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Das T, Anand U, Pal T, Mandal S, Kumar M, Radha, Gopalakrishnan AV, Lastra JMPDL, Dey A. Exploring the potential of CRISPR/Cas genome editing for vegetable crop improvement: An overview of challenges and approaches. Biotechnol Bioeng 2023; 120:1215-1228. [PMID: 36740587 DOI: 10.1002/bit.28344] [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: 06/02/2022] [Revised: 12/12/2022] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
Vegetables provide many nutrients in the form of fiber, vitamins, and minerals, which make them an important part of our diet. Numerous biotic and abiotic stresses can affect crop growth, quality, and yield. Traditional and modern breeding strategies to improve plant traits are slow and resource intensive. Therefore, it is necessary to find new approaches for crop improvement. Clustered regularly interspaced short palindromic repeats/CRISPR associated 9 (CRISPR/Cas9) is a genome editing tool that can be used to modify targeted genes for desirable traits with greater efficiency and accuracy. By using CRISPR/Cas9 editing to precisely mutate key genes, it is possible to rapidly generate new germplasm resources for the promotion of important agronomic traits. This is made possible by the availability of whole genome sequencing data and information on the function of genes responsible for important traits. In addition, CRISPR/Cas9 systems have revolutionized agriculture, making genome editing more versatile. Currently, genome editing of vegetable crops is limited to a few vegetable varieties (tomato, sweet potato, potato, carrot, squash, eggplant, etc.) due to lack of regeneration protocols and sufficient genome sequencing data. In this article, we summarize recent studies on the application of CRISPR/Cas9 in improving vegetable trait development and the potential for future improvement.
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Affiliation(s)
- Tuyelee Das
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Uttpal Anand
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Tarun Pal
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, Maharashtra, India
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - José M Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, IPNA-CSIC, Tenerife, Spain
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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Whole-Genome Transformation of Yeast Promotes Rare Host Mutations with a Single Causative SNP Enhancing Acetic Acid Tolerance. Mol Cell Biol 2022; 42:e0056021. [PMID: 35311587 PMCID: PMC9022575 DOI: 10.1128/mcb.00560-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Whole-genome (WG) transformation (WGT) with DNA from the same or another species has been used to obtain strains with superior traits. Very few examples have been reported in eukaryotes—most apparently involving integration of large fragments of foreign DNA into the host genome. We show that WGT of a haploid acetic acid-sensitive Saccharomyces cerevisiae strain with DNA from a tolerant strain, but not from nontolerant strains, generated many tolerant transformants, some of which were stable upon subculturing under nonselective conditions. The most tolerant stable transformant contained no foreign DNA but only seven nonsynonymous single nucleotide polymorphisms (SNPs), of which none was present in the donor genome. The SNF4 mutation c.[805G→T], generating Snf4E269*, was the main causative SNP. Allele exchange of SNF4E269* or snf4Δ in industrial strains with unrelated genetic backgrounds enhanced acetic acid tolerance during fermentation under industrially relevant conditions. Our work reveals a surprisingly small number of mutations introduced by WGT, which do not bear any sequence relatedness to the genomic DNA (gDNA) of the donor organism, including the causative mutation. Spontaneous mutagenesis under protection of a transient donor gDNA fragment, maintained as extrachromosomal circular DNA (eccDNA), might provide an explanation. Support for this mechanism was obtained by transformation with genomic DNA of a yeast strain containing NatMX and selection on medium with nourseothricin. Seven transformants were obtained that gradually lost their nourseothricin resistance upon subculturing in nonselective medium. Our work shows that WGT is an efficient strategy for rapidly generating and identifying superior alleles capable of improving selectable traits of interest in industrial yeast strains.
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Omics Profiles of Non-transgenic Scion Grafted on Transgenic RdDM Rootstock. Food Saf (Tokyo) 2022; 10:13-31. [PMID: 35510071 PMCID: PMC9008877 DOI: 10.14252/foodsafetyfscj.d-21-00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/16/2021] [Indexed: 11/21/2022] Open
Abstract
Grafting of commercial varieties onto transgenic stress-tolerant rootstocks is attractive
approach, because fruit from the non-transgenic plant body does not contain foreign genes.
RNA silencing can modulate gene expression and protect host plants from viruses and
insects, and small RNAs (sRNAs), key molecules of RNA silencing, can move systemically.
Here, to evaluate the safety of foods obtained from sRNA-recipient plant bodies, we
investigated the effects of rootstock-derived sRNAs involved in mediating RNA-directed DNA
methylation (RdDM) on non-transgenic scions. We used tobacco rootstocks showing RdDM
against the cauliflower mosaic virus (CaMV) 35S promoter. When scions harboring CaMV 35S
promoter sequence were grafted onto RdDM-inducing rootstocks, we found that RdDM-inducing
sRNAs were only weakly transported from the rootstocks to the scion, and we observed a low
level of DNA methylation of the CaMV 35S promoter in the scion. Next, wild-type (WT)
tobacco scions were grafted onto RdDM-inducing rootstocks (designated NT) or WT rootstocks
(designated NN), and scion leaves were subjected to multi-omics analyses. Our
transcriptomic analysis detected 55 differentially expressed genes between the NT and NN
samples. A principal component analysis of proteome profiles showed no significant
differences. In the positive and negative modes of LC-ESI-MS and GC-EI-MS analyses, we
found a large overlap between the metabolomic clusters of the NT and NN samples. In
contrast, the negative mode of a LC-ESI-MS analysis showed separation of clusters of NT
and NN metabolites, and we detected 6 peak groups that significantly differed. In
conclusion, we found that grafting onto RdDM-inducing rootstocks caused a low-level
transmission of sRNAs, resulting in limited DNA methylation in the scion. However, the
causal relationships between sRNA transmission and the very slight changes in the
transcriptomic and metabolomic profiles of the scions remains unclear. The safety
assessment points for grafting with RdDM rootstocks are discussed.
