1
|
Sun K, Fu K, Hu T, Shentu X, Yu X. Leveraging insect viruses and genetic manipulation for sustainable agricultural pest control. PEST MANAGEMENT SCIENCE 2024; 80:2515-2527. [PMID: 37948321 DOI: 10.1002/ps.7878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/16/2023] [Accepted: 11/11/2023] [Indexed: 11/12/2023]
Abstract
The potential of insect viruses in the biological control of agricultural pests is well-recognized, yet their practical application faces obstacles such as host specificity, variable virulence, and resource scarcity. High-throughput sequencing (HTS) technologies have significantly advanced our capabilities in discovering and identifying new insect viruses, thereby enriching the arsenal for pest management. Concurrently, progress in reverse genetics has facilitated the development of versatile viral expression vectors. These vectors have enhanced the specificity and effectiveness of insect viruses in targeting specific pests, offering a more precise approach to pest control. This review provides a comprehensive examination of the methodologies employed in the identification of insect viruses using HTS. Additionally, it explores the domain of genetically modified insect viruses and their associated challenges in pest management. The adoption of these cutting-edge approaches holds great promise for developing environmentally sustainable and effective pest control solutions. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Kai Sun
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Kang Fu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Tao Hu
- Zhejinag Seed Industry Group Xinchuang Bio-breeding Co., Ltd., Hangzhou, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| |
Collapse
|
2
|
Genome Editing: A Promising Approach for Achieving Abiotic Stress Tolerance in Plants. Int J Genomics 2022; 2022:5547231. [PMID: 35465040 PMCID: PMC9033345 DOI: 10.1155/2022/5547231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/24/2022] [Indexed: 12/26/2022] Open
Abstract
The susceptibility of crop plants towards abiotic stresses is highly threatening to assure global food security as it results in almost 50% annual yield loss. To address this issue, several strategies like plant breeding and genetic engineering have been used by researchers from time to time. However, these approaches are not sufficient to ensure stress resilience due to the complexity associated with the inheritance of abiotic stress adaptive traits. Thus, researchers were prompted to develop novel techniques with high precision that can address the challenges connected to the previous strategies. Genome editing is the latest approach that is in the limelight for improving the stress tolerance of plants. It has revolutionized crop research due to its versatility and precision. The present review is an update on the different genome editing tools used for crop improvement so far and the various challenges associated with them. It also highlights the emerging potential of genome editing for developing abiotic stress-resilient crops.
Collapse
|
3
|
Nazir R, Mandal S, Mitra S, Ghorai M, Das N, Jha NK, Majumder M, Pandey DK, Dey A. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated genome-editing toolkit to enhance salt stress tolerance in rice and wheat. PHYSIOLOGIA PLANTARUM 2022; 174:e13642. [PMID: 35099818 DOI: 10.1111/ppl.13642] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/02/2022] [Accepted: 01/27/2022] [Indexed: 05/14/2023]
Abstract
The rice and wheat agricultural system is the primary source of food for billions across the world. However, the productivity and long-term sustainability of rice and wheat are threatened by a large number of abiotic stresses, especially salinity stress. Salinity has a significant impact on plant development and productivity and is one of the leading causes of crop yield losses in agricultural soils worldwide. Over the last few decades, several attempts have been undertaken to enhance salinity stress tolerance, most of which have relied on traditional or molecular breeding approaches. These approaches have so far been insufficient in addressing the issues of abiotic stress. However, due to the availability of genome sequences for cereal crops like rice and wheat and the development of genome editing techniques like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9 (Cas9), it is now possible to "edit" genes and influence key traits. Here, we review the application of the CRISPR/Cas9 system in both rice (Oryza sativa L.) and wheat (Triticum aestivum L.) to develop salinity tolerant cultivars. The CRISPR/Cas genome editing toolkit holds great promise of producing cereal crops tolerant to salt stress to increase agriculture resilience with a strong impact on the environment and public health.
Collapse
Affiliation(s)
- Romaan Nazir
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Sicon Mitra
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, India
| | - Mimosa Ghorai
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Neela Das
- Department of Botany, Rishi Bankim Chandra College, Naihati, West Bengal, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, India
| | | | - Devendra Kumar Pandey
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| |
Collapse
|
4
|
Gomès É, Maillot P, Duchêne É. Molecular Tools for Adapting Viticulture to Climate Change. FRONTIERS IN PLANT SCIENCE 2021; 12:633846. [PMID: 33643361 PMCID: PMC7902699 DOI: 10.3389/fpls.2021.633846] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.
Collapse
Affiliation(s)
- Éric Gomès
- EGFV, University of Bordeaux – Bordeaux Sciences-Agro – INRAE, Villenave d’Ornon, France
| | - Pascale Maillot
- SVQV, INRAE – University of Strasbourg, Colmar, France
- University of Haute Alsace, Mulhouse, France
| | - Éric Duchêne
- SVQV, INRAE – University of Strasbourg, Colmar, France
| |
Collapse
|
5
|
Petersen BL, Möller SR, Mravec J, Jørgensen B, Christensen M, Liu Y, Wandall HH, Bennett EP, Yang Z. Improved CRISPR/Cas9 gene editing by fluorescence activated cell sorting of green fluorescence protein tagged protoplasts. BMC Biotechnol 2019; 19:36. [PMID: 31208390 PMCID: PMC6580576 DOI: 10.1186/s12896-019-0530-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/29/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND CRISPR/Cas9 is widely used for precise genetic editing in various organisms. CRISPR/Cas9 editing may in many plants be hampered by the presence of complex and high ploidy genomes and inefficient or poorly controlled delivery of the CRISPR/Cas9 components to gamete cells or cells with regenerative potential. Optimized strategies and methods to overcome these challenges are therefore in demand. RESULTS In this study we investigated the feasibility of improving CRISPR/Cas9 editing efficiency by Fluorescence Activated Cell Sorting (FACS) of protoplasts. We used Agrobacterium infiltration in leaves of Nicotiana benthamiana for delivery of viral replicons for high level expression of gRNAs designed to target two loci in the genome, NbPDS and NbRRA, together with the Cas9 nuclease in fusion with the 2A self-splicing sequence and GFP (Cas9-2A-GFP). Protoplasts isolated from the infiltrated leaves were then subjected to FACS for selection of GFP enriched protoplast populations. This procedure resulted in a 3-5 fold (from 20 to 30% in unsorted to more than 80% in sorted) increase in mutation frequencies as evidenced by restriction enzyme analysis and the Indel Detection by Amplicon Analysis, which allows for high throughput profiling and quantification of the generated mutations. CONCLUSIONS FACS of protoplasts expressing GFP tagged CRISPR/Cas9, delivered through A. tumefaciens leaf infiltration, facilitated clear CRISPR/Cas9 mediated mutation enrichment in selected protoplast populations.
