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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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Abstract
To confer resistance against pathogens and pests in plants, typically dominant resistance genes are deployed. However, because resistance is based on recognition of a single pathogen-derived molecular pattern, these narrow-spectrum genes are usually readily overcome. Disease arises from a compatible interaction between plant and pathogen. Hence, altering a plant gene that critically facilitates compatibility could provide a more broad-spectrum and durable type of resistance. Here, such susceptibility (S) genes are reviewed with a focus on the mechanisms underlying loss of compatibility. We distinguish three groups of S genes acting during different stages of infection: early pathogen establishment, modulation of host defenses, and pathogen sustenance. The many examples reviewed here show that S genes have the potential to be used in resistance breeding. However, because S genes have a function other than being a compatibility factor for the pathogen, the side effects caused by their mutation demands a one-by-one assessment of their usefulness for application.
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Da Ines O, White CI. Gene Site-Specific Insertion in Plants. SITE-DIRECTED INSERTION OF TRANSGENES 2013. [DOI: 10.1007/978-94-007-4531-5_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Grogan DW, Stengel KR. Recombination of synthetic oligonucleotides with prokaryotic chromosomes: substrate requirements of the Escherichia coli/lambdaRed and Sulfolobus acidocaldarius recombination systems. Mol Microbiol 2008; 69:1255-65. [PMID: 18631240 DOI: 10.1111/j.1365-2958.2008.06356.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to reveal functional properties of recombination involving short ssDNAs in hyperthermophilic archaea, we evaluated oligonucleotide-mediated transformation (OMT) in Sulfolobus acidocaldarius and Escherichia coli as a function of the molecular properties of the ssDNA substrates. Unmodified ssDNAs as short as 20-22 nt yielded recombinants in both organisms, as did longer DNAs forming as few as 2-5 base pairs on one side of the genomic mutation. The two OMT systems showed similar responses to certain end modifications of the oligonucleotides, but E. coli was found to require a 5' phosphate on 5'-limited ssDNA whereas this requirement was not evident in S. acidocaldarius. The ability of both E. coli and S. acidocaldarius to incorporate short, mismatched ssDNAs into their genomes raises questions about the biological significance of this capability, including its phylogenetic distribution among microorganisms and its impact on genome stability. These questions seem particularly relevant for S. acidocaldarius, as this archaeon has natural competence for OMT, encodes no MutSL homologues and thrives under environmental conditions that accelerate DNA decomposition.
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Affiliation(s)
- Dennis W Grogan
- Department of Biological Sciences, University of Cincinnati, 614 Rieveschl Hall, ML 0006, Cincinnati, OH 45221-0006, USA.
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Iida S, Terada R. Modification of endogenous natural genes by gene targeting in rice and other higher plants. PLANT MOLECULAR BIOLOGY 2005; 59:205-19. [PMID: 16217613 DOI: 10.1007/s11103-005-2162-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Accepted: 02/11/2005] [Indexed: 05/04/2023]
Abstract
The capability to modify a genomic sequence into a designed sequence is a powerful tool for biologists and breeders to elucidate the function of an individual gene and its cis-acting elements of multigene families in the genome. Gene targeting refers to the alteration of a specific DNA sequence in an endogenous gene at its original locus in the genome. In higher plants, however, the overwhelming occurrence of the random integration of transgenes by non-homologous end-joining is the main obstacle to develop efficient gene targeting. Two approaches have been undertaken to modify a genomic sequence in higher plants- chimeric RNA/DNA oligonucleotide-directed gene targeting to generate a site-specific base conversion, and homologous recombination-dependent gene targeting to produce either a base change or a gene replacement in a sequence-specific manner. The successful and reproducible targeting of an endogenous gene by homologous recombination, independently of gene-specific selection by employing a strong positive-negative selection, has been demonstrated for the first time in rice, an important staple food and a model plant for other cereal species. This review addresses the current status of targeting of an endogenous natural gene in rice and other higher plants and discusses possible models for Agrobacterium- mediated gene targeting by homologous recombination using a strong positive-negative selection.
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Affiliation(s)
- Shigeru Iida
- Division of Molecular Genetics, National Institutes of Natural Sciences, National Institute for Basic Biology, Myodaiji, Okazaki 444-8585, Japan.
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Puchta H. Towards the ideal GMP: homologous recombination and marker gene excision. JOURNAL OF PLANT PHYSIOLOGY 2003; 160:743-754. [PMID: 12940543 DOI: 10.1078/0176-1617-01027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A mayor aim of biotechnology is the establishment of techniques for the precise manipulation of plant genomes. Two major efforts have been undertaken over the last dozen years, one to set up techniques for site-specific alteration of the plant genome via homologous recombination ("gene targeting") and the other for the removal of selectable marker genes from transgenic plants. Unfortunately, despite multiple promising approaches that will be shortly described in this review no feasible gene targeting technique has been developed till now for crop plants. In contrast, several alternative procedures have been established successfully to remove selectable markers from plant genomes. Intriguingly besides techniques relying on transposons and site-specific recombinases, recent results indicate that homologous recombination might be a valuable alternative for the excision of marker genes.