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Effect of Transgenic Rootstock Grafting on the Omics Profiles in Tomato. Food Saf (Tokyo) 2021; 9:32-47. [PMID: 34249588 PMCID: PMC8254850 DOI: 10.14252/foodsafetyfscj.d-20-00032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/12/2021] [Indexed: 11/21/2022] Open
Abstract
Grafting of non-transgenic scion onto genetically modified (GM) rootstocks provides superior
agronomic traits in the GM rootstock, and excellent fruits can be produced for consumption. In
such grafted plants, the scion does not contain any foreign genes, but the fruit itself is
likely to be influenced directly or indirectly by the foreign genes in the rootstock. Before
market release of such fruit products, the effects of grafting onto GM rootstocks should be
determined from the perspective of safety use. Here, we evaluated the effects of a transgene
encoding β-glucuronidase (GUS) on the grafted tomato fruits as a model case. An edible tomato
cultivar, Stella Mini Tomato, was grafted onto GM Micro-Tom tomato plants that had been
transformed with the GUS gene. The grafted plants showed no difference in
their fruit development rate and fresh weight regardless of the presence or absence of the
GUS gene in the rootstock. The fruit samples were subjected to transcriptome
(NGS-illumina), proteome (shotgun LC-MS/MS), metabolome (LC-ESI-MS and GC-EI-MS), and general
food ingredient analyses. In addition, differentially detected items were identified between
the grafted plants onto rootstocks with or without transgenes (more than two-fold). The
transcriptome analysis detected approximately 18,500 expressed genes on average, and only 6
genes were identified as differentially expressed. Principal component analysis of 2,442 peaks
for peptides in proteome profiles showed no significant differences. In the LC-ESI-MS and
GC-EI-MS analyses, a total of 93 peak groups and 114 peak groups were identified, respectively,
and only 2 peak groups showed more than two-fold differences. The general food ingredient
analysis showed no significant differences in the fruits of Stella scions between GM and non-GM
Micro-Tom rootstocks. These multiple omics data showed that grafting on the rootstock harboring
the GUS transgene did not induce any genetic or metabolic variation in the
scion.
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Parker MT, Kunjapur AM. Deployment of Engineered Microbes: Contributions to the Bioeconomy and Considerations for Biosecurity. Health Secur 2021; 18:278-296. [PMID: 32816583 DOI: 10.1089/hs.2020.0010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Engineering at microscopic scales has an immense effect on the modern bioeconomy. Microbes contribute to such disparate markets as chemical manufacturing, fuel production, crop optimization, and pharmaceutical synthesis, to name a few. Due to new and emerging synthetic biology technologies, and the sophistication and control afforded by them, we are on the brink of deploying engineered microbes to not only enhance traditional applications but also to introduce these microbes to sectors, contexts, and formats not previously attempted. In microbially managed medicine, microbial engineering holds promise for increasing efficacy, improving tissue penetration, and sustaining treatment. In the environment, the most effective areas for deployment are in the management of crops and protection of ecosystems. However, caution is warranted before introducing engineered organisms to new environments where they may proliferate without control and could cause unforeseen effects. We summarize ideas and data that can inform identification and assessment of the risks that these tools present to ensure that realistic hazards are described and unrealistic ones do not hinder advancement. Further, because modes of containment are crucial complements to deployment, we describe the state of the art in microbial biocontainment strategies, current gaps, and how these gaps might be addressed through technological advances in synthetic engineering. Collectively, this work highlights engineered microbes as a foundational and expanding facet of the bioeconomy, projects their utility in upcoming deployments outside the laboratory, and identifies knowns and unknowns that will be necessary considerations and points of focus in this endeavor.
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Affiliation(s)
- Michael T Parker
- Michael T. Parker, PhD, is an Assistant Dean, Office of the Dean, Georgetown University, Washington, DC. Aditya M. Kunjapur, PhD, is an Assistant Professor, Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| | - Aditya M Kunjapur
- Michael T. Parker, PhD, is an Assistant Dean, Office of the Dean, Georgetown University, Washington, DC. Aditya M. Kunjapur, PhD, is an Assistant Professor, Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
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Deparis Q, Duitama J, Foulquié-Moreno MR, Thevelein JM. Whole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress. mBio 2021; 12:e03649-20. [PMID: 33758086 PMCID: PMC8092322 DOI: 10.1128/mbio.03649-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 11/20/2022] Open
Abstract
tRNAs are encoded by a large gene family, usually with several isogenic tRNAs interacting with the same codon. Mutations in the anticodon region of other tRNAs can overcome specific tRNA deficiencies. Phylogenetic analysis suggests that such mutations have occurred in evolution, but the driving force is unclear. We show that in yeast suppressor mutations in other tRNAs are able to overcome deficiency of the essential TRT2-encoded tRNAThrCGU at high temperature (40°C). Surprisingly, these tRNA suppressor mutations were obtained after whole-genome transformation with DNA from thermotolerant Kluyveromyces marxianus or Ogataea polymorpha strains but from which the mutations did apparently not originate. We suggest that transient presence of donor DNA in the host facilitates proliferation at high temperature and thus increases the chances for occurrence of spontaneous mutations suppressing defective growth at high temperature. Whole-genome sequence analysis of three transformants revealed only four to five nonsynonymous mutations of which one causing TRT2 anticodon stem stabilization and two anticodon mutations in non-threonyl-tRNAs, tRNALysCUU and tRNAeMetCAU, were causative. Both anticodon mutations suppressed lethality of TRT2 deletion and apparently caused the respective tRNAs to become novel substrates for threonyl-tRNA synthetase. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) data could not detect any significant mistranslation, and reverse transcription-quantitative PCR results contradicted induction of the unfolded protein response. We suggest that stress conditions have been a driving force in evolution for the selection of anticodon-switching mutations in tRNAs as revealed by phylogenetic analysis.IMPORTANCE In this work, we have identified for the first time the causative elements in a eukaryotic organism introduced by applying whole-genome transformation and responsible for the selectable trait of interest, i.e., high temperature tolerance. Surprisingly, the whole-genome transformants contained just a few single nucleotide polymorphisms (SNPs), which were unrelated to the sequence of the donor DNA. In each of three independent transformants, we have identified a SNP in a tRNA, either stabilizing the essential tRNAThrCGU at high temperature or switching the anticodon of tRNALysCUU or tRNAeMetCAU into CGU, which is apparently enough for in vivo recognition by threonyl-tRNA synthetase. LC-MS/MS analysis indeed indicated absence of significant mistranslation. Phylogenetic analysis showed that similar mutations have occurred throughout evolution and we suggest that stress conditions may have been a driving force for their selection. The low number of SNPs introduced by whole-genome transformation may favor its application for improvement of industrial yeast strains.