Collapse
Affiliation(s)
- Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Svenning Rune Möller
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Present Address: Centre for Novel Agricultural Products, University of York, Woodsmill Quay, Skeldergate, York, YO1 6DX UK
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Mikkel Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Present Address: UIT - Department of Chemistry, The Arctic University of Norway, Forskningsparken. 3, 9019 Tromsø, Norway
| | - Ying Liu
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Hans H. Wandall
- Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| |
Collapse
|
6
|
Naduthodi MIS, Mohanraju P, Südfeld C, D’Adamo S, Barbosa MJ, van der Oost J. CRISPR-Cas ribonucleoprotein mediated homology-directed repair for efficient targeted genome editing in microalgae Nannochloropsis oceanica IMET1. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:66. [PMID: 30962821 PMCID: PMC6432748 DOI: 10.1186/s13068-019-1401-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/09/2019] [Indexed: 06/07/2023]
Abstract
BACKGROUND Microalgae are considered as a sustainable feedstock for the production of biofuels and other value-added compounds. In particular, Nannochloropsis spp. stand out from other microalgal species due to their capabilities to accumulate both triacylglycerol (TAG) and polyunsaturated fatty acids (PUFAs). However, the commercialization of microalgae-derived products is primarily hindered by the high production costs compared to less sustainable alternatives. Efficient genome editing techniques leading to effective metabolic engineering could result in strains with enhanced productivities of interesting metabolites and thereby reduce the production costs. Competent CRISPR-based genome editing techniques have been reported in several microalgal species, and only very recently in Nannochloropsis spp. (2017). All the reported CRISPR-Cas-based systems in Nannochloropsis spp. rely on plasmid-borne constitutive expression of Cas9 and a specific guide, combined with repair of double-stranded breaks (DSB) by non-homologous end joining (NHEJ) for the target gene knockout. RESULTS In this study, we report for the first time an alternative approach for CRISPR-Cas-mediated genome editing in Nannochloropsis sp.; the Cas ribonucleoproteins (RNP) and an editing template were directly delivered into microalgal cells via electroporation, making Cas expression dispensable and homology-directed repair (HDR) possible with high efficiency. Apart from widely used SpCas9, Cas12a variants from three different bacterium were used for this approach. We observed that FnCas12a from Francisella novicida generated HDR-based targeted mutants with highest efficiency (up to 93% mutants among transformants) while AsCas12a from Acidaminococcus sp. resulted in the lowest efficiency. We initially show that the native homologous recombination (HR) system in N. oceanica IMET1 is not efficient for easy isolation of targeted mutants by HR. Cas9/sgRNA RNP delivery greatly enhanced HR at the target site, generating around 70% of positive mutant lines. CONCLUSION We show that the delivery of Cas RNP by electroporation can be an alternative approach to the presently reported plasmid-based Cas9 method for generating mutants of N. oceanica. The co-delivery of Cas-RNPs along with a dsDNA repair template efficiently enhanced HR at the target site, resulting in a remarkable higher percentage of positive mutant lines. Therefore, this approach can be used for efficient generation of targeted mutants in Nannochloropsis sp. In addition, we here report the activity of several Cas12a homologs in N. oceanica IMET1, identifying FnCas12a as the best performer for high efficiency targeted genome editing.
Collapse
Affiliation(s)
- Mihris Ibnu Saleem Naduthodi
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 PD Wageningen, The Netherlands
- Bioprocess Engineering Department, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 PD Wageningen, The Netherlands
| | - Christian Südfeld
- Bioprocess Engineering Department, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sarah D’Adamo
- Bioprocess Engineering Department, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maria J. Barbosa
- Bioprocess Engineering Department, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 PD Wageningen, The Netherlands
| |
Collapse
|
7
|
Sedeek KEM, Mahas A, Mahfouz M. Plant Genome Engineering for Targeted Improvement of Crop Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:114. [PMID: 30809237 PMCID: PMC6379297 DOI: 10.3389/fpls.2019.00114] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/23/2019] [Indexed: 05/18/2023]
Abstract
To improve food security, plant biology research aims to improve crop yield and tolerance to biotic and abiotic stress, as well as increasing the nutrient contents of food. Conventional breeding systems have allowed breeders to produce improved varieties of many crops; for example, hybrid grain crops show dramatic improvements in yield. However, many challenges remain and emerging technologies have the potential to address many of these challenges. For example, site-specific nucleases such as TALENs and CRISPR/Cas systems, which enable high-efficiency genome engineering across eukaryotic species, have revolutionized biological research and its applications in crop plants. These nucleases have been used in diverse plant species to generate a wide variety of site-specific genome modifications through strategies that include targeted mutagenesis and editing for various agricultural biotechnology applications. Moreover, CRISPR/Cas genome-wide screens make it possible to discover novel traits, expand the range of traits, and accelerate trait development in target crops that are key for food security. Here, we discuss the development and use of various site-specific nuclease systems for different plant genome-engineering applications. We highlight the existing opportunities to harness these technologies for targeted improvement of traits to enhance crop productivity and resilience to climate change. These cutting-edge genome-editing technologies are thus poised to reshape the future of agriculture and food security.
Collapse
Affiliation(s)
| | | | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| |
Collapse
|
8
|
Programmable Molecular Scissors: Applications of a New Tool for Genome Editing in Biotech. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:212-238. [PMID: 30641475 PMCID: PMC6330515 DOI: 10.1016/j.omtn.2018.11.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/23/2018] [Accepted: 11/23/2018] [Indexed: 01/04/2023]
Abstract
Targeted genome editing is an advanced technique that enables precise modification of the nucleic acid sequences in a genome. Genome editing is typically performed using tools, such as molecular scissors, to cut a defined location in a specific gene. Genome editing has impacted various fields of biotechnology, such as agriculture; biopharmaceutical production; studies on the structure, regulation, and function of the genome; and the creation of transgenic organisms and cell lines. Although genome editing is used frequently, it has several limitations. Here, we provide an overview of well-studied genome-editing nucleases, including single-stranded oligodeoxynucleotides (ssODNs), transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and CRISPR-Cas9 RNA-guided nucleases (CRISPR-Cas9). To this end, we describe the progress toward editable nuclease-based therapies and discuss the minimization of off-target mutagenesis. Future prospects of this challenging scientific field are also discussed.
