Construct design for CRISPR/Cas-based genome editing in plants

Md Mahmudul Hassan; Yingxiao Zhang; Guoliang Yuan; Kuntal De; Jin Gui Chen; Wellington Muchero; Gerald A. Tuskan; Yiping Qi; Xiaohan Yang

doi:10.1016/j.tplants.2021.06.015

Construct design for CRISPR/Cas-based genome editing in plants

Md Mahmudul Hassan, Yingxiao Zhang, Guoliang Yuan, Kuntal De, Jin Gui Chen, Wellington Muchero, Gerald A. Tuskan, Yiping Qi, Xiaohan Yang

Research output: Contribution to journal › Review article › peer-review

87 Scopus citations

Abstract

CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.

Original language	English
Pages (from-to)	1133-1152
Number of pages	20
Journal	Trends in Plant Science
Volume	26
Issue number	11
DOIs	https://doi.org/10.1016/j.tplants.2021.06.015
State	Published - Nov 2021

Funding

The authors are grateful to the anonymous reviewers for insightful comments and suggestions which greatly helped improve the manuscript. The writing of this manuscript is supported by the Center for Bioenergy Innovation (CBI), a U.S. Department of Energy (DOE) Research Centre supported by the Biological and Environmental Research (BER) program, the Laboratory Directed Research and Development (LDRD) program of Oak Ridge National Laboratory , and the U.S. DOE BER Genomic Science Program , as part of the Plant-Microbe Interfaces (PMI) and the Secure Ecosystem Engineering and Design (SEED) Scientific Focus Areas. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725. This work was also supported by the National Science Foundation Plant Genome Research Program grants (award no. IOS-1758745 and IOS-2029889 ), the U.S. Department of Agriculture Biotechnology Risk Assessment Grant Program competitive grants (award no. 2018-33522-28789 and 2020-33522-32274 ), Emergency Citrus Disease Research and Extension Program (award no. 2020-70029-33161 ), Agriculture and Food Research Initiative Agricultural Innovations Through Gene Editing Program (award no. 2021-67013-34554 ), Foundation for Food and Agriculture Research grant (award no. 593603 ), and Syngenta to Y.Q. The content of this publication is solely the responsibility of the authors and does not necessarily represent the official views of these funding agencies. Disclosure: this manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( http://energy.gov/downloads/doe-public-access-plan ). The authors are grateful to the anonymous reviewers for insightful comments and suggestions which greatly helped improve the manuscript. The writing of this manuscript is supported by the Center for Bioenergy Innovation (CBI), a U.S. Department of Energy (DOE) Research Centre supported by the Biological and Environmental Research (BER) program, the Laboratory Directed Research and Development (LDRD) program of Oak Ridge National Laboratory, and the U.S. DOE BER Genomic Science Program, as part of the Plant-Microbe Interfaces (PMI) and the Secure Ecosystem Engineering and Design (SEED) Scientific Focus Areas. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725. This work was also supported by the National Science Foundation Plant Genome Research Program grants (award no. IOS-1758745 and IOS-2029889), the U.S. Department of Agriculture Biotechnology Risk Assessment Grant Program competitive grants (award no. 2018-33522-28789 and 2020-33522-32274), Emergency Citrus Disease Research and Extension Program (award no. 2020-70029-33161), Agriculture and Food Research Initiative Agricultural Innovations Through Gene Editing Program (award no. 2021-67013-34554), Foundation for Food and Agriculture Research grant (award no. 593603), and Syngenta to Y.Q. The content of this publication is solely the responsibility of the authors and does not necessarily represent the official views of these funding agencies. Disclosure: this manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). M.M.H. and X.Y. conceived the idea. M.M.H. and Y.Z. led the writing and revision of the manuscript. G.Y. K.D. W.M. J.G.C. G.A.T. Y.Q. and X.Y. contributed to the manuscript revision. All authors accepted the final version of the manuscript. Y.Q. is a consultant for Inari Agriculture and CTC Genomics. The remaining authors declare no conflict of interests.

Funders	Funder number
Agriculture and Food Research Initiative Agricultural Innovations Through Gene Editing Program	2021-67013-34554
DOE Public Access Plan
National Science Foundation Plant Genome Research Program	IOS-2029889, IOS-1758745
Plant-Microbe Interfaces
Secure Ecosystem Engineering and Design
United States Government
U.S. Department of Energy
U.S. Department of Agriculture	2020-70029-33161, 2018-33522-28789, 2020-33522-32274
Biological and Environmental Research
Oak Ridge National Laboratory	DE-AC05-00OR22725
Foundation for Food and Agriculture Research	593603
Center for Bioenergy Innovation

Keywords

CRISPR/Cas
base editors
multiplex CRISPR
plant genome editing
prime editors

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10.1016/j.tplants.2021.06.015

Cite this

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title = "Construct design for CRISPR/Cas-based genome editing in plants",

abstract = "CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.",

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AU - Zhang, Yingxiao

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AU - Muchero, Wellington

AU - Tuskan, Gerald A.

AU - Qi, Yiping

AU - Yang, Xiaohan

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AB - CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.

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Construct design for CRISPR/Cas-based genome editing in plants

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