CRISPR-based tools for plant genome engineering

Abstract

Molecular tools adapted from bacterial CRISPR (clustered regulatory interspaced short palindromic repeat) adaptive immune systems have been demonstrated in an increasingly wide range of plant species. They have been applied for the induction of targeted mutations in one or more genes as well as for directing the integration of new DNA to specific genomic loci. The construction of molecular tools for multiplexed CRISPR-mediated editing in plants has been facilitated by cloning techniques that allow multiple sequences to be assembled together in a single cloning reaction. Modifications of the canonical Cas9 protein from Streptococcus pyogenes and the use of nucleases from other bacteria have increased the diversity of genomic sequences that can be targeted and allow the delivery of protein cargos such as transcriptional activators and repressors. Furthermore, the direct delivery of protein-RNA complexes to plant cells and tissues has enabled the production of engineered plants without the delivery or genomic integration of foreign DNA. Here, we review toolkits derived from bacterial CRISPR systems for targeted mutagenesis, gene delivery and modulation of gene expression in plants, focusing on their composition and the strategies employed to reprogramme them for the recognition of specific genomic targets.

The Swedish policy approach to directed mutagenesis in a European context

“…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 ).…”

“…The most widely known so far is the clustered regularly interspaced Abbreviations -CJEU, Court of Justice of the European Union; CRISPR, clustered regularly interspaced short palindromic repeats; EC, European Commission; EFSA, European Food Safety Authority; GMO, genetically modified organism; HLG SAM, high-level group of Scientific Advice Mechanism; JRC, Joint Research Centre; NCA, National Competent Authority; NPBTs, new plant breeding techniques; NTWG, new techniques working group; ODM, oligonucleotide-directed mutagenesis; RTDS, Rapid Trait Development System; SBA, Swedish Board of Agriculture; SDN, site-directed nuclease; TALENs, transcription activator-like effector nucleases; ZFNs, zinc finger nucleases. Paul III and Qi 2016, Samanta et al 2016, Stella and Montoya 2016, Arora and Narula 2017, Volpi e Silva and Patron 2017, Yin et al 2017, applications in plants (Brinegar et al 2017, Hilscher et al 2017, Ricroch et al 2017, Zhang et al 2017, as well as the historical development (Songstad et al 2017) and comparisons with other breeding techniques (Georges and Ray 2017).…”

Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review

“…70 The application of Golden Gate cloning or Gibson Assembly method, multiple gRNAs were assembled driven by different promoters. 151,152 developed a simple strategy to engineer endogenous tRNA through simple and robust method expanding targeting and multiplex editing through CRISPR/Cas9 system. The CRISPR/Cpf1 system had dual nuclease to cleave targeted DNA and its own CRISPR RNA.…”

A comparison of the EU regulatory approach to directed mutagenesis with that of other jurisdictions, consequences for international trade and potential steps forward

“…These techniques for directed mutagenesis include (inter alia) site-directed nuclease systems such as clustered regularly interspaced short palindromic repeats (CRISPR) together with a Cas (CRISPR associated) endonuclease protein, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), meganucleases and the nucleic acid-based oligonucleotide-directed mutagenesis (ODM). It is beyond the scope of this review to describe the genome editing techniques in detail or the various genetic alterations that these enable, however several recent reviews are available on various aspects, such as the technical details (NTWG, 2012, Chen & Gao, 2014Abdallah et al, 2016;Hilscher et al, 2017;HLG-SAM, 2017), specifically on CRISPR systems (Bortesi & Fischer, 2015;Ding et al, 2016;Paul & Qi, 2016;Samanta et al, 2016;Stella & Montoya, 2016;Arora & Narula, 2017;Volpi e Silva & Patron, 2017;Yin et al, 2017), applications in plants (Brinegar et al, 2017;Hilscher et al, 2017;Ricroch et al, 2017;Zhang et al, 2017), as well as the historical development (Songstad et al, 2017) and comparisons with other breeding techniques (Georges & Ray, 2017).…”