Abstract
Growing world population and deteriorating climate conditions necessitate the development of new crops with high yields and resilience. CRISPR–Cas-mediated genome engineering presents unparalleled opportunities to engineer crop varieties cheaper, easier and faster than ever. In this Review, we discuss how the CRISPR–Cas toolbox has rapidly expanded from Cas9 and Cas12 to include different Cas orthologues and engineered variants. We present various CRISPR–Cas-based methods, including base editing and prime editing, which are used for precise genome, epigenome and transcriptome engineering, and methods used to deliver the genome editors into plants, such as bacterial-mediated and viral-mediated transformation. We then discuss how promoter editing and chromosome engineering are used in crop breeding for trait engineering and fixation, and important applications of CRISPR–Cas in crop improvement, such as de novo domestication and enhancing tolerance to abiotic stresses. We conclude with discussing future prospects of plant genome engineering.
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A.T., C.P., J.S.C and Y.Q. researched data for the article, contributed substantially to discussion of the content, wrote the article and reviewed and/or edited the manuscript before submission. D.L. wrote the article and reviewed and/or edited the manuscript before submission.
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Glossary
- Activity window
-
Specific range of nucleotides within a target DNA sequence, where the base editor converts one nucleotide to another.
- Bystander mutations
-
Unintended genetic alterations that occur near the primary target site (often at adjacent bases within the activity window) owing to the activity of base editor.
- Cascade
-
An RNA-guided protein complex in type I CRISPR–Cas systems that recognizes target DNA sequences.
- CRISPR–Cas
-
Stands for clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein. A bacterial and archaeal adaptive immunity mechanism, in which CRISPR arrays (repeats interspersed with spacers) and Cas proteins identify and degrade viral nucleic acids.
- CRISPR RNA
-
In adaptive immunity in bacteria and archaea, a short RNA molecule that is complementary to a specific sequence of an invading nucleic acid and guides Cas proteins to cleave it.
- Crop yield potentials
-
Maximum possible agricultural outputs that can be achieved under optimal growing conditions. Represents the highest yield a crop can attain based on its genetic characteristics in the absence of limiting environmental factors.
- Filler DNA
-
Inadvertent integration of a segment(s) of the transduced plasmid DNA into the host genome at or near the site of the intended edit.
- Homology-directed repair
-
An error-free or high fidelity DNA double-strand break repair pathway, which uses a homologous template to guide repair, resulting in precise editing outcomes.
- Non-homologous end joining
-
An error-prone pathway of DNA double-strand break repair through direct joining of the DNA ends without requiring a homologous template. This process can introduce insertions or deletions of varying sizes.
- Primer-binding sequence
-
A short sequence included in the prime editing guide RNA that is complementary to the DNA strand targeted for editing; serves as the reverse transcriptase primer for initiation of DNA synthesis during the prime editing.
- Promoter bashing
-
Serial targeted deletions or mutagenesis of a promoter to optimize gene expression.
- Protospacer-adjacent motif
-
A short DNA sequence that is recognized by the Cas protein as a prerequisite for DNA targeting by a CRISPR–Cas system.
- Pyramiding mutations
-
Stacking or combining multiple beneficial genetic mutations or traits in a single organism, typically through selective breeding or genetic engineering.
- Replicons
-
DNA or RNA molecules capable of autonomous replication within a host cell, owing to harbouring sequences such as an origin of replication.
- Single guide RNA
-
(sgRNA). A fusion of CRISPR RNA and trans-activating CRISPR RNA. sgRNAs are used with certain Cas proteins such as Cas9 and Cas12b.
- Trans-activating CRISPR RNA
-
A short RNA encoded adjacent to the CRISPR locus, which can hybridize with the precursor CRISPR RNA and form a complex that guides the CRISPR-associated nuclease to the DNA target site.
- Transposase
-
An enzyme that catalyses the movement of transposable elements (or ‘jumping genes’) within the genome. It facilitates the excision of transposable elements from one location and their integration into another site in the DNA, contributing to genetic diversity.
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Tuncel, A., Pan, C., Clem, J.S. et al. CRISPR–Cas applications in agriculture and plant research. Nat Rev Mol Cell Biol 26, 419–441 (2025). https://doi.org/10.1038/s41580-025-00834-3
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DOI: https://doi.org/10.1038/s41580-025-00834-3
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