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Liu S, Zenda T, Tian Z, Huang Z. Metabolic pathways engineering for drought or/and heat tolerance in cereals. FRONTIERS IN PLANT SCIENCE 2023; 14:1111875. [PMID: 37810398 PMCID: PMC10557149 DOI: 10.3389/fpls.2023.1111875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.
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Affiliation(s)
- Songtao Liu
- Hebei Key Laboratory of Quality & Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Zaimin Tian
- Hebei Key Laboratory of Quality & Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Zhihong Huang
- Hebei Key Laboratory of Quality & Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
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Su W, Xu M, Radani Y, Yang L. Technological Development and Application of Plant Genetic Transformation. Int J Mol Sci 2023; 24:10646. [PMID: 37445824 DOI: 10.3390/ijms241310646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Genetic transformation is an important strategy for enhancing plant biomass or resistance in response to adverse environments and population growth by imparting desirable genetic characteristics. Research on plant genetic transformation technology can promote the functional analysis of plant genes, the utilization of excellent traits, and precise breeding. Various technologies of genetic transformation have been continuously discovered and developed for convenient manipulation and high efficiency, mainly involving the delivery of exogenous genes and regeneration of transformed plants. Here, currently developed genetic transformation technologies were expounded and compared. Agrobacterium-mediated gene delivery methods are commonly used as direct genetic transformation, as well as external force-mediated ways such as particle bombardment, electroporation, silicon carbide whiskers, and pollen tubes as indirect ones. The regeneration of transformed plants usually involves the de novo organogenesis or somatic embryogenesis pathway of the explants. Ectopic expression of morphogenetic transcription factors (Bbm, Wus2, and GRF-GIF) can significantly improve plant regeneration efficiency and enable the transformation of some hard-to-transform plant genotypes. Meanwhile, some limitations in these gene transfer methods were compared including genotype dependence, low transformation efficiency, and plant tissue damage, and recently developed flexible approaches for plant genotype transformation are discussed regarding how gene delivery and regeneration strategies can be optimized to overcome species and genotype dependence. This review summarizes the principles of various techniques for plant genetic transformation and discusses their application scope and limiting factors, which can provide a reference for plant transgenic breeding.
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Affiliation(s)
- Wenbin Su
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Mingyue Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yasmina Radani
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Sharma KK, Palakolanu SR, Bhattacharya J, Shankhapal AR, Bhatnagar-Mathur P. CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects. Front Genet 2022; 13:999207. [PMID: 36276961 PMCID: PMC9582247 DOI: 10.3389/fgene.2022.999207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022] Open
Abstract
Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.
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Affiliation(s)
- Kiran K. Sharma
- Sustainable Agriculture Programme, The Energy and Resources Institute (TERI), India Habitat Center, New Delhi, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, Telangana, India
| | - Aishwarya R. Shankhapal
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- International Maize and Wheat Improvement Center (CIMMYT), México, United Kingdom
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Chen H, Neubauer M, Wang JP. Enhancing HR Frequency for Precise Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:883421. [PMID: 35592579 PMCID: PMC9113527 DOI: 10.3389/fpls.2022.883421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.
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Affiliation(s)
- Hao Chen
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Matthew Neubauer
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Matchett-Oates L, Braich S, Spangenberg GC, Rochfort S, Cogan NOI. In silico analysis enabling informed design for genome editing in medicinal cannabis; gene families and variant characterisation. PLoS One 2021; 16:e0257413. [PMID: 34551006 PMCID: PMC8457487 DOI: 10.1371/journal.pone.0257413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cannabis has been used worldwide for centuries for industrial, recreational and medicinal use, however, to date no successful attempts at editing genes involved in cannabinoid biosynthesis have been reported. This study proposes and develops an in silico best practices approach for the design and implementation of genome editing technologies in cannabis to target all genes involved in cannabinoid biosynthesis. RESULTS A large dataset of reference genomes was accessed and mined to determine copy number variation and associated SNP variants for optimum target edit sites for genotype independent editing. Copy number variance and highly polymorphic gene sequences exist in the genome making genome editing using CRISPR, Zinc Fingers and TALENs technically difficult. Evaluation of allele or additional gene copies was determined through nucleotide and amino acid alignments with comparative sequence analysis performed. From determined gene copy number and presence of SNPs, multiple online CRISPR design tools were used to design sgRNA targeting every gene, accompanying allele and homologs throughout all involved pathways to create knockouts for further investigation. Universal sgRNA were designed for highly homologous sequences using MultiTargeter and visualised using Sequencher, creating unique sgRNA avoiding SNP and shared nucleotide locations targeting optimal edit sites. CONCLUSIONS Using this framework, the approach has wider applications to all plant species regardless of ploidy number or highly homologous gene sequences. SIGNIFICANCE STATEMENT Using this framework, a best-practice approach to genome editing is possible in all plant species, including cannabis, delivering a comprehensive in silico evaluation of the cannabinoid pathway diversity from a large set of whole genome sequences. Identification of SNP variants across all genes could improve genome editing potentially leading to novel applications across multiple disciplines, including agriculture and medicine.