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Affiliation(s)
- Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
- NovelYeast bv, Open Bio-Incubator, Erasmus High School, Brussels (Jette), Belgium
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Kok EJ, Glandorf DC, Prins TW, Visser RG. Food and environmental safety assessment of new plant varieties after the European Court decision: Process-triggered or product-based? Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Langner T, Kamoun S, Belhaj K. CRISPR Crops: Plant Genome Editing Toward Disease Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:479-512. [PMID: 29975607 DOI: 10.1146/annurev-phyto-080417-050158] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.
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Affiliation(s)
- Thorsten Langner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Khaoula Belhaj
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
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Hameed A, Zaidi SSEA, Shakir S, Mansoor S. Applications of New Breeding Technologies for Potato Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:925. [PMID: 30008733 PMCID: PMC6034203 DOI: 10.3389/fpls.2018.00925] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/11/2018] [Indexed: 05/17/2023]
Abstract
The first decade of genetic engineering primarily focused on quantitative crop improvement. With the advances in technology, the focus of agricultural biotechnology has shifted toward both quantitative and qualitative crop improvement, to deal with the challenges of food security and nutrition. Potato (Solanum tuberosum L.) is a solanaceous food crop having potential to feed the populating world. It can provide more carbohydrates, proteins, minerals, and vitamins per unit area of land as compared to other potential food crops, and is the major staple food in many developing countries. These aspects have driven the scientific attention to engineer potato for nutrition improvement, keeping the yield unaffected. Several studies have shown the improved nutritional value of potato tubers, for example by enhancing Amaranth Albumin-1 seed protein content, vitamin C content, β-carotene level, triacylglycerol, tuber methionine content, and amylose content, etc. Removal of anti-nutritional compounds like steroidal glycoalkaloids, acrylamide and food toxins is another research priority for scientists and breeders to improve potato tuber quality. Trait improvement using genetic engineering mostly involved the generation of transgenic products. The commercialization of these engineered products has been a challenge due to consumer preference and regulatory/ethical restrictions. In this context, new breeding technolgies like TALEN (transcription activator-like effector nucleases) and CRISPR/Cas9 (clustered regularly interspaced palindromic repeats/CRISPR-associated 9) have been employed to generate transgene-free products in a more precise, prompt and effective way. Moreover, the availability of potato genome sequence and efficient potato transformation systems have remarkably facilitated potato genetic engineering. Here we summarize the potato trait improvement and potential application of new breeding technologies (NBTs) to genetically improve the overall agronomic profile of potato.
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Affiliation(s)
- Amir Hameed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Syed Shan-e-Ali Zaidi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Sara Shakir
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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Emerging crossover technologies: How to organize a biotechnology that becomes mainstream? ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s10669-017-9666-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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11
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Potential impact of genome editing in world agriculture. Emerg Top Life Sci 2017; 1:117-133. [PMID: 33525764 DOI: 10.1042/etls20170010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/22/2017] [Accepted: 09/28/2017] [Indexed: 12/26/2022]
Abstract
Changeable biotic and abiotic stress factors that affect crop growth and productivity, alongside a drive to reduce the unintended consequences of plant protection products, will demand highly adaptive farm management practices as well as access to continually improved seed varieties. The former is limited mainly by cost and, in theory, could be implemented in relatively short time frames. The latter is fundamentally a longer-term activity where genome editing can play a major role. The first targets for genome editing will inevitably be loss-of-function alleles, because these are straightforward to generate. In addition, they are likely to focus on traits under simple genetic control and where the results of modification are already well understood from null alleles in existing gene pools or other knockout or silencing approaches such as induced mutations or RNA interference. In the longer term, genome editing will underpin more fundamental changes in agricultural performance and food quality, and ultimately will merge with the tools and philosophies of synthetic biology to underpin and enable new cellular systems, processes and organisms completely. The genetic changes required for simple allele edits or knockout phenotypes are synonymous with those found naturally in conventional breeding material and should be regulated as such. The more radical possibilities in the longer term will need societal engagement along with appropriate safety and ethical oversight.
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Trindade de Carvalho B, Holt S, Souffriau B, Lopes Brandão R, Foulquié-Moreno MR, Thevelein JM. Identification of Novel Alleles Conferring Superior Production of Rose Flavor Phenylethyl Acetate Using Polygenic Analysis in Yeast. mBio 2017; 8:e01173-17. [PMID: 29114020 PMCID: PMC5676035 DOI: 10.1128/mbio.01173-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/29/2017] [Indexed: 11/20/2022] Open
Abstract
Flavor compound metabolism is one of the last areas in metabolism where multiple genes encoding biosynthetic enzymes are still unknown. A major challenge is the involvement of side activities of enzymes having their main function in other areas of metabolism. We have applied pooled-segregant whole-genome sequence analysis to identify novel Saccharomyces cerevisiae genes affecting production of phenylethyl acetate (2-PEAc). This is a desirable flavor compound of major importance in alcoholic beverages imparting rose- and honey-like aromas, with production of high 2-PEAc levels considered a superior trait. Four quantitative trait loci (QTLs) responsible for high 2-PEAc production were identified, with two loci each showing linkage to the genomes of the BTC.1D and ER18 parents. The first two loci were investigated further. The causative genes were identified by reciprocal allele swapping into both parents using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9. The superior allele of the first major causative gene, FAS2, was dominant and contained two unique single nucleotide polymorphisms (SNPs) responsible for high 2-PEAc production that were not present in other sequenced yeast strains. FAS2 encodes the alpha subunit of the fatty acid synthetase complex. Surprisingly, the second causative gene was a mutant allele of TOR1, a gene involved in nitrogen regulation. Exchange of both superior alleles in the ER18 parent strain increased 2-PEAc production 70%, nearly to the same level as in the best superior segregant. Our results show that polygenic analysis combined with CRISPR/Cas9-mediated allele exchange is a powerful tool for identification of genes encoding missing metabolic enzymes and for development of industrial yeast strains generating novel flavor profiles in alcoholic beverages.IMPORTANCE Multiple reactions in flavor metabolism appear to be catalyzed by side activities of other enzymes that have been difficult to identify. We have applied genetic mapping of quantitative trait loci in the yeast Saccharomyces cerevisiae to identify mutant alleles of genes determining the production of phenylethyl acetate, an important flavor compound imparting rose- and honey-like aromas to alcoholic beverages. We identified a unique, dominant allele of FAS2 that supports high production of phenylethyl acetate. FAS2 encodes a subunit of the fatty acid synthetase complex and apparently exerts an important side activity on one or more alternative substrates in flavor compound synthesis. The second mutant allele contained a nonsense mutation in TOR1, a gene involved in nitrogen regulation of growth. Together the two alleles strongly increased the level of phenylethyl acetate. Our work highlights the potential of genetic mapping of quantitative phenotypic traits to identify novel enzymes and regulatory components in yeast metabolism, including regular metabolic enzymes with unknown side activities responsible for biosynthesis of specific flavor compounds. The superior alleles identified can be used to develop industrial yeast strains generating novel flavor profiles in alcoholic beverages.