Collapse
|
9
|
Fleming A, Abdalla EA, Maltecca C, Baes CF. Invited review: Reproductive and genomic technologies to optimize breeding strategies for genetic progress in dairy cattle. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-43-2018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Abstract. Dairy cattle breeders have exploited technological advances that have emerged in the past in regards to reproduction and genomics. The implementation of such technologies in routine breeding programs has permitted genetic gains in traditional milk production traits as well as, more recently, in low-heritability traits like health and fertility. As demand for dairy products increases, it is important for dairy breeders to optimize the use of available technologies and to consider the many emerging technologies that are currently being investigated in various fields. Here we review a number of technologies that have helped shape dairy breeding programs in the past and present, along with those potentially forthcoming. These tools have materialized in the areas of reproduction, genotyping and sequencing, genetic modification, and epigenetics. Although many of these technologies bring encouraging opportunities for genetic improvement of dairy cattle populations, their applications and benefits need to be weighed with their impacts on economics, genetic diversity, and society.
Collapse
|
10
|
|
11
|
Genome editing in livestock: Are we ready for a revolution in animal breeding industry? Transgenic Res 2017; 26:715-726. [DOI: 10.1007/s11248-017-0049-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 10/24/2017] [Indexed: 12/25/2022]
|
12
|
Abstract
New breeding techniques in plant agriculture exploded upon the scene about two years ago, in 2014. While these innovative plant breeding techniques, soon to be led by CRISPR/Cas9, initially appear to hold tremendous promise for plant breeding, if not a revolution for the industry, the question of how the products of these technologies will be regulated is rapidly becoming a key aspect of the technology's future potential. Regulation of innovative technologies and products has always lagged that of the science, but in the past decade, regulatory systems in many jurisdictions have become gridlocked as they try to regulate genetically modified (GM) crops. This regulatory incapability to efficiently assess and approve innovative new agricultural products is particularly important for new plant breeding techniques as if these techniques are classified as genetically modified breeding techniques, then their acceptance and future will diminish considerably as they will be rejected by the European Union. Conversely, if the techniques are accepted as conventional plant breeding, then the future is blindingly bright. This article examines the international debate about the regulation of new plant breeding techniques and then assesses how the Canadian regulatory system has approached the regulation of these technologies through two more public product approvals, GM apples and GM potatoes, then discusses other crop variety approval and those in the regulatory pipeline.
Collapse
Affiliation(s)
- Stuart J Smyth
- a Department of Agricultural and Resource Economics , University of Saskatchewan , Saskatoon , Saskatchewan , Canada
| |
Collapse
|
13
|
Genetic resistance - an alternative for controlling PRRS? Porcine Health Manag 2016; 2:27. [PMID: 28405453 PMCID: PMC5382513 DOI: 10.1186/s40813-016-0045-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/19/2016] [Indexed: 12/22/2022] Open
Abstract
PRRS is one of the most challenging diseases for world-wide pig production. Attempts for a sustainable control of this scourge by vaccination have not yet fully satisfied. With an increasing knowledge and methodology in disease resistance, a new world-wide endeavour has been started to support the combat of animal diseases, based on the existence of valuable gene variants with regard to any host-pathogen interaction. Several groups have produced a wealth of evidence for natural variability in resistance/susceptibility to PRRS in our commercial breeding lines. However, up to now, exploiting existing variation has failed because of the difficulty to detect the carriers of favourable and unfavourable alleles, especially with regard to such complex polygenic traits like resistance to PRRS. New hope comes from new genomic tools like next generation sequencing which have become extremely fast and low priced. Thus, research is booming world-wide and the jigsaw puzzle is filling up – slowly but steadily. On the other hand, knowledge from virological and biomedical basic research has opened the way for an “intervening way”, i.e. the modification of identified key genes that occupy key positions in PRRS pathogenesis, like CD163. CD163 was identified as the striking receptor in PRRSV entry and its knockout from the genome by gene editing has led to the production of pigs that were completely resistant to PRRSV – a milestone in modern pig breeding. However, at this early step, concerns remain about the acceptance of societies for gene edited products and regulation still awaits upgrading to the new technology. Further questions arise with regard to upcoming patents from an ethical and legal point of view. Eventually, the importance of CD163 for homeostasis, defence and immunity demands for more insight before its complete or partial silencing can be answered. Whatever path will be followed, even a partial abolishment of PRRSV replication will lead to a significant improvement of the disastrous herd situation, with a significant impact on welfare, performance, antimicrobial consumption and consumer protection. Genetics will be part of a future solution.
Collapse
|
14
|
Kanchiswamy CN. DNA-free genome editing methods for targeted crop improvement. PLANT CELL REPORTS 2016; 35:1469-74. [PMID: 27100964 DOI: 10.1007/s00299-016-1982-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/31/2016] [Indexed: 05/23/2023]
Abstract
Evolution of the next-generation clustered, regularly interspaced, short palindromic repeat/Cas9 (CRISPR/Cas9) genome editing tools, ribonucleoprotein (RNA)-guided endonuclease (RGEN) RNPs, is paving the way for developing DNA-free genetically edited crop plants. In this review, I discuss the various methods of RGEN RNPs tool delivery into plant cells and their limitations to adopt this technology to numerous crop plants. Furthermore, focus is given on the importance of developing DNA-free genome edited crop plants, including perennial crop plants. The possible regulation on the DNA-free, next-generation genome-edited crop plants is also highlighted.
Collapse
Affiliation(s)
- Chidananda Nagamangala Kanchiswamy
- Research and Innovation Centre, Genomics and Biology of Fruit Crop Department, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy.
| |
Collapse
|
15
|
Schaart JG, van de Wiel CCM, Lotz LAP, Smulders MJM. Opportunities for Products of New Plant Breeding Techniques. TRENDS IN PLANT SCIENCE 2016; 21:438-449. [PMID: 26654659 DOI: 10.1016/j.tplants.2015.11.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/30/2015] [Accepted: 11/06/2015] [Indexed: 05/21/2023]
Abstract
Various new plant breeding techniques (NPBT) have a similar aim, namely to produce improved crop varieties that are difficult to obtain through traditional breeding methods. Here, we review the opportunities for products created using NPBTs. We categorize products of these NPBTs into three product classes with a different degree of genetic modification. For each product class, recent examples are described to illustrate the potential for breeding new crops with improved traits. Finally, we touch upon the future applications of these methods, such as cisgenic potato genotypes in which specific combinations of Phytophthora infestans resistance genes have been stacked for use in durable cultivation, or the creation of new disease resistances by knocking out or removing S-genes using genome-editing techniques.