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Affiliation(s)
- L. Matchett-Oates
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - S. Braich
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - G. C. Spangenberg
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - S. Rochfort
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - N. O. I. Cogan
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
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6
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Matres JM, Hilscher J, Datta A, Armario-Nájera V, Baysal C, He W, Huang X, Zhu C, Valizadeh-Kamran R, Trijatmiko KR, Capell T, Christou P, Stoger E, Slamet-Loedin IH. Genome editing in cereal crops: an overview. Transgenic Res 2021; 30:461-498. [PMID: 34263445 PMCID: PMC8316241 DOI: 10.1007/s11248-021-00259-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/15/2021] [Indexed: 02/06/2023]
Abstract
Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of genome editing in the major cereal crops- rice, maize, wheat and barley. Genome editing has been used to achieve important agronomic and quality traits in cereals. These include adaptive traits to mitigate the effects of climate change, tolerance to biotic stresses, higher yields, more optimal plant architecture, improved grain quality and nutritional content, and safer products. Not all traits can be achieved through genome editing, and several technical and regulatory challenges need to be overcome for the technology to realize its full potential. Genome editing, however, has already revolutionized cereal crop improvement and is poised to shape future agricultural practices in conjunction with other breeding innovations.
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Affiliation(s)
- Jerlie Mhay Matres
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Akash Datta
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Victoria Armario-Nájera
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Xin Huang
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Rana Valizadeh-Kamran
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Kurniawan R Trijatmiko
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Inez H Slamet-Loedin
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines.
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Abstract
Conventional methods of DNA sequence insertion into plants, using Agrobacterium-mediated transformation or microprojectile bombardment, result in the integration of the DNA at random sites in the genome. These plants may exhibit altered agronomic traits as a consequence of disruption or silencing of genes that serve a critical function. Also, genes of interest inserted at random sites are often not expressed at the desired level. For these reasons, targeted DNA insertion at suitable genomic sites in plants is a desirable alternative. In this paper we review approaches of targeted DNA insertion in plant genomes, discuss current technical challenges, and describe promising applications of targeted DNA insertion for crop genetic improvement.
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8
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Kumar S, Rymarquis LA, Ezura H, Nekrasov V. Editorial: CRISPR-Cas in Agriculture: Opportunities and Challenges. FRONTIERS IN PLANT SCIENCE 2021; 12:672329. [PMID: 33841487 PMCID: PMC8034289 DOI: 10.3389/fpls.2021.672329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 05/29/2023]
Affiliation(s)
| | | | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Japan
| | - Vladimir Nekrasov
- Plant Sciences Department, Rothamsted Research, Harpenden, United Kingdom
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Barone P, Wu E, Lenderts B, Anand A, Gordon-Kamm W, Svitashev S, Kumar S. Efficient Gene Targeting in Maize Using Inducible CRISPR-Cas9 and Marker-free Donor Template. MOLECULAR PLANT 2020; 13:1219-1227. [PMID: 32574856 DOI: 10.1016/j.molp.2020.06.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 05/26/2023]
Abstract
CRISPR-Cas9 is a powerful tool for generating targeted mutations and genomic deletions. However, precise gene insertion or sequence replacement remains a major hurdle before application of CRISPR-Cas9 technology is fully realized in plant breeding. Here, we report high-frequency, selectable marker-free intra-genomic gene targeting (GT) in maize. Heat shock-inducible Cas9 was used for generating targeted double-strand breaks and simultaneous mobilization of the donor template from pre-integrated T-DNA. The construct was designed such that release of the donor template and subsequent DNA repair activated expression of the selectable marker gene within the donor locus. This approach generated up to 4.7% targeted insertion of the donor sequence into the target locus in T0 plants, with up to 86% detected donor template release and 99% mutation rate being observed at the donor loci and the genomic target site, respectively. Unlike previous in planta or intra-genomic homologous recombination reports in which the original chimeric GT plants required extensive progeny screening in the next generation to identify non-chimeric GT individuals, our method provides non-chimeric heritable GT in one generation.
