system for simultaneous activation of up to four genes in plants. Our results suggest that mTALE-Act is even more effective than CRISPR-Act2.0 in most cases tested. In addition, we explored tissue-specific gene activation using positive feedback loops. Interestingly, our study revealed that certain endogenous genes are more amenable than others to transcriptional activation, and tightly regulated genes may cause target gene silencing when perturbed by activation probes. Hence, these new tools could be used to investigate gene regulatory networks and their control mechanisms. Assembly of multiplex CRISPR-Act2.0 and mTALE-Act systems are both based on streamlined and PCR-independent Golden Gate and Gateway cloning strategies, which will facilitate transcriptional activation applications in both dicots and monocots.
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Affiliation(s)
- Levi G Lowder
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jianping Zhou
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology and Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Yiping Qi
- Department of Biology, East Carolina University, Greenville, NC 27858, USA; Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
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Eriksson D, Brinch-Pedersen H, Chawade A, Holme IB, Hvoslef-Eide TAK, Ritala A, Teeri TH, Thorstensen T. Scandinavian perspectives on plant gene technology: applications, policies and progress. PHYSIOLOGIA PLANTARUM 2018; 162:219-238. [PMID: 29080293 DOI: 10.1111/ppl.12661] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/10/2017] [Accepted: 10/25/2017] [Indexed: 05/29/2023]
Abstract
Plant research and breeding has a long and successful history in the Scandinavian countries, Denmark, Finland, Norway and Sweden. Researchers in the region have been early in adopting plant gene technologies as they developed. This review gives a background, as well as discuss the current and future progress of plant gene technology in these four countries. Country-specific details of the regulation of genetically modified plants are described, as well as similarities and differences in the approach to regulation of novel genome-editing techniques. Also, the development of a sustainable bioeconomy may encompass the application of plant gene technology and we discuss whether or not this is reflected in current associated national strategies. In addition, country-specific information about the opinion of the public and other stakeholders on plant gene technology is presented, together with a country-wise political comparison and a discussion of the potential reciprocal influence between public opinion and the political process of policy development. The Scandinavian region is unique in several aspects, such as climate and certain agriculturally related regulations, and at the same time the region is vulnerable to changes in plant breeding investments due to the relatively small market sizes. It is therefore important to discuss the role and regulation of innovative solutions in Scandinavian plant research and breeding.
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Affiliation(s)
- Dennis Eriksson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden
| | - Henrik Brinch-Pedersen
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden
| | - Inger B Holme
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, 4300 Slagelse, Denmark
| | - Trine A K Hvoslef-Eide
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Anneli Ritala
- VTT Technical Research Centre of Finland Ltd., P.O.Box 1000, FI-02044 Espoo, Finland
| | - Teemu H Teeri
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, 00014 Finland
| | - Tage Thorstensen
- Department of Biotechnology and Molecular Genetics, Norwegian Institute of Bioeconomy Research, P.O. Box 115 NO-1431, Ås, Norway
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Li C, Hao M, Wang W, Wang H, Chen F, Chu W, Zhang B, Mei D, Cheng H, Hu Q. An Efficient CRISPR/Cas9 Platform for Rapidly Generating Simultaneous Mutagenesis of Multiple Gene Homoeologs in Allotetraploid Oilseed Rape. FRONTIERS IN PLANT SCIENCE 2018; 9:442. [PMID: 29731757 PMCID: PMC5920024 DOI: 10.3389/fpls.2018.00442] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/21/2018] [Indexed: 05/20/2023]
Abstract
With the rapid development of sequence specific nucleases (SSNs) for genome targeting, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) is now considered the most promising method for functional genetic researches, as well as genetic improvement in crop plants. However, the gene redundancy feature within the allotetraploid rapeseed genome is one of the major obstacles for simultaneous modification of different homologs in the first generation. In addition, large scale screening to identify mutated transgenic plants is very time-and labor-consuming using the conventional restriction enzyme-based approaches. In this study, a streamlined rapeseed CRISPR-Cas9 genome editing platform was developed through synthesizing a premade U6-26 driven sgRNA expression cassette and optimizing polyacrylamide gel electrophoresis (PAGE)-based screening approach. In our experiment, a sgRNA was constructed to target five rapeseed SPL3 homologous gene copies, BnSPL3-A5/BnSPL3-A4/BnSPL3-C3/BnSPL3-C4/BnSPL3-Cnn. High-throughput sequencing analysis demonstrated that the editing frequency of CRISPR/Cas9-induced mutagenesis ranged from 96.8 to 100.0% in plants with obvious heteroduplexed PAGE bands, otherwise this proportion was only 0.00-60.8%. Consistent with those molecular analyses, Bnspl3 mutants exhibited developmental delay phenotype in the first generation. In summary, our data suggest that this set of CRISPR/Cas9 platform is qualified for rapidly generating and identifying simultaneous mutagenesis of multiple gene homologs in allotetraploid rapeseed.