Collapse
Affiliation(s)
- Jan G Schaart
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands.
| | | | - Lambertus A P Lotz
- Wageningen UR Agrosystems Research, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Marinus J M Smulders
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| |
Collapse
|
16
|
Malyska A, Bolla R, Twardowski T. The Role of Public Opinion in Shaping Trajectories of Agricultural Biotechnology. Trends Biotechnol 2016; 34:530-534. [PMID: 27059762 DOI: 10.1016/j.tibtech.2016.03.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 11/16/2022]
Abstract
Science and technology are not autonomous entities and research trajectories are largely influenced by public opinion. The role of political decisions becomes especially evident in light of rapidly developing new breeding techniques (NBTs) and other genome editing methods for crop improvement. Decisions on how those new techniques should be regulated may not be based entirely on scientific rationale, and even if it is decided that crops produced by NBTs do not fall under the umbrella of genetically modified organisms (GMOs), their commercialization is by no means certain at this time. If and when adopted regulations do not comply with the public's perception of risks, policy makers will find themselves under pressure to ban or restrict the use of the respective products.
Collapse
Affiliation(s)
| | - Robert Bolla
- Tin Duck Consulting Chesterfield, St Louis County, MO, USA
| | - Tomasz Twardowski
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
17
|
Reid W, O'Brochta DA. Applications of genome editing in insects. CURRENT OPINION IN INSECT SCIENCE 2016; 13:43-54. [PMID: 27436552 DOI: 10.1016/j.cois.2015.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/14/2023]
Abstract
Insect genome editing was first reported 1991 in Drosophila melanogaster but the technology used was not portable to other species. Not until the recent development of facile, engineered DNA endonuclease systems has gene editing become widely available to insect scientists. Most applications in insects to date have been technical in nature but this is rapidly changing. Functional genomics and genetics-based insect control efforts will be major beneficiaries of the application of contemporary gene editing technologies. Engineered endonucleases like Cas9 make it possible to create powerful and effective gene drive systems that could be used to reduce or even eradicate specific insect populations. 'Best practices' for using Cas9-based editing are beginning to emerge making it easier and more effective to design and use but gene editing technologies still require traditional means of delivery in order to introduce them into somatic and germ cells of insects-microinjection of developing embryos. This constrains the use of these technologies by insect scientists. Insects created using editing technologies challenge existing governmental regulatory structures designed to manage genetically modified organisms.
Collapse
Affiliation(s)
- William Reid
- Institute for Bioscience and Biotechnology Research, Department of Entomology, University of Maryland, College Park, 9600 Gudelsky Drive, Rockville, MD 20850, United States
| | - David A O'Brochta
- Institute for Bioscience and Biotechnology Research, Department of Entomology, University of Maryland, College Park, 9600 Gudelsky Drive, Rockville, MD 20850, United States.
| |
Collapse
|
18
|
Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, Kim JS, Velasco R, Nagamangala Kanchiswamy C. DNA-Free Genetically Edited Grapevine and Apple Protoplast Using CRISPR/Cas9 Ribonucleoproteins. FRONTIERS IN PLANT SCIENCE 2016; 7:1904. [PMID: 28066464 PMCID: PMC5170842 DOI: 10.3389/fpls.2016.01904] [Citation(s) in RCA: 306] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/01/2016] [Indexed: 05/11/2023]
Abstract
The combined availability of whole genome sequences and genome editing tools is set to revolutionize the field of fruit biotechnology by enabling the introduction of targeted genetic changes with unprecedented control and accuracy, both to explore emergent phenotypes and to introduce new functionalities. Although plasmid-mediated delivery of genome editing components to plant cells is very efficient, it also presents some drawbacks, such as possible random integration of plasmid sequences in the host genome. Additionally, it may well be intercepted by current process-based GMO regulations, complicating the path to commercialization of improved varieties. Here, we explore direct delivery of purified CRISPR/Cas9 ribonucleoproteins (RNPs) to the protoplast of grape cultivar Chardonnay and apple cultivar such as Golden delicious fruit crop plants for efficient targeted mutagenesis. We targeted MLO-7, a susceptible gene in order to increase resistance to powdery mildew in grape cultivar and DIPM-1, DIPM-2, and DIPM-4 in the apple to increase resistance to fire blight disease. Furthermore, efficient protoplast transformation, the molar ratio of Cas9 and sgRNAs were optimized for each grape and apple cultivar. The targeted mutagenesis insertion and deletion rate was analyzed using targeted deep sequencing. Our results demonstrate that direct delivery of CRISPR/Cas9 RNPs to the protoplast system enables targeted gene editing and paves the way to the generation of DNA-free genome edited grapevine and apple plants.
Collapse
Affiliation(s)
- Mickael Malnoy
- Research and Innovation Centre, Genomics and Biology of Fruit Crop Department, Fondazione Edmund MachTrento, Italy
- *Correspondence: Mickael Malnoy, Chidananda Nagamangala Kanchiswamy,
| | - Roberto Viola
- Research and Innovation Centre, Genomics and Biology of Fruit Crop Department, Fondazione Edmund MachTrento, Italy
| | | | | | | | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic ScienceSeoul, Republic of Korea
- Department of Chemistry, Seoul National UniversitySeoul, Republic of Korea
| | - Riccardo Velasco
- Research and Innovation Centre, Genomics and Biology of Fruit Crop Department, Fondazione Edmund MachTrento, Italy
| | - Chidananda Nagamangala Kanchiswamy
- Research and Innovation Centre, Genomics and Biology of Fruit Crop Department, Fondazione Edmund MachTrento, Italy
- *Correspondence: Mickael Malnoy, Chidananda Nagamangala Kanchiswamy,
| |
Collapse
|
19
|
|
20
|
Kanchiswamy CN, Malnoy M, Velasco R, Kim JS, Viola R. Non-GMO genetically edited crop plants. Trends Biotechnol 2015; 33:489-91. [PMID: 25978870 DOI: 10.1016/j.tibtech.2015.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 01/14/2023]
Abstract
Direct delivery of purified Cas9 protein with guide RNA into plant cells, as opposed to plasmid-mediated delivery, displays high efficiency and reduced off-target effects. Following regeneration from edited cells, the ensuing plant is also likely to bypass genetically modified organism (GMO) legislation as the genome editing complex is degraded in the recipient cells.