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Affiliation(s)
| | - Emily Wu
- Corteva Agriscience™, Johnston, IA 50131, USA
| | | | - Ajith Anand
- Corteva Agriscience™, Johnston, IA 50131, USA
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Gao H, Mutti J, Young JK, Yang M, Schroder M, Lenderts B, Wang L, Peterson D, St. Clair G, Jones S, Feigenbutz L, Marsh W, Zeng M, Wagner S, Farrell J, Snopek K, Scelonge C, Sopko X, Sander JD, Betts S, Cigan AM, Chilcoat ND. Complex Trait Loci in Maize Enabled by CRISPR-Cas9 Mediated Gene Insertion. FRONTIERS IN PLANT SCIENCE 2020; 11:535. [PMID: 32431725 PMCID: PMC7214728 DOI: 10.3389/fpls.2020.00535] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/08/2020] [Indexed: 05/03/2023]
Abstract
Modern maize hybrids often contain biotech and native traits. To-date all biotech traits have been randomly inserted in the genome. Consequently, developing hybrids with multiple traits is expensive, time-consuming, and complex. Here we report using CRISPR-Cas9 to generate a complex trait locus (CTL) to facilitate trait stacking. A CTL consists of multiple preselected sites positioned within a small well-characterized chromosomal region where trait genes are inserted. We generated individual lines, each carrying a site-specific insertion landing pad (SSILP) that was targeted to a preselected site and capable of efficiently receiving a transgene via recombinase-mediated cassette exchange. The selected sites supported consistent transgene expression and the SSILP insertion had no effect on grain yield. We demonstrated that two traits residing at different sites within a CTL can be combined via genetic recombination. CTL technology is a major step forward in the development of multi-trait maize hybrids.
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Affiliation(s)
- Huirong Gao
- Research and Development, Corteva Agriscience, Johnston, IA, United States
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Eckerstorfer MF, Dolezel M, Heissenberger A, Miklau M, Reichenbecher W, Steinbrecher RA, Waßmann F. An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs). Front Bioeng Biotechnol 2019; 7:31. [PMID: 30891445 PMCID: PMC6413072 DOI: 10.3389/fbioe.2019.00031] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/05/2019] [Indexed: 12/23/2022] Open
Abstract
The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.
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Affiliation(s)
| | - Marion Dolezel
- Department Landuse & Biosafety, Environment Agency Austria, Vienna, Austria
| | | | - Marianne Miklau
- Department Landuse & Biosafety, Environment Agency Austria, Vienna, Austria
| | - Wolfram Reichenbecher
- Department GMO Regulation, Biosafety, Federal Agency for Nature Conservation, Bonn, Germany
| | | | - Friedrich Waßmann
- Department GMO Regulation, Biosafety, Federal Agency for Nature Conservation, Bonn, Germany
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12
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Mall T, Gupta M, Dhadialla TS, Rodrigo S. Overview of Biotechnology-Derived Herbicide Tolerance and Insect Resistance Traits in Plant Agriculture. Methods Mol Biol 2019; 1864:313-342. [PMID: 30415345 DOI: 10.1007/978-1-4939-8778-8_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biotechnology has been central for the acceleration of crop improvement over the last two decades. Since 1994, when the first commercial biotechnology-derived tomato crop was commercialized, the cultivated area for genetically modified crops has reached 185.1 million hactares worldwide. Both the number of crops and the number of traits developed using biotechnology have accounted for this increase. Among the most impactful biotechnology-derived traits are insect resistance and herbicide tolerance, which have greatly contributed to the worldwide increase in agricultural productivity and stabilization of food security. In this chapter, we provide an overview of the history of the biotechnology-derived input traits, the existing genetically engineered commercial crop products carrying insect resistance and herbicide tolerance traits, as well as a perspective on how new technologies could further impact the development of new traits in crops. With the projection of the world population to increase to 9.8 billion by the year 2050 and reduction in available farmland, one of the biggest challenges will be to provide sustainable nourishment to the projected population. Biotechnology will continue to be the key enabler for development of insect resistance and herbicide tolerance traits to overcome that imminent challenge.
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Affiliation(s)
- Tejinder Mall
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
| | - Manju Gupta
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
| | | | - Sarria Rodrigo
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA.