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Affiliation(s)
- Chao Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Wenxiang Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Fan Chen
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Wen Chu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
- Hongtao Cheng
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
- *Correspondence: Qiong Hu
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Dalla Costa L, Malnoy M, Gribaudo I. Breeding next generation tree fruits: technical and legal challenges. HORTICULTURE RESEARCH 2017; 4:17067. [PMID: 29238598 PMCID: PMC5717367 DOI: 10.1038/hortres.2017.67] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/15/2017] [Accepted: 10/18/2017] [Indexed: 05/04/2023]
Abstract
The new plant breeding technologies (NPBTs) have recently emerged as powerful tools in the context of 'green' biotechnologies. They have wide potential compared to classical genetic engineering and they are attracting the interest of politicians, stakeholders and citizens due to the revolutionary impact they may have on agriculture. Cisgenesis and genome editing potentially allow to obtain pathogen-resistant plants or plants with enhanced qualitative traits by introducing or disrupting specific genes in shorter times compared to traditional breeding programs and by means of minimal modifications in the plant genome. Grapevine, the most important fruit crop in the world from an economical point of view, is a peculiar case for NPBTs because of the load of cultural aspects, varietal traditions and consumer demands, which hinder the use of classical breeding techniques and, furthermore, the application of genetic engineering to wine grape cultivars. Here we explore the technical challenges which may hamper the application of cisgenesis and genome editing to this perennial plant, in particular focusing on the bottlenecks of the Agrobacterium-mediated gene transfer. In addition, strategies to eliminate undesired sequences from the genome and to choose proper target sites are discussed in light of peculiar features of this species. Furthermore is reported an update of the international legislative frameworks regulating NPBT products which shows conflicting positions and, in the case of the European Union, a prolonged lack of regulation.
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Affiliation(s)
- Lorenza Dalla Costa
- Research and Innovation Centre, Fondazione Edmund Mach, via E Mach 1, San Michele a/Adige 38010, Italy
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, via E Mach 1, San Michele a/Adige 38010, Italy
| | - Ivana Gribaudo
- IPSP-CNR, Institute for Sustainable Plant Protection, National Research Council, Strada delle Cacce 73, Torino I-10135, Italy
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35
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Opportunities for genome editing in vegetable crops. Emerg Top Life Sci 2017; 1:193-207. [DOI: 10.1042/etls20170033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 11/17/2022]
Abstract
Vegetables include high-value crops with health-promoting effects and reduced environmental impact. The availability of genomic and biotechnological tools in certain species, coupled with the recent development of new breeding techniques based on precise editing of DNA, provides unique opportunities to finally take advantage of the past decades of detailed genetic analyses, thus making improvement of traits related to quality and stress tolerance achievable in a reasonable time frame. Recent reports of such approaches in vegetables illustrate the feasibility of obtaining multiple homozygous mutations in a single generation, heritable by the progeny, using stable or transient transformation approaches, which may not rely on the integration of unwanted foreign DNA. Application of these approaches to currently non-sequenced/tissue culture recalcitrant crops will contribute to meet the challenges posed by the increase in population and climate change.