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Affiliation(s)
- Bruna Trindade de Carvalho
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Sylvester Holt
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Ben Souffriau
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Rogelio Lopes Brandão
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, ICEB II, Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, CEP 35, Ouro Preto, Brazil
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
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Limera C, Sabbadini S, Sweet JB, Mezzetti B. New Biotechnological Tools for the Genetic Improvement of Major Woody Fruit Species. FRONTIERS IN PLANT SCIENCE 2017; 8:1418. [PMID: 28861099 PMCID: PMC5559511 DOI: 10.3389/fpls.2017.01418] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/31/2017] [Indexed: 05/09/2023]
Abstract
The improvement of woody fruit species by traditional plant breeding techniques has several limitations mainly caused by their high degree of heterozygosity, the length of their juvenile phase and auto-incompatibility. The development of new biotechnological tools (NBTs), such as RNA interference (RNAi), trans-grafting, cisgenesis/intragenesis, and genome editing tools, like zinc-finger and CRISPR/Cas9, has introduced the possibility of more precise and faster genetic modifications of plants. This aspect is of particular importance for the introduction or modification of specific traits in woody fruit species while maintaining unchanged general characteristics of a selected cultivar. Moreover, some of these new tools give the possibility to obtain transgene-free modified fruit tree genomes, which should increase consumer's acceptance. Over the decades biotechnological tools have undergone rapid development and there is a continuous addition of new and valuable techniques for plant breeders. This makes it possible to create desirable woody fruit varieties in a fast and more efficient way to meet the demand for sustainable agricultural productivity. Although, NBTs have a common goal i.e., precise, fast, and efficient crop improvement, individually they are markedly different in approach and characteristics from each other. In this review we describe in detail their mechanisms and applications for the improvement of fruit trees and consider the relationship between these biotechnological tools and the EU biosafety regulations applied to the plants and products obtained through these techniques.
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Affiliation(s)
- Cecilia Limera
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Silvia Sabbadini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Jeremy B. Sweet
- J. T. Environmental Consultants LtdCambridge, United Kingdom
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
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van Hove L, Gillund F. Is it only the regulatory status? Broadening the debate on cisgenic plants. ENVIRONMENTAL SCIENCES EUROPE 2017; 29:22. [PMID: 28680789 PMCID: PMC5487859 DOI: 10.1186/s12302-017-0120-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/12/2017] [Indexed: 05/30/2023]
Abstract
In current debates on emerging technologies for plant breeding in Europe, much attention has been given to the regulatory status of these techniques and their public acceptance. At present, both genetically modified plants with cisgenic approaches-using genes from crossable species-as well as transgenic approaches-using genes from different species-fall under GMO regulation in the EU and both are mandatorily labelled as GMOs. Researchers involved in the early development of cisgenic GM plants convey the message that the potential use and acceptance of cisgenic approaches will be seriously hindered if GMO regulations are not adjusted. Although the similar treatment and labelling of transgenic and cisgenic plants may be a legitimate concern for the marketability of a cisgenic GM plant, there are concerns around their commercialization that reach beyond the current focus on (de)regulation. In this paper, we will use the development of the cisgenic GM potato that aims to overcome 'late blight'-the most devastating potato disease worldwide-as a case to argue that it is important to recognize, reflect and respond to broader concerns than the dominant focus on the regulatory 'burden' and consumer acceptance. Based on insights we gained from discussing this case with diverse stakeholders within the agricultural sector and potato production in Norway during a series of workshops, we elaborate on additional issues such as the (technical) solution offered; different understandings of the late blight problem; the durability of the potato plant resistance; and patenting and ownership. Hence, this paper contributes to empirical knowledge on stakeholder perspectives on emerging plant breeding technologies, underscoring the importance to broaden the scope of the debate on the opportunities and challenges of agricultural biotechnologies, such as cisgenic GM plants. The paper offers policy-relevant input to ongoing efforts to broaden the scope of risk assessments of agricultural biotechnologies. We aim to contribute to the recognition of the complex socio-ecological, legal and political dimensions in which these technological developments are entangled as a means to acknowledge, discuss and respond to these concerns and thereby contribute to more comprehensive and responsible developments within agricultural biotechnology.