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13
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Trait stacking in modern agriculture: application of genome editing tools. Emerg Top Life Sci 2017; 1:151-160. [PMID: 33525762 DOI: 10.1042/etls20170012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 11/17/2022]
Abstract
Advances in plant transgenic technology in the 20th century overcame the major hurdle for transfer of genetic material between species. This not only enabled fundamental insights into plant biology, but also revolutionized commercial agriculture. Adoption of transgenic plants in industrial agriculture has reduced pesticide application, while bringing significant increase in crop yields and farmers' profits. The progress made in transgenic technology over the last three decades paved the way mainly for simple single-gene insect and herbicide tolerance (HT) trait products. Modern agriculture demands stacking and pyramiding of complex traits that provide broad-spectrum insect and HT with other agronomic traits. In addition, more recent developments in genome editing provide unique opportunities to create precise on-demand genome modifications to enhance crop productivity. The major challenge for the plant biotech industry therefore remains to combine multiple forms of traits needed to create commercially viable stacked product. This review provides a historical perspective of conventional breeding stacks, current status of molecular stacks and future developments needed to enable genome-editing technology for trait stacking.
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Davies JP, Kumar S, Sastry-Dent L. Use of Zinc-Finger Nucleases for Crop Improvement. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:47-63. [PMID: 28712500 DOI: 10.1016/bs.pmbts.2017.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the past two decades, new technologies enabling targeted modification of plant genomes have been developed. Among these are zinc-finger nucleases (ZFNs) which are composed of engineered zinc-finger DNA-binding domains fused with a nuclease, generally the FokI nuclease. The zinc-finger domains are composed of a series of four to six 30 amino acid domains that can bind to trinucleotide sequences giving the entire DNA-binding domain specificity to 12-18 nucleotides. Since the FokI nuclease functions as a dimer, pairs of zinc-finger domains are designed to bind upstream and downstream of the cut site which increases the specificity of the complete ZFN to 24-36 nucleotides. The ability of these engineered nucleases to create targeted double-stranded breaks at designated locations throughout the genome has enabled precise deletion, addition, and editing of genes. These techniques are being used to create new genetic variation by deleting or editing endogenous gene sequences and enhancing the efficiency of transgenic product development through targeted insertion of transgenes to specific genomic locations and to sequentially add and/or delete transgenes from existing transgenic events.
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15
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Beringer J, Chen W, Garton R, Sardesai N, Wang PH, Zhou N, Gupta M, Wu H. Comparison of the impact of viral and plant-derived promoters regulating selectable marker gene on maize transformation and transgene expression. PLANT CELL REPORTS 2017; 36:519-528. [PMID: 28160062 PMCID: PMC5360835 DOI: 10.1007/s00299-017-2099-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/02/2017] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE The choice of promoter regulating the selectable marker gene impacts transformation efficiency, copy number and the expression of selectable marker and flanking genes in maize. Viral or plant-derived constitutive promoters are often used to regulate selectable marker genes. We compared two viral promoters, cauliflower mosaic virus (CaMV 35T) and sugarcane bacilliform virus (SCBV) with two plant promoters, rice actin1 (OsAct1) and maize ubiquitin 1 (ZmUbi1) to drive aryloxyalkanoate dioxygenase (aad-1) selectable marker gene in maize inbred line B104. ZmUbi1- and OsAct1-containing constructs demonstrated higher transformation frequencies (43.8 and 41.4%, respectively) than the two viral promoter constructs, CaMV 35T (25%) and SCBV (8%). Interestingly, a higher percentage of single copy events were recovered for SCBV (82.1%) and CaMV 35T (59.3%) promoter constructs, compared to the two plant-derived promoters, OsAct1 (40.0%), and ZmUbi1 (27.6%). Analysis of protein expression suggested that the viral promoter CaMV 35T expressed significantly higher AAD-1 protein (174.6 ng/cm2) than the OsAct1 promoter (12.6 ng/cm2) in T0 leaf tissue. When measured in T2 callus tissue, the two viral promoters both had higher expression and more variability than the two plant-derived promoters. A potential explanation for why viral promoters produce lower transformation efficiencies but higher percentages of low copy number events is discussed. In addition, viral promoters regulating aad-1 were found to influence the expression of upstream flanking genes in both T0 leaf and T2 callus tissue.