Collapse
Affiliation(s)
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Gwanak-ro 1, Gwanak-gu, Seoul 151-747, South Korea; Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 151-747, South Korea
| | - Roberto Viola
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010 San Michele all'Adige (TN), Italy
| |
Collapse
|
21
|
Luo S, Li J, Stoddard TJ, Baltes NJ, Demorest ZL, Clasen BM, Coffman A, Retterath A, Mathis L, Voytas DF, Zhang F. Non-transgenic Plant Genome Editing Using Purified Sequence-Specific Nucleases. MOLECULAR PLANT 2015; 8:1425-7. [PMID: 26074033 DOI: 10.1016/j.molp.2015.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/13/2015] [Accepted: 05/27/2015] [Indexed: 05/19/2023]
Affiliation(s)
- Song Luo
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA.
| | - Jin Li
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Thomas J Stoddard
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Nicholas J Baltes
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Zachary L Demorest
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Benjamin M Clasen
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Andrew Coffman
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Adam Retterath
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Luc Mathis
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Daniel F Voytas
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| | - Feng Zhang
- Cellectis Plant Sciences, 600 County Road D West, Suite 8, New Brighton, MN 55112, USA
| |
Collapse
|
22
|
Lucht JM. Public Acceptance of Plant Biotechnology and GM Crops. Viruses 2015; 7:4254-81. [PMID: 26264020 PMCID: PMC4576180 DOI: 10.3390/v7082819] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 01/16/2023] Open
Abstract
A wide gap exists between the rapid acceptance of genetically modified (GM) crops for cultivation by farmers in many countries and in the global markets for food and feed, and the often-limited acceptance by consumers. This review contrasts the advances of practical applications of agricultural biotechnology with the divergent paths-also affecting the development of virus resistant transgenic crops-of political and regulatory frameworks for GM crops and food in different parts of the world. These have also shaped the different opinions of consumers. Important factors influencing consumer's attitudes are the perception of risks and benefits, knowledge and trust, and personal values. Recent political and societal developments show a hardening of the negative environment for agricultural biotechnology in Europe, a growing discussion-including calls for labeling of GM food-in the USA, and a careful development in China towards a possible authorization of GM rice that takes the societal discussions into account. New breeding techniques address some consumers' concerns with transgenic crops, but it is not clear yet how consumers' attitudes towards them will develop. Discussions about agriculture would be more productive, if they would focus less on technologies, but on common aims and underlying values.
Collapse
Affiliation(s)
- Jan M Lucht
- Scienceindustries, Swiss Business Association Chemistry Pharma Biotech, P.O. Box 1826, Zurich CH-8021, Switzerland.
| |
Collapse
|
23
|
Dossa GS, Sparks A, Cruz CV, Oliva R. Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems. FRONTIERS IN PLANT SCIENCE 2015; 6:305. [PMID: 25999970 PMCID: PMC4419666 DOI: 10.3389/fpls.2015.00305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/16/2015] [Indexed: 05/29/2023]
Abstract
Attempting to achieve long-lasting and stable resistance using uniformly deployed rice varieties is not a sustainable approach. The real situation appears to be much more complex and dynamic, one in which pathogens quickly adapt to resistant varieties. To prevent disease epidemics, deployment should be customized and this decision will require interdisciplinary actions. This perspective article aims to highlight the current progress on disease resistance deployment to control bacterial blight in rice. Although the model system rice-Xanthomonas oryzae pv. oryzae has distinctive features that underpin the need for a case-by-case analysis, strategies to integrate those elements into a unique decision tool could be easily extended to other crops.
Collapse
Affiliation(s)
- Gerbert S. Dossa
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
| | - Adam Sparks
- Crop and Environmental Sciences Division, International Rice Research Institute, Metro Manila, Philippines
| | - Casiana Vera Cruz
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| | - Ricardo Oliva
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| |
Collapse
|
24
|
Rajendran SRCK, Yau YY, Pandey D, Kumar A. CRISPR-Cas9 Based Genome Engineering: Opportunities in Agri-Food-Nutrition and Healthcare. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:261-75. [PMID: 25871888 DOI: 10.1089/omi.2015.0023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recently developed strategies and techniques that make use of the vast amount of genetic information to perform targeted perturbations in the genome of living organisms are collectively referred to as genome engineering. The wide array of applications made possible by the use of this technology range from agriculture to healthcare. This, along with the applications involving basic biological research, has made it a very dynamic and active field of research. This review focuses on the CRISPR system from its discovery and role in bacterial adaptive immunity to the most recent developments, and its possible applications in agriculture and modern medicine.
Collapse
Affiliation(s)
- Subin Raj Cheri Kunnumal Rajendran
- 1 Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology , Pantnagar, U.S. Nagar, Uttarakhand, India
| | | | | | | |
Collapse
|
25
|
Govindarajan S, Mannervik B, Silverman JA, Wright K, Regitsky D, Hegazy U, Purcell TJ, Welch M, Minshull J, Gustafsson C. Mapping of amino acid substitutions conferring herbicide resistance in wheat glutathione transferase. ACS Synth Biol 2015; 4:221-7. [PMID: 24905764 DOI: 10.1021/sb500242x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have used design of experiments (DOE) and systematic variance to efficiently explore glutathione transferase substrate specificities caused by amino acid substitutions. Amino acid substitutions selected using phylogenetic analysis were synthetically combined using a DOE design to create an information-rich set of gene variants, termed infologs. We used machine learning to identify and quantify protein sequence-function relationships against 14 different substrates. The resulting models were quantitative and predictive, serving as a guide for engineering of glutathione transferase activity toward a diverse set of herbicides. Predictive quantitative models like those presented here have broad applicability for bioengineering.