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Affiliation(s)
- Lilian van Hove
- Society, Ecology and Ethics Department, GenØk Centre for Biosafety, SIVA Innovation Centre, 9294 Tromsø, Norway
| | - Frøydis Gillund
- Society, Ecology and Ethics Department, GenØk Centre for Biosafety, SIVA Innovation Centre, 9294 Tromsø, Norway
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Pacher M, Puchta H. From classical mutagenesis to nuclease-based breeding - directing natural DNA repair for a natural end-product. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:819-833. [PMID: 28027431 DOI: 10.1111/tpj.13469] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/22/2016] [Accepted: 12/22/2016] [Indexed: 05/18/2023]
Abstract
Production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damage in an error-prone way. In the case of radiation, multiple double-strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site-directed nucleases (SDNs) - also referred to as sequence-specific nucleases - like the CRISPR/Cas system has enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at pre-defined sites in plant genomes. As these changes are not necessarily associated with the permanent integration of foreign DNA, the obtained organisms per se cannot be regarded as genetically modified as there is no way to distinguish them from natural variants. This applies to changes induced by DSBs as well as single-strand breaks, and involves repair by non-homologous end-joining and homologous recombination. The recent development of SDN-based 'DNA-free' approaches makes mutagenesis strategies in classical breeding indistinguishable from SDN-derived targeted genome modifications, even in regard to current regulatory rules. With the advent of new SDN technologies, much faster and more precise genome editing becomes available at reasonable cost, and potentially without requiring time-consuming deregulation of newly created phenotypes. This review will focus on classical mutagenesis breeding and the application of newly developed SDNs in order to emphasize similarities in the context of the regulatory situation for genetically modified crop plants.
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Affiliation(s)
- Michael Pacher
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, PO 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, PO 6980, 76049, Karlsruhe, Germany
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Wolt JD. Safety, Security, and Policy Considerations for Plant Genome Editing. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:215-241. [PMID: 28712498 DOI: 10.1016/bs.pmbts.2017.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome editing with engineered nucleases (GEEN) is increasingly used as a tool for gene discovery and trait development in crops through generation of targeted changes in endogenous genes. The development of the CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein), in particular, has enabled widespread use of genome editing. Research to date has not comprehensively addressed genome-editing specificity and off-target mismatches that may result in unintended changes within plant genomes or the potential for gene drive initiation. Governance and regulatory considerations for bioengineered crops derived from using GEEN will require greater clarity as to target specificity, the potential for mismatched edits, unanticipated downstream effects of off-target mutations, and assurance that genome reagents do not occur in finished products. Since governance and regulatory decision making involves robust standards of evidence extending from the laboratory to the postcommercial marketplace, developers of genome-edited crops must anticipate significant engagement and investment to address questions of regulators and civil society.
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Affiliation(s)
- Jeffrey D Wolt
- Biosafety Institute for Genetically Modified Agricultural Products, Iowa State University, Ames, IA, United States; Crop Bioengineering Consortium, Iowa State University, Ames, IA, United States.
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Eriksson D, Ammann KH. A Universally Acceptable View on the Adoption of Improved Plant Breeding Techniques. FRONTIERS IN PLANT SCIENCE 2017; 7:1999. [PMID: 28105036 PMCID: PMC5215382 DOI: 10.3389/fpls.2016.01999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/16/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Dennis Eriksson
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
| | - Klaus H. Ammann
- Institute of Plant Sciences, University of BernBern, Switzerland
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Davison J, Ammann K. New GMO regulations for old: Determining a new future for EU crop biotechnology. GM CROPS & FOOD 2017; 8:13-34. [PMID: 28278120 PMCID: PMC5592979 DOI: 10.1080/21645698.2017.1289305] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
In this review, current EU GMO regulations are subjected to a point-by point analysis to determine their suitability for agriculture in modern Europe. Our analysis concerns present GMO regulations as well as suggestions for possible new regulations for genome editing and New Breeding Techniques (for which no regulations presently exist). Firstly, the present GMO regulations stem from the early days of recombinant DNA and are not adapted to current scientific understanding on this subject. Scientific understanding of GMOs has changed and these regulations are now, not only unfit for their original purpose, but, the purpose itself is now no longer scientifically valid. Indeed, they defy scientific, economic, and even common, sense. A major EU regulatory preconception is that GM crops are basically different from their parent crops. Thus, the EU regulations are "process based" regulations that discriminate against GMOs simply because they are GMOs. However current scientific evidence shows a blending of classical crops and their GMO counterparts with no clear demarcation line between them. Canada has a "product based" approach and determines the safety of each new crop variety independently of the process used to obtain it. We advise that the EC re-writes it outdated regulations and moves toward such a product based approach. Secondly, over the last few years new genomic editing techniques (sometimes called New Breeding Techniques) have evolved. These techniques are basically mutagenesis techniques that can generate genomic diversity and have vast potential for crop improvement. They are not GMO based techniques (any more than mutagenesis is a GMO technique), since in many cases no new DNA is introduced. Thus they cannot simply be lumped together with GMOs (as many anti-GMO NGOs would prefer). The EU currently has no regulations to cover these new techniques. In this review, we make suggestions as to how these new gene edited crops may be regulated. The EU is at a turning point where the wrong decision could destroy European agricultural competitively for decades to come.
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Affiliation(s)
- John Davison
- Research Director (retired), Institut National de la Recherche Agronomique (INRA), Versailles, France
| | - Klaus Ammann
- Former Director of the Botanical Garden, University of Bern, Bern, Switzerland
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19
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Genome Editing in Plants: An Overview of Tools and Applications. INTERNATIONAL JOURNAL OF AGRONOMY 2017. [DOI: 10.1155/2017/7315351] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence of genome manipulation methods promises a real revolution in biotechnology and genetic engineering. Targeted editing of the genomes of living organisms not only permits investigations into the understanding of the fundamental basis of biological systems but also allows addressing a wide range of goals towards improving productivity and quality of crops. This includes the creation of plants with valuable compositional properties and with traits that confer resistance to various biotic and abiotic stresses. During the past few years, several novel genome editing systems have been developed; these include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These exciting new methods, briefly reviewed herein, have proved themselves as effective and reliable tools for the genetic improvement of plants.