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Affiliation(s)
- Jeffrey Beringer
- Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Wei Chen
- Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Russell Garton
- Covance, Inc., 8211 SciCor Drive, Indianapolis, IN, 46214, USA
| | - Nagesh Sardesai
- Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Po-Hao Wang
- Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Ning Zhou
- Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Manju Gupta
- Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Huixia Wu
- Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
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16
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Kumar S, Worden A, Novak S, Lee R, Petolino JF. A trait stacking system via intra-genomic homologous recombination. PLANTA 2016; 244:1157-1166. [PMID: 27663725 DOI: 10.1007/s00425-016-2595-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/05/2016] [Indexed: 05/24/2023]
Abstract
MAIN CONCLUSION A gene targeting method has been developed, which allows the conversion of 'breeding stacks', containing unlinked transgenes into a 'molecular stack' and thereby circumventing the breeding challenges associated with transgene segregation. A gene targeting method has been developed for converting two unlinked trait loci into a single locus transgene stack. The method utilizes intra-genomic homologous recombination (IGHR) between stably integrated target and donor loci which share sequence homology and nuclease cleavage sites whereby the donor contains a promoterless herbicide resistance transgene. Upon crossing with a zinc finger nuclease (ZFN)-expressing plant, double-strand breaks (DSB) are created in both the stably integrated target and donor loci. DSBs flanking the donor locus result in intra-genomic mobilization of a promoterless selectable marker-containing donor sequence, which can be utilized as a template for homology-directed repair of a concomitant DSB at the target locus resulting in a functional selectable marker via nuclease-mediated cassette exchange (NMCE). The method was successfully demonstrated in maize using a glyphosate tolerance gene as a donor whereby up to 3.3 % of the resulting progeny embryos cultured on selection medium regenerated plants with the donor sequence integrated into the target locus. The process could be extended to multiple cycles of trait stacking by virtue of a unique intron sequence homology for NMCE between the target and the donor loci. This is the first report that describes NMCE via IGHR, thereby enabling trait stacking using conventional crossing.
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Affiliation(s)
- Sandeep Kumar
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Andrew Worden
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Stephen Novak
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Ryan Lee
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Joseph F Petolino
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
- Biotechnology Department, Ivy Tech Community College, 9301 East 59th Street, Indianapolis, IN, 46216, USA
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17
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Ma X, Zhu Q, Chen Y, Liu YG. CRISPR/Cas9 Platforms for Genome Editing in Plants: Developments and Applications. MOLECULAR PLANT 2016; 9:961-74. [PMID: 27108381 DOI: 10.1016/j.molp.2016.04.009] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 05/19/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (Cas9) genome editing system (CRISPR/Cas9) is adapted from the prokaryotic type II adaptive immunity system. The CRISPR/Cas9 tool surpasses other programmable nucleases, such as ZFNs and TALENs, for its simplicity and high efficiency. Various plant-specific CRISPR/Cas9 vector systems have been established for adaption of this technology to many plant species. In this review, we present an overview of current advances on applications of this technology in plants, emphasizing general considerations for establishment of CRISPR/Cas9 vector platforms, strategies for multiplex editing, methods for analyzing the induced mutations, factors affecting editing efficiency and specificity, and features of the induced mutations and applications of the CRISPR/Cas9 system in plants. In addition, we provide a perspective on the challenges of CRISPR/Cas9 technology and its significance for basic plant research and crop genetic improvement.
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Affiliation(s)
- Xingliang Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yuanling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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18
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Cardi T, Neal Stewart C. Progress of targeted genome modification approaches in higher plants. PLANT CELL REPORTS 2016; 35:1401-16. [PMID: 27025856 DOI: 10.1007/s00299-016-1975-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/21/2016] [Indexed: 05/07/2023]
Abstract
Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.
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Affiliation(s)
- Teodoro Cardi
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Centro di Ricerca per l'Orticoltura, Via Cavalleggeri 25, 84098, Pontecagnano, Italy.
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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19
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Liu D, Hu R, Palla KJ, Tuskan GA, Yang X. Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:70-7. [PMID: 26896588 DOI: 10.1016/j.pbi.2016.01.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 05/18/2023]
Abstract
Genome editing with site-specific nucleases has become a powerful tool for functional characterization of plant genes and genetic improvement of agricultural crops. Among the various site-specific nuclease-based technologies available for genome editing, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems have shown the greatest potential for rapid and efficient editing of genomes in plant species. This article reviews the current status of application of CRISPR/Cas9 to plant genomics research, with a focus on loss-of-function and gain-of-function analysis of individual genes in the context of perennial plants and the potential application of CRISPR/Cas9 to perturbation of gene expression, and identification and analysis of gene modules as part of an accelerated domestication and synthetic biology effort.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA.
