Targeted modification of plant genomes for precision crop breeding

Hilscher, Julia; Buerstmayr, Hermann; Stöger, Eva

doi:10.1002/biot.201600173

Cited by 65 publications

(56 citation statements)

References 87 publications

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“…Currently, three different categories for SDN‐mediated genome modifications have been defined (Podevin et al ., ; Hilscher et al ., ) based on the European Union (EU) New Techniques Working Group (NTWG; European Commission et al .) classification of ZFN activity and regulatory purposes: SDN1 covers the application of a SDN without an additional donor DNA or repair template.…”

Section: Classification Of Gene and Genome Editing Eventsmentioning

confidence: 99%

From classical mutagenesis to nuclease‐based breeding – directing natural DNA repair for a natural end‐product

2017

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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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Section: Classification Of Gene and Genome Editing Eventsmentioning

confidence: 99%

From classical mutagenesis to nuclease‐based breeding – directing natural DNA repair for a natural end‐product

2017

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“…The most widely known so far is the clustered regularly interspaced short palindromic repeats (CRISPR) system, including a CRISPR associated (Cas) endonuclease protein, while zinc finger nucleases, transcription activator‐like effector nucleases (TALENs) and the nucleic acid‐based oligonucleotide‐directed mutagenesis (ODM) are also routinely applied. It is beyond the scope of this review to describe the genome editing techniques in detail; however, several recent reviews are available on various aspects, such as the technical details (NTWG , Chen and Gao , Abdallah et al , Hilscher et al , HLG SAM , entire issue of Plant Biotechnology Journal ), specifically on CRISPR systems (Bortesi and Fischer , Ding et al , Paul III and Qi , Samanta et al , Stella and Montoya , Arora and Narula , Volpi e Silva and Patron , Yin et al ), applications in plants (Brinegar et al , Hilscher et al , Ricroch et al , Zhang et al ), as well as the historical development (Songstad et al ) and comparisons with other breeding techniques (Georges and Ray ).…”

Section: Introductionmentioning

confidence: 99%

The Swedish policy approach to directed mutagenesis in a European context

Eriksson

2018

Physiologia Plantarum

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This review describes the Swedish approach to directed mutagenesis in plants and puts it in a comparative European perspective. Directed mutagenesis is accomplished by a number of genome editing techniques; however, the legal status of these techniques and their resulting products is uncertain in the European Union (EU) as there is no political consensus on whether or not these should be regulated as genetically modified organisms (GMOs). A number of cases have developed over the past few years, putting the GMO regulatory framework to the test. These include oilseed rape developed by oligonucleotide-directed mutagenesis, Arabidopsis developed by clustered regularly interspaced short palindromic repeat-Cas9, and the case on mutagenesis for which the French Court requested a preliminary ruling from the Court of Justice of the EU. In this review, the involvement of the Swedish Government and governmental authorities in these cases is described and compared with that of other EU member states and/or EU entity statements and reports. Various approaches to the definition of recombinant nucleic acids are also discussed, as this is crucial for the EU GMO definition thus affecting the legal status of products developed by directed mutagenesis.

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“…In the US, no regulatory oversight was deemed necessary by USDA-APHIS (e.g., waxy maize, high oleic acid soybean mentioned above under ‘Product quality’ and sweet14 -based blight resistance in rice under ‘Disease resistance’, see for further examples Table 1 of Hilscher et al 2016). In Europe, there is no definitive legal analysis yet.…”

Section: Regulatory and Ip Issuesmentioning

confidence: 99%

“…Similarly to zinc finger nucleases (ZFN) and TALENs, CRISPR-Cas is able to make a double-strand break (DSB) at a precisely specified location in the genome, but it is much more versatile and easy to use, because the specificity of the target sequence is achieved by a separate guide RNA (gRNA) that can be easily designed and readily synthesised rather than by the protein structure itself (ZFN, TALEN). The use in plants has recently been reviewed by Luo et al (2016), Paul and Qi (2016), Hilscher et al (2016), and Rani et al (2016). …”

Section: Introductionmentioning

confidence: 99%

New traits in crops produced by genome editing techniques based on deletions

Wiel

Schaart

Lotz

et al. 2017

Plant Biotechnol Rep

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One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs, or CRISPR-Cas9. The programmable nuclease is used to induce a double-strand break in the DNA, while the repair is left to the plant cell itself, and mistakes are introduced, while the cell is repairing the double-strand break using the relatively error-prone NHEJ pathway. From a biological point of view, it could be considered as a form of targeted mutagenesis. We first discuss improvements and new technical variants for SDN-1, in particular employing CRISPR-Cas, and subsequently explore the effectiveness of targeted deletions that eliminate the function of a gene, as an approach to generate novel traits useful for improving agricultural sustainability, including disease resistances. We compare them with examples of deletions that resulted in novel functionality as known from crop domestication and classical mutation breeding (both using radiation and chemical mutagens). Finally, we touch upon regulatory and access and benefit sharing issues regarding the plants produced.

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Targeted modification of plant genomes for precision crop breeding

Cited by 65 publications

References 87 publications

From classical mutagenesis to nuclease‐based breeding – directing natural DNA repair for a natural end‐product

From classical mutagenesis to nuclease‐based breeding – directing natural DNA repair for a natural end‐product

The Swedish policy approach to directed mutagenesis in a European context

New traits in crops produced by genome editing techniques based on deletions

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