Genome Editing in Agriculture: Technical and Practical Considerations

Abstract

The advent of precise genome-editing tools has revolutionized the way we create new plant varieties. Three groups of tools are now available, classified according to their mechanism of action: Programmable sequence-specific nucleases, base-editing enzymes, and oligonucleotides. The corresponding techniques not only lead to different outcomes, but also have implications for the public acceptance and regulatory approval of genome-edited plants. Despite the high efficiency and precision of the tools, there are still major bottlenecks in the generation of new and improved varieties, including the efficient delivery of the genome-editing reagents, the selection of desired events, and the regeneration of intact plants. In this review, we evaluate current delivery and regeneration methods, discuss their suitability for important crop species, and consider the practical aspects of applying the different genome-editing techniques in agriculture.

Trend of Biotechnology Applications in Pest Management: A Review

“…NBTs include emerging techniques that are more broadly and commonly referred to as 'genome editing' that aim to manipulate DNA at specific locations to rapidly generate potentially useful traits. Genome editing of crop plants is a rapidly advancing technology whereby targeted mutations can be introduced into a plant genome in a highly specific manner and with great precision (Georges and Ray, 2017;Townson, 2017;Jansing et al, 2019). Genome editing, which consists of targeting and digesting DNA at a specific site in the genome is an important tool for improved basic understanding of plant gene function analysis.…”

“…Thus, it is a more precise and accurate technology to effectively develop more productive, highly nutritious and climate-resilient crops (Wolter et al, 2019). However, the regulatory framework that covers genome-edited crops in different countries has a major impact on their development and marketability (Jansing et al, 2019) Eckerstorfer et al, (2019) listed the range of nGMs techniques namely (i) Genome editing with site-directed nucleases (SDNs), e.g., using clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-9 (CAS) system directed nucleases, transcription activator-like effector nuclease (TALENs), zinc-finger nucleases (3 ZFNs) or meganucleases. SDN-based techniques can also be applied for multiplex genome editing and "base editing" as well as for modification of transcriptional regulation; (ii) Genome editing directed by synthetic oligonucleotides, referred to as oligonucleotidedirected mutagenesis (ODM)also known as the Rapid Trait Development System (RTDS); (iii) RNA dependent/directed DNA methylation (RdDM);an approach for modifying epigenetic regulation of gene expression; (iv) Cisgenesis and intragenesis; (v) Transgrafting, in particular the use of GM-rootstocks in grafting; (vi) Agro-infiltration, (vii) Haploid induction and accelerated breeding, i.e., examples of techniques developed to assist complex breeding schemes Among these genome-editing technologies, the CRISPR-Cas9 system has become the tool of choice for gene manipulation and has been extensively used in the last five years because of its, novelty, simplicity, affordability, and feasibility (Sticklen, 2015;Barakate and Stephens, 2016;Bernard et al, 2019).…”

Citrus Genetic Engineering for Disease Resistance: Past, Present and Future

“…Genome editing, a specific and efficient tool for generating useful novel phenotypes, surely represents a great technical innovation in plant breeding. Generally, genome-editing technology employs three types of engineered endonucleases: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR/Cas) for site-specific cleavage and the emerging CRISPR/Cas9 is comparatively easy to prepare, affordable, and can be scaled up better than ZFNs and TALENs [119,120,121]. Though developed recently, CRISPR/Cas9 technology has already been established in several important plant species through gene mutation, repression, activation, and epigenome editing, such as rice [122], wheat [123], maize [124], and some horticultural crops, including tomato, petunia, citrus, grape, potato, carrot, and apple [125,126,127,128,129].…”

“…Novel genome-editing systems help introduce stably inherited point modifications in the plant genome and allow the creation of non-transgenic plants [175,176], which may meet the challenges faced by citrus breeders, such as the quest to develop productive, disease-resistant varieties with tasty, high-quality, and nutrient-packed fruit. In contrast to ZFNs and TALENs, second-generation genome editing techniques like CRISPR-Cas9 and CRISPR/Cpf1 involve easier design and execution methodologies that are also more time- and cost-effective [120], both of which are currently the best studied and most widely used CRISPR systems in plants. In citrus, the canker susceptibility gene CsLOB1 and canker immunity response gene CsWRKY22 have been modified at the promoter region or coding region by CRISPR/Cas9 [45,46,47,49] and the citrus CsPDS gene was also effectively modified via a new improved CRISPR/Cpf1 system [48].…”

CRISPR/Cas9: A Robust Genome-Editing Tool with Versatile Functions and Endless Application

“…Jansing and colleagues (2019) reviewed the technical and practical consideration of genome editing in agriculture, particularly focusing on the current delivery method of the CRISPR/Cas9 system into plant cells and their regeneration methods. They also discussed the suitability of CRISPR/Cas9 for improving different traits of agriculturally important crops [ 8 ]. Among all crops, significant progress has been made in rice using CRISPR/Cas genome editing technology.…”