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20
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Vanhaeren H, Inzé D, Gonzalez N. Plant Growth Beyond Limits. TRENDS IN PLANT SCIENCE 2016; 21:102-109. [PMID: 26739421 DOI: 10.1016/j.tplants.2015.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 05/09/2023]
Abstract
Growth processes, governed by complex genetic networks in a coordinated manner, are determining factors for numerous crop traits. Many components of these networks, described in Arabidopsis and to a lesser extent in crops, enhance organ growth when perturbed. However, translating our understanding of plant growth into crop improvement has been very limited. We argue here that this lack of success is due to the fact that modifying the expression of single genes in a complex growth regulatory network might be buffered by other components of the network. We discuss the observation that simultaneous perturbations of multiple genes have more pronounced effects, and present novel perspectives to use knowledge of growth regulatory networks to enhance crop yield in a targeted manner.
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Affiliation(s)
- Hannes Vanhaeren
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
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21
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Petolino JF, Kumar S. Transgenic trait deployment using designed nucleases. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:503-9. [PMID: 26332789 DOI: 10.1111/pbi.12457] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/08/2015] [Accepted: 07/16/2015] [Indexed: 05/09/2023]
Abstract
The demand for crops requiring increasingly complex combinations of transgenes poses unique challenges for transgenic trait deployment. Future value-adding traits such as those associated with crop performance are expected to involve multiple transgenes. Random integration of transgenes not only results in unpredictable expression and potential unwanted side effects but stacking multiple, randomly integrated, independently segregating transgenes creates breeding challenges during introgression and product development. Designed nucleases enable the creation of targeted DNA double-strand breaks at specified genomic locations whereby repair can result in targeted transgene integration leading to precise alterations in DNA sequences for plant genome editing, including the targeting of a transgene to a genomic locus that supports high-level and stable transgene expression without interfering with resident gene function. In addition, targeted DNA integration via designed nucleases allows for the addition of transgenes into previously integrated transgenic loci to create stacked products. The currently reported frequencies of independently generated transgenic events obtained with site-specific transgene integration without the aid of selection for targeting are very low. A modular, positive selection-based gene targeting strategy has been developed involving cassette exchange of selectable marker genes which allows for targeted events to be preferentially selected, over multiple cycles of sequential transformation. This, combined with the demonstration of intragenomic recombination following crossing of transgenic events that contain stably integrated donor and target DNA constructs with nuclease-expressing plants, points towards the future of trait stacking that is less dependent on high-efficiency transformation.
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22
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Forsyth A, Weeks T, Richael C, Duan H. Transcription Activator-Like Effector Nucleases (TALEN)-Mediated Targeted DNA Insertion in Potato Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1572. [PMID: 27826306 PMCID: PMC5078815 DOI: 10.3389/fpls.2016.01572] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/05/2016] [Indexed: 05/19/2023]
Abstract
Targeted DNA integration into known locations in the genome has potential advantages over the random insertional events typically achieved using conventional means of genetic modification. Specifically integrated transgenes are guaranteed to co-segregate, and expression level is more predictable, which makes downstream characterization and line selection more manageable. Because the site of DNA integration is known, the steps to deregulation of transgenic crops may be simplified. Here we describe a method that combines transcription activator-like effector nuclease (TALEN)-mediated induction of double strand breaks (DSBs) and non-autonomous marker selection to insert a transgene into a pre-selected, transcriptionally active region in the potato genome. In our experiment, TALEN was designed to create a DSB in the genome sequence following an endogenous constitutive promoter. A cytokinin vector was utilized for TALENs expression and prevention of stable integration of the nucleases. The donor vector contained a gene of interest cassette and a promoter-less plant-derived herbicide resistant gene positioned near the T-DNA left border which was used to select desired transgenic events. Our results indicated that TALEN induced T-DNA integration occurred with high frequency and resulting events have consistent expression of the gene of interest. Interestingly, it was found that, in most lines integration took place through one sided homology directed repair despite the minimal homologous sequence at the right border. An efficient transient assay for TALEN activity verification is also described.