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Mikami M, Toki S, Endo M. In Planta Processing of the SpCas9-gRNA Complex. PLANT & CELL PHYSIOLOGY 2017; 58:1857-1867. [PMID: 29040704 PMCID: PMC5921533 DOI: 10.1093/pcp/pcx154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/09/2017] [Indexed: 05/19/2023]
Abstract
In CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9)-mediated genome editing in plants, Streptococcus pyogenes Cas9 (SpCas9) protein and the required guide RNA (gRNA) are, in most cases, expressed from a stably integrated transgene. Generally, SpCas9 protein is expressed from an RNA polymerase (pol) II promoter, while gRNA is expressed from a pol III promoter. However, pol III promoters have not been much characterized other than in model plants, making it difficult to select appropriate promoters for specific applications, while pol II transcripts have to be processed to generate functional gRNAs. Recently, successful processing of a pol II transcript into functional gRNAs using ribozyme or Csy4-RNA cleavage systems has been demonstrated. Here, we show that functional gRNAs can be efficiently processed using SpCas9 protein and plant endogenous RNA cleavage systems without the need for a specific RNA processing system. In our system, SpCas9 RNA and gRNA are both transcribed as a single RNA using a single pol II promoter; translated SpCas9 protein can be bound to this RNA and, finally, extra RNA sequences are trimmed by plant RNA processing systems to form a functional SpCas9-gRNA complex. The efficiency of targeted mutagenesis using our novel SpCas9-gRNA fused system was comparable with that of the SpCas9-gRNA system with ribozyme sequence, achieving rates of up to 100% in rice. Our results could be useful in developing stable SpCas9-gRNA expression systems and in RNA virus vector-mediated genome editing systems in plants.
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Affiliation(s)
- Masafumi Mikami
- Graduate School of Nanobioscience, Yokohama City University, 22- 2 Seto, Yokohama, Kanagawa 236-0027, Japan
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Seiichi Toki
- Graduate School of Nanobioscience, Yokohama City University, 22- 2 Seto, Yokohama, Kanagawa 236-0027, Japan
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Yokohama, Kanagawa 244-0813, Japan
| | - Masaki Endo
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Samodelov SL, Zurbriggen MD. Quantitatively Understanding Plant Signaling: Novel Theoretical-Experimental Approaches. TRENDS IN PLANT SCIENCE 2017; 22:685-704. [PMID: 28668509 DOI: 10.1016/j.tplants.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
With the need to respond to and integrate a multitude of external and internal stimuli, plant signaling is highly complex, exhibiting signaling component redundancy and high interconnectedness between individual pathways. We review here novel theoretical-experimental approaches in manipulating plant signaling towards the goal of a comprehensive understanding and targeted quantitative control of plant processes. We highlight approaches taken in the field of synthetic biology used in other systems and discuss their applicability in plants. Finally, we introduce existing tools for the quantitative analysis and monitoring of plant signaling and the integration of experimentally obtained quantitative data into mathematical models. Incorporating principles of synthetic biology into plant sciences more widely will lead this field forward in both fundamental and applied research.
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Affiliation(s)
- Sophia L Samodelov
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany.
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38
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Malzahn A, Lowder L, Qi Y. Plant genome editing with TALEN and CRISPR. Cell Biosci 2017; 7:21. [PMID: 28451378 PMCID: PMC5404292 DOI: 10.1186/s13578-017-0148-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 11/10/2022] Open
Abstract
Genome editing promises giant leaps forward in advancing biotechnology, agriculture, and basic research. The process relies on the use of sequence specific nucleases (SSNs) to make DNA double stranded breaks at user defined genomic loci, which are subsequently repaired by two main DNA repair pathways: non-homologous end joining (NHEJ) and homology directed repair (HDR). NHEJ can result in frameshift mutations that often create genetic knockouts. These knockout lines are useful for functional and reverse genetic studies but also have applications in agriculture. HDR has a variety of applications as it can be used for gene replacement, gene stacking, and for creating various fusion proteins. In recent years, transcription activator-like effector nucleases and clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR associated protein 9 or CRISPR from Prevotella and Francisella 1 have emerged as the preferred SSNs for research purposes. Here, we review their applications in plant research, discuss current limitations, and predict future research directions in plant genome editing.