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Marchant GE, Stevens YA. A new window of opportunity to reject process-based biotechnology regulation. GM CROPS & FOOD 2016; 6:233-42. [PMID: 26930116 DOI: 10.1080/21645698.2015.1134406] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The question of whether biotechnology regulation should be based on the process or the product has long been debated, with different jurisdictions adopting different approaches. The European Union has adopted a process-based approach, Canada has adopted a product-based approach, and the United States has implemented a hybrid system. With the recent proliferation of new methods of genetic modification, such as gene editing, process-based regulatory systems, which are premised on a binary system of transgenic and conventional approaches, will become increasingly obsolete and unsustainable. To avoid unreasonable, unfair and arbitrary results, nations that have adopted process-based approaches will need to migrate to a product-based approach that considers the novelty and risks of the individual trait, rather than the process by which that trait was produced. This commentary suggests some approaches for the design of such a product-based approach.
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Affiliation(s)
- Gary E Marchant
- a Center for Law, Science & Innovation; Sandra Day O'Connor College of Law; Arizona State University ; Tempe , AZ USA
| | - Yvonne A Stevens
- a Center for Law, Science & Innovation; Sandra Day O'Connor College of Law; Arizona State University ; Tempe , AZ USA
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21
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Jones HD. Future of breeding by genome editing is in the hands of regulators. GM CROPS & FOOD 2016; 6:223-32. [PMID: 26930115 DOI: 10.1080/21645698.2015.1134405] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We are witnessing the timely convergence of several technologies that together will have significant impact on research, human health and in animal and plant breeding. The exponential increase in genome and expressed sequence data, the ability to compile, analyze and mine these data via sophisticated bioinformatics procedures on high-powered computers, and developments in various molecular and in-vitro cellular techniques combine to underpin novel developments in research and commercial biotechnology. Arguably the most important of these is genome editing which encompasses a suite of site directed nucleases (SDN) that can be designed to cut, or otherwise modify predetermined DNA sequences in the genome and result in targeted insertions, deletions, or other changes for genetic improvement. It is a powerful and adaptive technology for animal and plant science, with huge relevance for plant and animal breeding. But this promise will be realized only if the regulatory oversite is proportionate to the potential hazards and has broad support from consumers, researchers and commercial interests. Despite significant progress in research and development and one genome edited crop close to commercialization, in most regions of the world it still remains unclear how or whether this fledgling technology will be regulated. The various risk management authorities and biotechnology regulators have a unique opportunity to set up a logical, appropriate and workable regulatory framework for gene editing that, unlike the situation for GMOs, would have broad support from stakeholders.
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22
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Gaffney J, Anderson J, Franks C, Collinson S, MacRobert J, Woldemariam W, Albertsen M. Robust seed systems, emerging technologies, and hybrid crops for Africa. GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT 2016. [DOI: 10.1016/j.gfs.2016.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Lamichhane JR, Devos Y, Beckie HJ, Owen MDK, Tillie P, Messéan A, Kudsk P. Integrated weed management systems with herbicide-tolerant crops in the European Union: lessons learnt from home and abroad. Crit Rev Biotechnol 2016; 37:459-475. [PMID: 27173634 DOI: 10.1080/07388551.2016.1180588] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Conventionally bred (CHT) and genetically modified herbicide-tolerant (GMHT) crops have changed weed management practices and made an important contribution to the global production of some commodity crops. However, a concern is that farm management practices associated with the cultivation of herbicide-tolerant (HT) crops further deplete farmland biodiversity and accelerate the evolution of herbicide-resistant (HR) weeds. Diversification in crop systems and weed management practices can enhance farmland biodiversity, and reduce the risk of weeds evolving herbicide resistance. Therefore, HT crops are most effective and sustainable as a component of an integrated weed management (IWM) system. IWM advocates the use of multiple effective strategies or tactics to manage weed populations in a manner that is economically and environmentally sound. In practice, however, the potential benefits of IWM with HT crops are seldom realized because a wide range of technical and socio-economic factors hamper the transition to IWM. Here, we discuss the major factors that limit the integration of HT crops and their associated farm management practices in IWM systems. Based on the experience gained in countries where CHT or GMHT crops are widely grown and the increased familiarity with their management, we propose five actions to facilitate the integration of HT crops in IWM systems within the European Union.
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Affiliation(s)
| | - Yann Devos
- b GMO Unit, European Food Safety Authority (EFSA) , Parma , Italy
| | - Hugh J Beckie
- c Agriculture and Agri-Food Canada , Saskatoon , Saskatchewan , Canada
| | | | - Pascal Tillie
- e European Commission-Joint Research Centre (JRC), Institute for Prospective Technological Studies (IPTS) , Seville , Spain
| | - Antoine Messéan
- a Eco-Innov Research Unit, INRA , Thiverval-Grignon , France
| | - Per Kudsk
- f Department of Agroecology , Aarhus University , Slagelse , Denmark
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24
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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.
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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
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25
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Khatodia S, Bhatotia K, Passricha N, Khurana SMP, Tuteja N. The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops. FRONTIERS IN PLANT SCIENCE 2016; 7:506. [PMID: 27148329 PMCID: PMC4835450 DOI: 10.3389/fpls.2016.00506] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2016] [Indexed: 05/18/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double-stranded breaks with only a short RNA sequence to confer recognition of the target in animals and plants. Development of genetically edited (GE) crops similar to those developed by conventional or mutation breeding using this potential technique makes it a promising and extremely versatile tool for providing sustainable productive agriculture for better feeding of rapidly growing population in a changing climate. The emerging areas of research for the genome editing in plants include interrogating gene function, rewiring the regulatory signaling networks and sgRNA library for high-throughput loss-of-function screening. In this review, we have described the broad applicability of the Cas9 nuclease mediated targeted plant genome editing for development of designer crops. The regulatory uncertainty and social acceptance of plant breeding by Cas9 genome editing have also been described. With this powerful and innovative technique the designer GE non-GM plants could further advance climate resilient and sustainable agriculture in the future and maximizing yield by combating abiotic and biotic stresses.