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23
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Sun Y, Li J, Xia L. Precise Genome Modification via Sequence-Specific Nucleases-Mediated Gene Targeting for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2016; 7:1928. [PMID: 28066481 PMCID: PMC5167731 DOI: 10.3389/fpls.2016.01928] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/05/2016] [Indexed: 05/17/2023]
Abstract
Genome editing technologies enable precise modifications of DNA sequences in vivo and offer a great promise for harnessing plant genes in crop improvement. The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks by sequence-specific nucleases (SSNs) to initiate DNA repair reactions that are based on either non-homologous end joining (NHEJ) or homology-directed repair (HDR). While complete knock-outs and loss-of-function mutations generated by NHEJ are very valuable in defining gene functions, their applications in crop improvement are somewhat limited because many agriculturally important traits are conferred by random point mutations or indels at specific loci in either the genes' encoding or promoter regions. Therefore, genome modification through SSNs-mediated HDR for gene targeting (GT) that enables either gene replacement or knock-in will provide an unprecedented ability to facilitate plant breeding by allowing introduction of precise point mutations and new gene functions, or integration of foreign genes at specific and desired "safe" harbor in a predefined manner. The emergence of three programmable SSNs, such as zinc finger nucleases, transcriptional activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems has revolutionized genome modification in plants in a more controlled manner. However, while targeted mutagenesis is becoming routine in plants, the potential of GT technology has not been well realized for traits improvement in crops, mainly due to the fact that NHEJ predominates DNA repair process in somatic cells and competes with the HDR pathway, and thus HDR-mediated GT is a relative rare event in plants. Here, we review recent research findings mainly focusing on development and applications of precise GT in plants using three SSNs systems described above, and the potential mechanisms underlying HDR events in plant cells. We then address the challenges and propose future perspectives in order to facilitate the implementation of precise genome modification through SSNs-mediated GT for crop improvement in a global context.
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Kumar S, Barone P, Smith M. Gene targeting and transgene stacking using intra genomic homologous recombination in plants. PLANT METHODS 2016; 12:11. [PMID: 26839580 PMCID: PMC4736180 DOI: 10.1186/s13007-016-0111-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/14/2016] [Indexed: 05/04/2023]
Abstract
Modern agriculture has created a demand for plant biotechnology products that provide durable resistance to insect pests, tolerance of herbicide applications for weed control, and agronomic traits tailored for specific geographies. These transgenic trait products require a modular and sequential multigene stacking platform that is supported by precise genome engineering technology. Designed nucleases have emerged as potent tools for creating targeted DNA double strand breaks (DSBs). Exogenously supplied donor DNA can repair the targeted DSB by a process known as gene targeting (GT), resulting in a desired modification of the target genome. The potential of GT technology has not been fully realized for trait deployment in agriculture, mainly because of inefficient transformation and plant regeneration systems in a majority of crop plants and genotypes. This challenge of transgene stacking in plants could be overcome by Intra-Genomic Homologous Recombination (IGHR) that converts independently segregating unlinked donor and target transgenic loci into a genetically linked molecular stack. The method requires stable integration of the donor DNA into the plant genome followed by intra-genomic mobilization. IGHR complements conventional breeding with genetic transformation and designed nucleases to provide a flexible transgene stacking and trait deployment platform.
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Affiliation(s)
- Sandeep Kumar
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46286 USA
| | - Pierluigi Barone
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46286 USA
| | - Michelle Smith
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46286 USA
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Wang C, Li C, Leslie CA, Sun Q, Guo X, Yang K. Molecular cloning and heterologous expression analysis of JrVTE1 gene from walnut ( Juglans regia). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:222. [PMID: 26612974 PMCID: PMC4648991 DOI: 10.1007/s11032-015-0414-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
Tocopherol cyclase (VTE1) plays a key role in promoting the production of γ-tocopherol and improving total tocopherol content in photosynthetic organisms. Walnut is an important source of tocopherols in the human diet, and γ-tocopherol is the major tocopherol compound in walnut kernels. In this study, a full-length cDNA of the VTE1 gene was isolated from walnut using RT-PCR and RACE, and designated as JrVTE1. The full-length cDNA of the JrVTE1 gene contained a 1353-bp open-reading frame encoding a 451-amino-acid protein with a calculated molecular weight of 49.5 kDa. The deduced JrVTE1 protein had a considerable homology with other plant VTE1s and belonged to the tocopherol cyclase family. Functional characterization of JrVTE1 by heterologous expression was carried out in E. coli BL21 (DE3) and microshoot lines of the fruit trees jujube (Zizyphus jujuba var. spinosa) and pear (Pyrus communis) cultivar 'Old Home'. JrVTE1 in E. coli expressed as a 50 kDa protein, as expected. One or two copies of the transferred JrVTE1 gene were detected in the genomes of representative transgenic lines (from the initial transgenic plants) of jujube and pear by gel blots analysis. Over-expression of JrVTE1 in jujube and pear resulted in an accumulation of tocopherol and a shift in tocopherol composition in leaf, root and stem tissues. In the transgenic jujube, the total tocopherol content increased by 29.8 μg/g in the stems of line J3, 43.7 and 22.5 μg/g in the roots and leaves of line J1, respectively, whereas in the transgenic pear it increased by 47.3 μg/g in the leaf of line P3, and 16.7 and 10.4 μg/g in roots and stems of line P9, respectively. In the examined tissues of transgenic plants, the highest accumulation rate was the γ-tocopherol. These results indicate that JrVTE1 is one of the rate-limiting enzymes for tocopherol production and could be used to improve the tocopherol content of tree crops through genetic engineering.
