Crop bioengineering via gene editing: reshaping the future of agriculture

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Abstract

Genome-editing technologies have revolutionized research in plant biology, with major implications for agriculture and worldwide food security, particularly in the face of challenges such as climate change and increasing human populations. Among these technologies, clustered regularly interspaced short palindromic repeats [CRISPR]–CRISPR-associated protein [Cas] systems are now widely used for editing crop plant genomes. In this review, we provide an overview of CRISPR–Cas technology and its most significant applications for improving crop sustainability. We also review current and potential technological advances that will aid in the future breeding of crops to enhance food security worldwide. Finally, we discuss the obstacles and challenges that must be overcome to realize the maximum potential of genome-editing technologies for future crop and food production.

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Most cited references 160

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RNA-guided human genome engineering via Cas9.

P. Mali, L. YANG, K. Esvelt … (2013)

Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cells. We show that this process relies on CRISPR components; is sequence-specific; and, upon simultaneous introduction of multiple gRNAs, can effect multiplex editing of target loci. We also compute a genome-wide resource of ~190 K unique gRNAs targeting ~40.5% of human exons. Our results establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.

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Search-and-replace genome editing without double-strand breaks or donor DNA

Andrew Anzalone, Peyton B. Randolph, Jessie Davis … (2019)

Summary Most genetic variants that contribute to disease 1 are challenging to correct efficiently and without excess byproducts 2–5 . Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed >175 edits in human cells including targeted insertions, deletions, and all 12 types of point mutations without requiring double-strand breaks or donor DNA templates. We applied prime editing in human cells to correct efficiently and with few byproducts the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay-Sachs disease (requiring a deletion in HEXA), to install a protective transversion in PRNP, and to precisely insert various tags and epitopes into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, complementary strengths and weaknesses compared to base editing, and much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle can correct up to 89% of known genetic variants associated with human diseases.

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Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

Nicole M. Gaudelli, Alexis Komor, Holly A. Rees … (2017)

Summary The spontaneous deamination of cytosine is a major source of C•G to T•A transitions, which account for half of known human pathogenic point mutations. The ability to efficiently convert target A•T base pairs to G•C therefore could advance the study and treatment of genetic diseases. While the deamination of adenine yields inosine, which is treated as guanine by polymerases, no enzymes are known to deaminate adenine in DNA. Here we report adenine base editors (ABEs) that mediate conversion of A•T to G•C in genomic DNA. We evolved a tRNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs (e.g., ABE7.10), that convert target A•T to G•C base pairs efficiently (~50% in human cells) with very high product purity (typically ≥ 99.9%) and very low rates of indels (typically ≤ 0.1%). ABEs introduce point mutations more efficiently and cleanly than a current Cas9 nuclease-based method, induce less off-target genome modification than Cas9, and can install disease-correcting or disease-suppressing mutations in human cells. Together with our previous base editors, ABEs advance genome editing by enabling the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage.

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Author and article information

Contributors

Magdy Mahfouz:

ORCID: http://orcid.org/0000-0002-0616-6365

magdy.mahfouz@kaust.edu.sa

Journal

Journal ID (nlm-ta): Plant Cell Rep

Journal ID (iso-abbrev): Plant Cell Rep

Title: Plant Cell Reports

Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )

ISSN (Print): 0721-7714

ISSN (Electronic): 1432-203X

Publication date (Electronic): 18 March 2024

Publication date PMC-release: 18 March 2024

Publication date (Print): 2024

Volume: 43

Issue: 4

Electronic Location Identifier: 98

Affiliations

Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), ( https://ror.org/01q3tbs38) 23955-6900 Thuwal, Saudi Arabia

Author notes

Communicated by Wusheng Liu.

Author information

Magdy Mahfouz http://orcid.org/0000-0002-0616-6365

Article

Publisher ID: 3183

DOI: 10.1007/s00299-024-03183-1

PMC ID: 10944814

PubMed ID: 38494539

SO-VID: 5c4053c5-fe93-476d-9221-faae52236a92

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 25 December 2023

Date accepted : 23 February 2024

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ScienceOpen disciplines: Plant science & Botany

Keywords: crispr/cas system,crop engineering,trait engineering,food security,genome editing

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ScienceOpen disciplines: Plant science & Botany

Keywords: crispr/cas system, crop engineering, trait engineering, food security, genome editing

Crop bioengineering via gene editing: reshaping the future of agriculture

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Climate Change: Open Access

Most cited references 160

RNA-guided human genome engineering via Cas9.

Search-and-replace genome editing without double-strand breaks or donor DNA

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

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