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      CRISPR/Cas9-gene editing approaches in plant breeding

      review-article
      Author(s): a , b , c , d , e , f
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: GM Crops & Food
      Publisher: Taylor & Francis
      Keywords: Agriculture, Crispr/Cas9, gene editing, genome, plant breeding

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          ABSTRACT

          CRISPR/Cas9 gene editing system is recently developed robust genome editing technology for accelerating plant breeding. Various modifications of this editing system have been established for adaptability in plant varieties as well as for its improved efficiency and portability. This review provides an in-depth look at the various strategies for synthesizing gRNAs for efficient delivery in plant cells, including chemical synthesis and in vitro transcription. It also covers traditional analytical tools and emerging developments in detection methods to analyze CRISPR/Cas9 mediated mutation in plant breeding. Additionally, the review outlines the various analytical tools which are used to detect and analyze CRISPR/Cas9 mediated mutations, such as next-generation sequencing, restriction enzyme analysis, and southern blotting. Finally, the review discusses emerging detection methods, including digital PCR and qPCR. Hence, CRISPR/Cas9 has great potential for transforming agriculture and opening avenues for new advancements in the system for gene editing in plants.

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          Most cited references149

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          A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

          Martin Jinek, Krzysztof Chylinski, Ines Fonfara … (2012)
          Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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            Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

            John Doench, Nicolò Fusi, Meagan Sullender … (2016)
            CRISPR-Cas9-based genetic screens are a powerful new tool in biology. By simply altering the sequence of the single-guide RNA (sgRNA), Cas9 can be reprogrammed to target different sites in the genome with relative ease, but the on-target activity and off-target effects of individual sgRNAs can vary widely. Here, we use recently-devised sgRNA design rules to create human and mouse genome-wide libraries, perform positive and negative selection screens and observe that the use of these rules produced improved results. Additionally, we profile the off-target activity of thousands of sgRNAs and develop a metric to predict off-target sites. We incorporate these findings from large-scale, empirical data to improve our computational design rules and create optimized sgRNA libraries that maximize on-target activity and minimize off-target effects to enable more effective and efficient genetic screens and genome engineering.
            Article 0 comments Cited 1222 times – based on 0 reviews     Review now
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              Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.

              Bernd Zetsche, Jonathan S. Gootenberg, Omar Abudayyeh … (2015)
              The microbial adaptive immune system CRISPR mediates defense against foreign genetic elements through two classes of RNA-guided nuclease effectors. Class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characterized Cas9. Here, we report characterization of Cpf1, a putative class 2 CRISPR effector. We demonstrate that Cpf1 mediates robust DNA interference with features distinct from Cas9. Cpf1 is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif. Moreover, Cpf1 cleaves DNA via a staggered DNA double-stranded break. Out of 16 Cpf1-family proteins, we identified two candidate enzymes from Acidaminococcus and Lachnospiraceae, with efficient genome-editing activity in human cells. Identifying this mechanism of interference broadens our understanding of CRISPR-Cas systems and advances their genome editing applications.
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                Author and article information

                Journal
                Journal ID (nlm-ta): GM Crops Food
                Journal ID (iso-abbrev): GM Crops Food
                Title: GM Crops & Food
                Publisher: Taylor & Francis
                ISSN (Print): 2164-5698
                ISSN (Electronic): 2164-5701
                Publication date (Electronic, pub): 19 September 2023
                Publication date (Electronic, collection): 2023
                Publication date PMC-release: 19 September 2023
                Volume: 14
                Issue: 1
                Pages: 1-17
                Affiliations
                [a ]School of Applied Natural Science, Adama Science and Technology University; , Adama, Ethiopia
                [b ]School of Agriculture, Forestry & Fisheries, Himgiri Zee University; , Dehradun, Uttarakhand, India
                [c ]Department of Plant Pathology, Dr Yashwant Singh Parmar University of Horticulture and Forestry; , Nauni, Solan, Himachal Pradesh, India
                [d ]Department of Agronomy, School of Agriculture, Lovely professional university; , Phagwara, Punjab, India
                [e ]Division of Genetics and Tree Improvement, Forest Research Institute; , Dehradun, Uttarakhand, India
                [f ]Department of Fruit Science, Dr Yashwant Singh Parmar University of Horticulture and Forestry; , Nauni, Solan, Himachal Pradesh, India
                Author notes
                CONTACT Himanshu Saini saini.biotech@ 123456gmail.com School of Agriculture, Forestry & Fisheries, Himgiri Zee University; , Dehradun, Uttarakhand, India
                Author information
                https://orcid.org/0009-0000-7852-6262
                Article
                Publisher ID: 2256930
                DOI: 10.1080/21645698.2023.2256930
                PMC ID: 10512805
                PubMed ID: 37725519
                SO-VID: f353260a-2d3e-4b5d-99ba-f2e350b1d4f8
                Copyright © © 2023 The Author(s). Published with license by Taylor & Francis Group, LLC.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

                History
                Page count
                Figures: 1, Tables: 1, References: 149, Pages: 17
                Categories
                Subject: Review Article
                Subject: Review

                Keywords: agriculture,crispr/cas9,gene editing,genome,plant breeding
                Data availability:
                Keywords: agriculture, crispr/cas9, gene editing, genome, plant breeding

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