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Affiliation(s)
- Cancan Wang
- />College of Forestry, Shandong Agricultural University, Taian, 271018 Shandong Province People’s Republic of China
- />Shandong Taishan Forest Ecosystem Research Station, Taian, 271018 People’s Republic of China
| | - Chuanrong Li
- />College of Forestry, Shandong Agricultural University, Taian, 271018 Shandong Province People’s Republic of China
- />Shandong Taishan Forest Ecosystem Research Station, Taian, 271018 People’s Republic of China
| | - Charles A. Leslie
- />Department of Plant Sciences, University of California-Davis, Davis, CA 95616 USA
| | - Qingrong Sun
- />Shandong Institute of Pomology, Taian, 271018 Shandong Province People’s Republic of China
| | - Xianfeng Guo
- />College of Forestry, Shandong Agricultural University, Taian, 271018 Shandong Province People’s Republic of China
| | - Keqiang Yang
- />College of Forestry, Shandong Agricultural University, Taian, 271018 Shandong Province People’s Republic of China
- />Shandong Taishan Forest Ecosystem Research Station, Taian, 271018 People’s Republic of China
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26
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Nandy S, Zhao S, Pathak BP, Manoharan M, Srivastava V. Gene stacking in plant cell using recombinases for gene integration and nucleases for marker gene deletion. BMC Biotechnol 2015; 15:93. [PMID: 26452472 PMCID: PMC4600305 DOI: 10.1186/s12896-015-0212-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/01/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Practical approaches for multigene transformation and gene stacking are extremely important for engineering complex traits and adding new traits in transgenic crops. Trait deployment by gene stacking would greatly simplify downstream plant breeding and trait introgression into cultivars. Gene stacking into pre-determined genomic sites depends on mechanisms of targeted DNA integration and recycling of selectable marker genes. Targeted integrations into chromosomal breaks, created by nucleases, require large transformation efforts. Recombinases such as Cre-lox, on the other hand, efficiently drive site-specific integrations in plants. However, the reversibility of Cre-lox recombination, due to the incorporation of two cis-positioned lox sites, presents a major bottleneck in its application in gene stacking. Here, we describe a strategy of resolving this bottleneck through excision of one of the cis-positioned lox, embedded in the marker gene, by nuclease activity. METHODS All transgenic lines were developed by particle bombardment of rice callus with plasmid constructs. Standard molecular approach was used for building the constructs. Transgene loci were analyzed by PCR, Southern hybridization, and DNA sequencing. RESULTS We developed a highly efficient gene stacking method by utilizing powerful recombinases such as Cre-lox and FLP-FRT, for site-specific gene integrations, and nucleases for marker gene excisions. We generated Cre-mediated site-specific integration locus in rice and showed excision of marker gene by I-SceI at ~20 % efficiency, seamlessly connecting genes in the locus. Next, we showed ZFN could be used for marker excision, and the locus can be targeted again by recombinases. Hence, we extended the power of recombinases to gene stacking application in plants. Finally, we show that heat-inducible I-SceI is also suitable for marker excision, and therefore could serve as an important tool in streamlining this gene stacking platform. CONCLUSIONS A practical approach for gene stacking in plant cell was developed that allows targeted gene insertions through rounds of transformation, a method needed for introducing new traits into transgenic lines for their rapid deployment in the field. By using Cre-lox, a powerful site-specific recombination system, this method greatly improves gene stacking efficiency, and through the application of nucleases develops marker-free, seamless stack of genes at pre-determined chromosomal sites.
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Affiliation(s)
- Soumen Nandy
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Shan Zhao
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Bhuvan P Pathak
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Muthusamy Manoharan
- Department of Agriculture, 144 Woodard Hall, University of Arkansas at Pine Bluff, Pine Bluff, AR, 71601, USA.
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
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