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Affiliation(s)
- Surender Khatodia
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Kirti Bhatotia
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Nishat Passricha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - S. M. P. Khurana
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
- Amity Institute of Microbial Technology, Amity UniversityNoida, India
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26
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Wolt JD, Wang K, Yang B. The Regulatory Status of Genome-edited Crops. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:510-8. [PMID: 26251102 PMCID: PMC5042095 DOI: 10.1111/pbi.12444] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/24/2015] [Accepted: 07/03/2015] [Indexed: 05/18/2023]
Abstract
Genome editing with engineered nucleases (GEEN) represents a highly specific and efficient tool for crop improvement with the potential to rapidly generate useful novel phenotypes/traits. Genome editing techniques initiate specifically targeted double strand breaks facilitating DNA-repair pathways that lead to base additions or deletions by non-homologous end joining as well as targeted gene replacements or transgene insertions involving homology-directed repair mechanisms. Many of these techniques and the ancillary processes they employ generate phenotypic variation that is indistinguishable from that obtained through natural means or conventional mutagenesis; and therefore, they do not readily fit current definitions of genetically engineered or genetically modified used within most regulatory regimes. Addressing ambiguities regarding the regulatory status of genome editing techniques is critical to their application for development of economically useful crop traits. Continued regulatory focus on the process used, rather than the nature of the novel phenotype developed, results in confusion on the part of regulators, product developers, and the public alike and creates uncertainty as of the use of genome engineering tools for crop improvement.
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Affiliation(s)
- Jeffrey D Wolt
- Department of Agronomy, Iowa State University, Ames, IA, USA
- Biosafety Institute for Genetically Modified Agricultural Products, Iowa State University, Ames, IA, USA
- Crop Bioengineering Consortium, Iowa State University, Ames, IA, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, USA
- Crop Bioengineering Consortium, Iowa State University, Ames, IA, USA
| | - Bing Yang
- Crop Bioengineering Consortium, Iowa State University, Ames, IA, USA
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
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27
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Pauwels K, De Keersmaecker SC, De Schrijver A, du Jardin P, Roosens NH, Herman P. Next-generation sequencing as a tool for the molecular characterisation and risk assessment of genetically modified plants: Added value or not? Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.07.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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28
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Olsen A, Lütken H, Hegelund JN, Müller R. Ethylene resistance in flowering ornamental plants - improvements and future perspectives. HORTICULTURE RESEARCH 2015; 2:15038. [PMID: 26504580 PMCID: PMC4591681 DOI: 10.1038/hortres.2015.38] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 05/20/2023]
Abstract
Various strategies of plant breeding have been attempted in order to improve the ethylene resistance of flowering ornamental plants. These approaches span from conventional techniques such as simple cross-pollination to new breeding techniques which modify the plants genetically such as precise genome-editing. The main strategies target the ethylene pathway directly; others focus on changing the ethylene pathway indirectly via pathways that are known to be antagonistic to the ethylene pathway, e.g. increasing cytokinin levels. Many of the known elements of the ethylene pathway have been addressed experimentally with the aim of modulating the overall response of the plant to ethylene. Elements of the ethylene pathway that appear particularly promising in this respect include ethylene receptors as ETR1, and transcription factors such as EIN3. Both direct and indirect approaches seem to be successful, nevertheless, although genetic transformation using recombinant DNA has the ability to save much time in the breeding process, they are not readily used by breeders yet. This is primarily due to legislative issues, economic issues, difficulties of implementing this technology in some ornamental plants, as well as how these techniques are publically perceived, particularly in Europe. Recently, newer and more precise genome-editing techniques have become available and they are already being implemented in some crops. New breeding techniques may help change the current situation and pave the way toward a legal and public acceptance if products of these technologies are indistinguishable from plants obtained by conventional techniques.
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Affiliation(s)
- Andreas Olsen
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 9-13, 2630 Taastrup, Denmark
| | - Henrik Lütken
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 9-13, 2630 Taastrup, Denmark
| | - Josefine Nymark Hegelund
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 9-13, 2630 Taastrup, Denmark
| | - Renate Müller
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 9-13, 2630 Taastrup, Denmark
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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.
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30
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Johnson RA, Gurevich V, Filler S, Samach A, Levy AA. Comparative assessments of CRISPR-Cas nucleases' cleavage efficiency in planta. PLANT MOLECULAR BIOLOGY 2015; 87:143-56. [PMID: 25403732 DOI: 10.1007/s11103-014-0266-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 11/12/2014] [Indexed: 05/21/2023]
Abstract
Custom-designed nucleases can enable precise plant genome editing by catalyzing DNA-breakage at specific targets to stimulate targeted mutagenesis or gene replacement. The CRISPR-Cas system, with its target-specifying RNA molecule to direct the Cas9 nuclease, is a recent addition to existing nucleases that bind and cleave the target through linked protein domains (e.g. TALENs and zinc-finger nucleases). We have conducted a comparative study of these different types of custom-designed nucleases and we have assessed various components of the CRISPR-Cas system. For this purpose, we have adapted our previously reported assay for cleavage-dependent luciferase gene correction in Nicotiana benthamiana leaves (Johnson et al. in Plant Mol Biol 82(3):207-221, 2013). We found that cleavage by CRISPR-Cas was more efficient than cleavage of the same target by TALENs. We also compared the cleavage efficiency of the Streptococcus pyogenes Cas9 protein based on expression using three different Cas9 gene variants. We found significant differences in cleavage efficiency between these variants, with human and Arabidopsis thaliana codon-optimized genes having the highest cleavage efficiencies. We compared the activity of 12 de novo-designed single synthetic guide RNA (sgRNA) constructs, and found their cleavage efficiency varied drastically when using the same Cas9 nuclease. Finally, we show that, for one of the targets tested with our assay, we could induce a germinally-transmitted deletion in a repeat array in A. thaliana. This work emphasizes the efficiency of the CRISPR-Cas system in plants. It also shows that further work is needed to be able to predict the optimal design of sgRNAs or Cas9 variants.