Collapse
Affiliation(s)
- Sridhar Govindarajan
- DNA2.0, Inc., 1140 O’Brien
Drive, Suite A, Menlo Park, California 94025, United States
| | - Bengt Mannervik
- Department
of Neurochemistry, Stockholm University, SE-10691 Stockholm, Sweden
| | - Joshua A. Silverman
- Calysta, 1140 O’Brien Drive, Suite
B, Menlo Park, California 94025, United States
| | - Kathy Wright
- DNA2.0, Inc., 1140 O’Brien
Drive, Suite A, Menlo Park, California 94025, United States
| | - Drew Regitsky
- Calysta, 1140 O’Brien Drive, Suite
B, Menlo Park, California 94025, United States
| | - Usama Hegazy
- National Research Centre, Dokki, Cairo 12311, Egypt
| | - Thomas J. Purcell
- DNA2.0, Inc., 1140 O’Brien
Drive, Suite A, Menlo Park, California 94025, United States
| | - Mark Welch
- DNA2.0, Inc., 1140 O’Brien
Drive, Suite A, Menlo Park, California 94025, United States
| | - Jeremy Minshull
- DNA2.0, Inc., 1140 O’Brien
Drive, Suite A, Menlo Park, California 94025, United States
| | - Claes Gustafsson
- DNA2.0, Inc., 1140 O’Brien
Drive, Suite A, Menlo Park, California 94025, United States
| |
Collapse
|
26
|
|
27
|
|
28
|
Affiliation(s)
- Huw D Jones
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| |
Collapse
|
29
|
Abstract
Novel targeted genetic modification (TagMo) techniques for plants have the potential to increase the speed and ease of genetic modification and fall outside existing regulatory authority. We conducted 31 interviews with expert-stakeholders to explore the differing visions they have for the future of plant TagMo environmental regulation. To guide our analysis we review the tenets of anticipatory governance in light of future studies literature on emerging technology, focusing on how to contribute to reflexivity by making explicit the assumptions within envisioned futures. Our findings reveal that the environmental regulation futures articulated by expert-stakeholders could be classified into three categories—optimistic, pragmatic, and critical—based on their differing underlying assumptions concerning what constitutes environmental risk and the adequacy of existing U.S. genetically modified plant regulations. By gathering these diverse perspectives on the future and studying how they differ, we hope to further the anticipatory governance-informed engagement with regulation and foster a more productive discussion of plant TagMo regulation.
Collapse
|
30
|
Laible G, Wei J, Wagner S. Improving livestock for agriculture - technological progress from random transgenesis to precision genome editing heralds a new era. Biotechnol J 2014; 10:109-20. [DOI: 10.1002/biot.201400193] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/04/2014] [Accepted: 11/24/2014] [Indexed: 12/17/2022]
|
31
|
Boch J, Bonas U, Lahaye T. TAL effectors--pathogen strategies and plant resistance engineering. THE NEW PHYTOLOGIST 2014; 204:823-32. [PMID: 25539004 DOI: 10.1111/nph.13015] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcription activator-like effectors (TALEs) from plant pathogenic Xanthomonas spp. and the related RipTALs from Ralstonia solanacearum are DNA-binding proteins with a modular DNA-binding domain. This domain is both predictable and programmable, which simplifies elucidation of TALE function in planta and facilitates generation of DNA-binding modules with desired specificity for biotechnological approaches. Recently identified TALE host target genes that either promote or stop bacterial disease provide new insights into how expression of TALE genes affects the plant–pathogen interaction. Since its elucidation the TALE code has been continuously refined and now provides a mature tool that, in combination with transcriptome profiling, allows rapid isolation of novel TALE target genes. The TALE code is also the basis for synthetic promoter-traps that mediate recognition of TALE or RipTAL proteins in engineered plants. In this review, we will summarize recent findings in plant-focused TALE research. In addition, we will provide an outline of the newly established gene isolation approach for TALE or RipTAL host target genes with an emphasis on potential pitfalls.
Collapse
|
32
|
Sprink T, Metje J, Hartung F. Plant genome editing by novel tools: TALEN and other sequence specific nucleases. Curr Opin Biotechnol 2014; 32:47-53. [PMID: 25448232 DOI: 10.1016/j.copbio.2014.11.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 10/30/2014] [Accepted: 11/10/2014] [Indexed: 01/08/2023]
Abstract
Genome editing technologies using sequence specific nucleases (SSNs) became a tremendously powerful and precise tool for reverse genetic approaches and applied biology. Transcription activator-like effector nucleases (TALENs) in particular, consisting of a free designable DNA binding domain and a nuclease, have been exploited today by a huge number of approaches in many different organisms. The convenience of designing the DNA binding domain and straightforward protocols for their assembly, as well as the broad number of applications in different scientific fields made it Natures method of the year 2011. TALENs act as molecular scissors by introducing double strand breaks (DSBs) to the DNA at a given location. The DSBs are subsequently repaired by the cell itself using different repair pathways such as non-homologous end joining (NHEJ) or homologous recombination (HR). These mechanisms can lead to deletions, insertions, replacements or larger chromosomal rearrangements. By offering a template DNA it is possible to channel the repair in direction of HR. In this article we review the recent findings in the field of SSN approaches with emphasis on plants.
Collapse
Affiliation(s)
- Thorben Sprink
- Julius Kühn Institut, Institute for Biosafety in Plant Biotechnology, Erwin Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Janina Metje
- Max Plank Institute for Biophysical Chemistry, Research Group Autophagy, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Hartung
- Julius Kühn Institut, Institute for Biosafety in Plant Biotechnology, Erwin Baur-Str. 27, 06484 Quedlinburg, Germany.
| |
Collapse
|
33
|
Yuan L, Grotewold E. Metabolic engineering to enhance the value of plants as green factories. Metab Eng 2014; 27:83-91. [PMID: 25461830 DOI: 10.1016/j.ymben.2014.11.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 11/08/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022]
Abstract
The promise of plants to serve as the green factories of the future is ever increasing. Plants have been used traditionally for construction, energy, food and feed. Bioactive compounds primarily derived from specialized plant metabolism continue to serve as important scaffold molecules for pharmaceutical drug production. Yet, the past few years have witnessed a growing interest on plants as the ultimate harvesters of carbon and energy from the sun, providing carbohydrate and lipid biofuels that would contribute to balancing atmospheric carbon. How can the metabolic output from plants be increased even further, and what are the bottlenecks? Here, we present what we perceive to be the main opportunities and challenges associated with increasing the efficiency of plants as chemical factories. We offer some perspectives on when it makes sense to use plants as production systems because the amount of biomass needed makes any other system unfeasible. However, there are other instances in which plants serve as great sources of biological catalysts, yet are not necessarily the best-suited systems for production. We also present emerging opportunities for manipulating plant genomes to make plant synthetic biology a reality.