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Affiliation(s)
- Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
| | - Levi Lowder
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850 USA
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Wolt JD. Safety, Security, and Policy Considerations for Plant Genome Editing. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:215-241. [PMID: 28712498 DOI: 10.1016/bs.pmbts.2017.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome editing with engineered nucleases (GEEN) is increasingly used as a tool for gene discovery and trait development in crops through generation of targeted changes in endogenous genes. The development of the CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein), in particular, has enabled widespread use of genome editing. Research to date has not comprehensively addressed genome-editing specificity and off-target mismatches that may result in unintended changes within plant genomes or the potential for gene drive initiation. Governance and regulatory considerations for bioengineered crops derived from using GEEN will require greater clarity as to target specificity, the potential for mismatched edits, unanticipated downstream effects of off-target mutations, and assurance that genome reagents do not occur in finished products. Since governance and regulatory decision making involves robust standards of evidence extending from the laboratory to the postcommercial marketplace, developers of genome-edited crops must anticipate significant engagement and investment to address questions of regulators and civil society.
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Affiliation(s)
- Jeffrey D Wolt
- Biosafety Institute for Genetically Modified Agricultural Products, Iowa State University, Ames, IA, United States; Crop Bioengineering Consortium, Iowa State University, Ames, IA, United States.
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40
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Fondong VN. The Search for Resistance to Cassava Mosaic Geminiviruses: How Much We Have Accomplished, and What Lies Ahead. FRONTIERS IN PLANT SCIENCE 2017; 8:408. [PMID: 28392798 PMCID: PMC5365051 DOI: 10.3389/fpls.2017.00408] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/09/2017] [Indexed: 05/23/2023]
Abstract
The cassava mosaic disease (CMD), which occurs in all cassava growing regions of Africa and the Indian subcontinent, is caused by cassava mosaic geminiviruses (CMGs). CMGs are considered to be the most damaging vector-borne plant pathogens. So far, the most successful approach used to control these viruses has been the transfer of a polygenic recessive resistance locus, designated CMD1, from wild cassava to cassava cultivars. Further progress in harnessing natural resistance to contain CMGs has come from the discovery of the dominant monogenic resistance locus, CMD2, in some West African cassava cultivars. CMD2 has been combined with CMD1 through genetic crosses. Because of the limitations of the cassava breeding approach, especially with regard to time required to produce a variety and the loss of preferred agronomic attributes, efforts have been directed toward the deployment of genetic engineering approaches. Most of these approaches have been centered on RNA silencing strategies, developed mainly in the model plant Nicotiana benthamiana. Early RNA silencing platforms assessed for CMG resistance have been use of viral genes for co-suppression, antisense suppression or for hairpin RNAs-mediated gene silencing. Here, progress and challenges in the deployment of these approaches in the control of CMGs are discussed. Novel functional genomics approaches with potential to overcome some of the drawbacks of the current strategies are also discussed.
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Affiliation(s)
- Vincent N. Fondong
- Department of Biological Sciences, Delaware State UniversityDover, DE, USA
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41
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Genome Editing in Plants: An Overview of Tools and Applications. INTERNATIONAL JOURNAL OF AGRONOMY 2017. [DOI: 10.1155/2017/7315351] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence of genome manipulation methods promises a real revolution in biotechnology and genetic engineering. Targeted editing of the genomes of living organisms not only permits investigations into the understanding of the fundamental basis of biological systems but also allows addressing a wide range of goals towards improving productivity and quality of crops. This includes the creation of plants with valuable compositional properties and with traits that confer resistance to various biotic and abiotic stresses. During the past few years, several novel genome editing systems have been developed; these include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These exciting new methods, briefly reviewed herein, have proved themselves as effective and reliable tools for the genetic improvement of plants.
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