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Affiliation(s)
- Holger Puchta
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany.
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Segal DJ, Stege JT, Barbas CF. Zinc fingers and a green thumb: manipulating gene expression in plants. CURRENT OPINION IN PLANT BIOLOGY 2003; 6:163-168. [PMID: 12667874 DOI: 10.1016/s1369-5266(03)00007-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Artificial transcription factors can be rapidly constructed from predefined zinc-finger modules to regulate virtually any gene. Stable, heritable up- and downregulation of endogenous genes has been demonstrated in transgenic plants. These advances promise new approaches for creating functional knockouts and conditional overexpression, and for other gene discovery and manipulation applications in plants.
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Affiliation(s)
- David J Segal
- The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Dekker M, Brouwers C, te Riele H. Targeted gene modification in mismatch-repair-deficient embryonic stem cells by single-stranded DNA oligonucleotides. Nucleic Acids Res 2003; 31:e27. [PMID: 12626726 PMCID: PMC152881 DOI: 10.1093/nar/gng027] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Gene targeting through homologous recombination in murine embryonic stem (ES) cells is already strongly suppressed by DNA mismatch-repair (MMR)-dependent anti-recombination when targeting construct and target locus differ at <1% of the nucleotide positions. We demonstrate that MMR activity also raises a strong impediment to gene modification mediated by small synthetic DNA oligonucleotide sequences. In the absence of the DNA MMR gene MSH2, synthetic single-stranded deoxyribo-oligonucleotides can be used to site-specifically modify the ES cell genome. We show that PCR-based procedures can be used to identify and clone modified cells. By this method we have substituted a single codon in the retinoblastoma gene.
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Affiliation(s)
- Marleen Dekker
- Division of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Abstract
Since the mid 1990s, genetically modified (GM) crops have been grown commercially in Canada on a scale that has increased steadily over the years. An intense debate ensued, as elsewhere, and many fears were expressed regarding not only the technology itself but some of the main GM crops being grown. It would seem appropriate at this time to examine how these novel crops compare to crops bred by more traditional means and what impacts these GM crops have had based on experience and not merely on conjecture. To begin, we will put things in a historical perspective and recall how domestication and conventional plant breeding have shaped the crops of today. Then, we will describe briefly the distinctive features of GM plants (obtained so far mainly by nuclear transgenesis) and how these novel crops are regulated in Canada. We will then give two examples of widely grown GM crops in Canada (insect-resistant corn and herbicide-tolerant canola) and examine the main questions that were raised as well as the actual impacts these crops have had on the farm. These examples will help us outline some of the limitations of the current generation of GM plants and, finally, we will try to get a glimpse of the future by examining some recent technical developments in the field of recombinant DNA technologies applied to plant breeding.
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Affiliation(s)
- François J Belzile
- Département de phytologie, 1243 Pavillon C.-E. Marchand, Université Laval, Quebec, Canada G1K 7P4.
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Riechmann JL. Transcriptional regulation: a genomic overview. THE ARABIDOPSIS BOOK 2002; 1:e0085. [PMID: 22303220 PMCID: PMC3243377 DOI: 10.1199/tab.0085] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic principles and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription.
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Affiliation(s)
- José Luis Riechmann
- Mendel Biotechnology, 21375 Cabot Blvd., Hayward, CA 94545, USA
- California Institute of Technology, Division of Biology 156-29, Pasadena, CA 91125
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Abstract
After the elucidation of the sequence of the yeast genome a major effort was started to elucidate the biological function of all open reading frames of this organisms by targeted gene replacement via homologous recombination. The establishment of the complete sequence of the genome of Arabidopsis thaliana would principally allow a similar approach. However, over the past dozen years all attempts to establish an efficient gene targeting technique in flowering plants were in the end not successful. In contrast, in Physcomitrella patens an efficient gene targeting procedure has been set up, making the moss a valuable model system for plant molecular biologists. But also for flowering plants recently several new approaches--some of them based on the availability of the genomic sequence of Arabidopsis--were initiated that might finally result on the set up of a general applicable technique. Beside the production of hyper-recombinogenic plants either via expression or suppression of specific gene functions or via undirected mutagenesis, the application of chimeric oligonucleotides might result in major progress.
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Affiliation(s)
- Holger Puchta
- Institut fur Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany.
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