Collapse
Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, United States
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS), Department of Molecular Genetics and Department of Horticulture and Crop Science, The Ohio State University, 012 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, United States.
| |
Collapse
|
34
|
Voytas DF, Gao C. Precision genome engineering and agriculture: opportunities and regulatory challenges. PLoS Biol 2014; 12:e1001877. [PMID: 24915127 PMCID: PMC4051594 DOI: 10.1371/journal.pbio.1001877] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Plant agriculture is poised at a technological inflection point. Recent advances in genome engineering make it possible to precisely alter DNA sequences in living cells, providing unprecedented control over a plant's genetic material. Potential future crops derived through genome engineering include those that better withstand pests, that have enhanced nutritional value, and that are able to grow on marginal lands. In many instances, crops with such traits will be created by altering only a few nucleotides among the billions that comprise plant genomes. As such, and with the appropriate regulatory structures in place, crops created through genome engineering might prove to be more acceptable to the public than plants that carry foreign DNA in their genomes. Public perception and the performance of the engineered crop varieties will determine the extent to which this powerful technology contributes towards securing the world's food supply.
Collapse
Affiliation(s)
- Daniel F. Voytas
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail: (DFV); (CG)
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (DFV); (CG)
| |
Collapse
|
35
|
Hartung F, Schiemann J. Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:742-52. [PMID: 24330272 DOI: 10.1111/tpj.12413] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 12/04/2013] [Accepted: 12/09/2013] [Indexed: 05/04/2023]
Abstract
Several new plant breeding techniques (NPBTs) have been developed during the last decade, and make it possible to precisely perform genome modifications in plants. The major problem, other than technical aspects, is the vagueness of regulation concerning these new techniques. Since the definition of eight NPBTs by a European expert group in 2007, there has been an ongoing debate on whether the resulting plants and their products are covered by GMO legislation. Obviously, cover by GMO legislation would severely hamper the use of NPBT, because genetically modified plants must pass a costly and time-consuming GMO approval procedure in the EU. In this review, we compare some of the NPBTs defined by the EU expert group with classical breeding techniques and conventional transgenic plants. The list of NPBTs may be shortened (or extended) during the international discussion process initiated by the Organization for Economic Co-operation and Development. From the scientific point of view, it may be argued that plants developed by NPBTs are often indistinguishable from classically bred plants and are not expected to possess higher risks for health and the environment. In light of the debate on the future regulation of NPBTs and the accumulated evidence on the biosafety of genetically modified plants that have been commercialized and risk-assessed worldwide, it may be suggested that plants modified by crop genetic improvement technologies, including genetic modification, NPBTs or other future techniques, should be evaluated according to the new trait and the resulting end product rather than the technique used to create the new plant variety.
Collapse
Affiliation(s)
- Frank Hartung
- Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin Baur Straße 27, D-06484, Quedlinburg, Germany
| | | |
Collapse
|
36
|
Chen K, Gao C. Targeted genome modification technologies and their applications in crop improvements. PLANT CELL REPORTS 2014; 33:575-83. [PMID: 24277082 DOI: 10.1007/s00299-013-1539-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 11/03/2013] [Accepted: 11/04/2013] [Indexed: 05/20/2023]
Abstract
Recent advances in genome engineering indicate that innovative crops developed by targeted genome modification (TGM) using site-specific nucleases (SSNs) have the potential to avoid the regulatory issues raised by genetically modified organisms. These powerful SSNs tools, comprising zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regulatory interspaced short palindromic repeats/CRISPR-associated systems, enable precise genome engineering by introducing DNA double-strand breaks that subsequently trigger DNA repair pathways involving either non-homologous end-joining or homologous recombination. Here, we review developments in genome-editing tools, summarize their applications in crop organisms, and discuss future prospects. We also highlight the ability of these tools to create non-transgenic TGM plants for next-generation crop breeding.
Collapse
Affiliation(s)
- Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | | |
Collapse
|
37
|
Smyth SJ, McDonald J, Falck-Zepeda J. Investment, regulation, and uncertainty: managing new plant breeding techniques. GM CROPS & FOOD 2013; 5:44-57. [PMID: 24499745 PMCID: PMC5033172 DOI: 10.4161/gmcr.27465] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
As with any technological innovation, time refines the technology, improving upon the original version of the innovative product. The initial GM crops had single traits for either herbicide tolerance or insect resistance. Current varieties have both of these traits stacked together and in many cases other abiotic and biotic traits have also been stacked. This innovation requires investment. While this is relatively straight forward, certain conditions need to exist such that investments can be facilitated. The principle requirement for investment is that regulatory frameworks render consistent and timely decisions. If the certainty of regulatory outcomes weakens, the potential for changes in investment patterns increases.
This article provides a summary background to the leading plant breeding technologies that are either currently being used to develop new crop varieties or are in the pipeline to be applied to plant breeding within the next few years. Challenges for existing regulatory systems are highlighted. Utilizing an option value approach from investment literature, an assessment of uncertainty regarding the regulatory approval for these varying techniques is undertaken. This research highlights which technology development options have the greatest degree of uncertainty and hence, which ones might be expected to see an investment decline.
Collapse
Affiliation(s)
- Stuart J Smyth
- Department Bioresource Policy, Business and Economics; University of Saskatchewan; Saskatoon, SK Canada
| | - Jillian McDonald
- Department Bioresource Policy, Business and Economics; University of Saskatchewan; Saskatoon, SK Canada
| | - Jose Falck-Zepeda
- International Food Policy Research Institute (IFPRI); Washington, DC USA
| |
Collapse
|
38
|
Whitford R, Fleury D, Reif JC, Garcia M, Okada T, Korzun V, Langridge P. Hybrid breeding in wheat: technologies to improve hybrid wheat seed production. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5411-28. [PMID: 24179097 DOI: 10.1093/jxb/ert333] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Global food security demands the development and delivery of new technologies to increase and secure cereal production on finite arable land without increasing water and fertilizer use. There are several options for boosting wheat yields, but most offer only small yield increases. Wheat is an inbred plant, and hybrids hold the potential to deliver a major lift in yield and will open a wide range of new breeding opportunities. A series of technological advances are needed as a base for hybrid wheat programmes. These start with major changes in floral development and architecture to separate the sexes and force outcrossing. Male sterility provides the best method to block self-fertilization, and modifying the flower structure will enhance pollen access. The recent explosion in genomic resources and technologies provides new opportunities to overcome these limitations. This review outlines the problems with existing hybrid wheat breeding systems and explores molecular-based technologies that could improve the hybrid production system to reduce hybrid seed production costs, a prerequisite for a commercial hybrid wheat system.