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Affiliation(s)
- Ross A Johnson
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel,
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Whelan AI, Lema MA. Regulatory framework for gene editing and other new breeding techniques (NBTs) in Argentina. GM CROPS & FOOD 2015; 6:253-65. [PMID: 26552666 PMCID: PMC5033209 DOI: 10.1080/21645698.2015.1114698] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 10/22/2022]
Abstract
"New Breeding Techniques" (NBTs) are a group of recent innovations in plant breeding using molecular biology tools. It is becoming evident that NBTs can introduce advantageous traits for agriculture that could be commercially available very soon However, there is still a need of clarifying its regulatory status, particularly in regards to worldwide regulations on Genetically Modified Organisms (GMOs). This article reviews the meaning of the NBTs concept, performs an overall regulatory analysis of these technologies and reports the first regulation in the world that is applied to these technologies, which was issued by the Argentine Government.
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Key Words
- CPB, Cartagena Protocol on Biosafety;
- DNA, Deoxyribonucleic acid;
- GMO regulation
- GMO, genetically modified organisms;
- LMO, Living modified organism;
- MNs, Mega Nucleases;
- NBTs
- NBTs, New Breeding Techniques;
- ODM, Oligonucleotide-Directed Mutation;
- RNA, Ribonucleic acid;
- RNAi, RNA interference
- RdDM, RNA-Dependent DNA Methylation;
- SDN, Site –Directed Nucleases;
- TALENs, TAL Effector Nucleases;
- ZFNs, Zinc Finger Nucleases;
- agriculture
- biosafety
- gene editing
- gene targeting
- genetic modification
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Affiliation(s)
- Agustina I Whelan
- Biotechnology Directorate; Secretariat of Agriculture; Livestock and Fisheries; Buenos Aires, Argentina
- National University of Quilmes; Bernal, Argentina
| | - Martin A Lema
- Biotechnology Directorate; Secretariat of Agriculture; Livestock and Fisheries; Buenos Aires, Argentina
- National University of Quilmes; Bernal, Argentina
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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.
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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.
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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
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Lin H, Qin S. Tipping points in seaweed genetic engineering: scaling up opportunities in the next decade. Mar Drugs 2014; 12:3025-45. [PMID: 24857961 PMCID: PMC4052329 DOI: 10.3390/md12053025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/04/2014] [Accepted: 04/25/2014] [Indexed: 12/30/2022] Open
Abstract
Seaweed genetic engineering is a transgenic expression system with unique features compared with those of heterotrophic prokaryotes and higher plants. This study discusses several newly sequenced seaweed nuclear genomes and the necessity that research on vector design should consider endogenous promoters, codon optimization, and gene copy number. Seaweed viruses and artificial transposons can be applied as transformation methods after acquiring a comprehensive understanding of the mechanism of viral infections in seaweeds and transposon patterns in seaweed genomes. After cultivating transgenic algal cells and tissues in a photobioreactor, a biosafety assessment of genetically modified (GM) seaweeds must be conducted before open-sea application. We propose a set of programs for the evaluation of gene flow from GM seaweeds to local/geographical environments. The effective implementation of such programs requires fundamentally systematic and interdisciplinary studies on algal physiology and genetics, marine hydrology, reproductive biology, and ecology.
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Affiliation(s)
- Hanzhi Lin
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ 08901, USA.
| | - Song Qin
- Key Lab of Coastal Biology and Bio-resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai 264003, China.
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Devos Y, Aguilera J, Diveki Z, Gomes A, Liu Y, Paoletti C, du Jardin P, Herman L, Perry JN, Waigmann E. EFSA's scientific activities and achievements on the risk assessment of genetically modified organisms (GMOs) during its first decade of existence: looking back and ahead. Transgenic Res 2013; 23:1-25. [PMID: 23963741 DOI: 10.1007/s11248-013-9741-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/14/2013] [Indexed: 12/13/2022]
Abstract
Genetically modified organisms (GMOs) and derived food and feed products are subject to a risk analysis and regulatory approval before they can enter the market in the European Union (EU). In this risk analysis process, the role of the European Food Safety Authority (EFSA), which was created in 2002 in response to multiple food crises, is to independently assess and provide scientific advice to risk managers on any possible risks that the use of GMOs may pose to human and animal health and the environment. EFSA's scientific advice is elaborated by its GMO Panel with the scientific support of several working groups and EFSA's GMO Unit. This review presents EFSA's scientific activities and highlights its achievements on the risk assessment of GMOs for the first 10 years of its existence. Since 2002, EFSA has issued 69 scientific opinions on genetically modified (GM) plant market registration applications, of which 62 for import and processing for food and feed uses, six for cultivation and one for the use of pollen (as or in food), and 19 scientific opinions on applications for marketing products made with GM microorganisms. Several guidelines for the risk assessment of GM plants, GM microorganisms and GM animals, as well as on specific issues such as post-market environmental monitoring (PMEM) were elaborated. EFSA also provided scientific advice upon request of the European Commission on safeguard clause and emergency measures invoked by EU Member States, annual PMEM reports, the potential risks of new biotechnology-based plant breeding techniques, evaluations of previously assessed GMOs in the light of new scientific publications, and the use of antibiotic resistance marker genes in GM plants. Future challenges relevant to the risk assessment of GMOs are discussed. EFSA's risk assessments of GMO applications ensure that data are analysed and presented in a way that facilitates scientifically sound decisions that protect human and animal health and the environment.
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Affiliation(s)
- Yann Devos
- GMO Unit, European Food Safety Authority (EFSA), Via Carlo Magno 1, 43126, Parma, Italy,
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Engineering nucleases for gene targeting: safety and regulatory considerations. N Biotechnol 2013; 31:18-27. [PMID: 23851284 DOI: 10.1016/j.nbt.2013.07.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/24/2013] [Accepted: 07/03/2013] [Indexed: 12/26/2022]
Abstract
Nuclease-based gene targeting (NBGT) represents a significant breakthrough in targeted genome editing since it is applicable from single-celled protozoa to human, including several species of economic importance. Along with the fast progress in NBGT and the increasing availability of customized nucleases, more data are available about off-target effects associated with the use of this approach. We discuss how NBGT may offer a new perspective for genetic modification, we address some aspects crucial for a safety improvement of the corresponding techniques and we also briefly relate the use of NBGT applications and products to the regulatory oversight.
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