Collapse
Affiliation(s)
- Ryan Whitford
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
| | | | | | | | | | | | | |
Collapse
|
39
|
Dubouzet JG, Strabala TJ, Wagner A. Potential transgenic routes to increase tree biomass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 212:72-101. [PMID: 24094056 DOI: 10.1016/j.plantsci.2013.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 05/05/2023]
Abstract
Biomass is a prime target for genetic engineering in forestry because increased biomass yield will benefit most downstream applications such as timber, fiber, pulp, paper, and bioenergy production. Transgenesis can increase biomass by improving resource acquisition and product utilization and by enhancing competitive ability for solar energy, water, and mineral nutrients. Transgenes that affect juvenility, winter dormancy, and flowering have been shown to influence biomass as well. Transgenic approaches have increased yield potential by mitigating the adverse effects of prevailing stress factors in the environment. Simultaneous introduction of multiple genes for resistance to various stress factors into trees may help forest trees cope with multiple or changing environments. We propose multi-trait engineering for tree crops, simultaneously deploying multiple independent genes to address a set of genetically uncorrelated traits that are important for crop improvement. This strategy increases the probability of unpredictable (synergistic or detrimental) interactions that may substantially affect the overall phenotype and its long-term performance. The very limited ability to predict the physiological processes that may be impacted by such a strategy requires vigilance and care during implementation. Hence, we recommend close monitoring of the resultant transgenic genotypes in multi-year, multi-location field trials.
Collapse
|
40
|
Kuzhabekova A, Kuzma J. Mapping the emerging field of genome editing. TECHNOLOGY ANALYSIS & STRATEGIC MANAGEMENT 2013. [DOI: 10.1080/09537325.2013.850657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
41
|
Holme IB, Wendt T, Holm PB. Intragenesis and cisgenesis as alternatives to transgenic crop development. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:395-407. [PMID: 23421562 DOI: 10.1111/pbi.12055] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 05/21/2023]
Abstract
One of the major concerns of the general public about transgenic crops relates to the mixing of genetic materials between species that cannot hybridize by natural means. To meet this concern, the two transformation concepts cisgenesis and intragenesis were developed as alternatives to transgenesis. Both concepts imply that plants must only be transformed with genetic material derived from the species itself or from closely related species capable of sexual hybridization. Furthermore, foreign sequences such as selection genes and vector-backbone sequences should be absent. Intragenesis differs from cisgenesis by allowing use of new gene combinations created by in vitro rearrangements of functional genetic elements. Several surveys show higher public acceptance of intragenic/cisgenic crops compared to transgenic crops. Thus, although the intragenic and cisgenic concepts were introduced internationally only 9 and 7 years ago, several different traits in a variety of crops have currently been modified according to these concepts. Five of these crops are now in field trials and two have pending applications for deregulation. Currently, intragenic/cisgenic plants are regulated as transgenic plants worldwide. However, as the gene pool exploited by intragenesis and cisgenesis are identical to the gene pool available for conventional breeding, less comprehensive regulatory measures are expected. The regulation of intragenic/cisgenic crops is presently under evaluation in the EU and in the US regulators are considering if a subgroup of these crops should be exempted from regulation. It is accordingly possible that the intragenic/cisgenic route will be of major significance for future plant breeding.
Collapse
Affiliation(s)
- Inger Bæksted Holme
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Research Centre Flakkebjerg, Slagelse, Denmark.
| | | | | |
Collapse
|
42
|
Podevin N, Davies HV, Hartung F, Nogué F, Casacuberta JM. Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding. Trends Biotechnol 2013; 31:375-83. [PMID: 23601269 DOI: 10.1016/j.tibtech.2013.03.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/11/2013] [Accepted: 03/11/2013] [Indexed: 12/17/2022]
Abstract
Conventional plant breeding exploits existing genetic variability and introduces new variability by mutagenesis. This has proven highly successful in securing food supplies for an ever-growing human population. The use of genetically modified plants is a complementary approach but all plant breeding techniques have limitations. Here, we discuss how the recent evolution of targeted mutagenesis and DNA insertion techniques based on tailor-made site-directed nucleases (SDNs) provides opportunities to overcome such limitations. Plant breeding companies are exploiting SDNs to develop a new generation of crops with new and improved traits. Nevertheless, some technical limitations as well as significant uncertainties on the regulatory status of SDNs may challenge their use for commercial plant breeding.
Collapse
Affiliation(s)
- Nancy Podevin
- The European Food Safety Authority-EFSA, Via Carlo Magno 1A, Parma, Italy
| | | | | | | | | |
Collapse
|
43
|
|
44
|
Transgenic or not? No simple answer! New biotechnology-based plant breeding techniques and the regulatory landscape. EMBO Rep 2012; 13:1057-61. [PMID: 23154464 PMCID: PMC3512411 DOI: 10.1038/embor.2012.168] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
|
45
|
Curtin SJ, Voytas DF, Stupar RM. Genome Engineering of Crops with Designer Nucleases. THE PLANT GENOME 2012; 5:42-50. [PMID: 0 DOI: 10.3835/plantgenome2012.06.0008] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Shaun J. Curtin
- Dep. of Agronomy and Plant Genetics; Univ. of Minnesota; St. Paul MN 55108
| | - Daniel F. Voytas
- Dep. of Genetics, Cell Biology, and Development and Center for Genome Engineering; Univ. of Minnesota; Minneapolis MN 55455
| | - Robert M. Stupar
- Dep. of Agronomy and Plant Genetics; Univ. of Minnesota; St. Paul MN 55108
| |
Collapse
|
46
|
Tan WS, Carlson DF, Walton MW, Fahrenkrug SC, Hackett PB. Precision editing of large animal genomes. ADVANCES IN GENETICS 2012; 80:37-97. [PMID: 23084873 PMCID: PMC3683964 DOI: 10.1016/b978-0-12-404742-6.00002-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transgenic animals are an important source of protein and nutrition for most humans and will play key roles in satisfying the increasing demand for food in an ever-increasing world population. The past decade has experienced a revolution in the development of methods that permit the introduction of specific alterations to complex genomes. This precision will enhance genome-based improvement of farm animals for food production. Precision genetics also will enhance the development of therapeutic biomaterials and models of human disease as resources for the development of advanced patient therapies.
Collapse
Affiliation(s)
- Wenfang Spring Tan
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | | |
Collapse
|