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Precise plant genome editing using base editors and prime editors

Abstract

The development of CRISPR–Cas systems has sparked a genome editing revolution in plant genetics and breeding. These sequence-specific RNA-guided nucleases can induce DNA double-stranded breaks, resulting in mutations by imprecise non-homologous end joining (NHEJ) repair or precise DNA sequence replacement by homology-directed repair (HDR). However, HDR is highly inefficient in many plant species, which has greatly limited precise genome editing in plants. To fill the vital gap in precision editing, base editing and prime editing technologies have recently been developed and demonstrated in numerous plant species. These technologies, which are mainly based on Cas9 nickases, can introduce precise changes into the target genome at a single-base resolution. This Review provides a timely overview of the current status of base editors and prime editors in plants, covering both technological developments and biological applications.

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Fig. 1: Cytosine and adenine base editing in nuclear DNA.
Fig. 2: C-to-G and dual (simultaneous C-to-T and A-to-G) base editing in nuclear DNA.
Fig. 3: Base editing in organellar DNA.
Fig. 4: Base editing in RNA.
Fig. 5: Prime editing.
Fig. 6: Base editing and prime editing applications for different kinds of genetic modifications.
Fig. 7: Examples of crop improvement by base editing and prime editing.

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Acknowledgements

Owing to space limitations, we could not cite all of the related literature and we apologize to the authors whose work was not cited in this Review. This work was supported by the National Science Foundation Plant Genome Research Program grants (award nos IOS-1758745 and IOS-2029889), the US Department of Agriculture Biotechnology Risk Assessment Grant Program competitive grants (award nos 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 & Agriculture Research grant (award no. 593603), Maryland Innovation Initiative Funding (award no. 1120-012_2) and Syngenta to Y.Q. K.A.M. acknowledges funding from the Indian Council of Agricultural Research (ICAR), New Delhi, in the form of the Plan Scheme—‘Incentivizing Research in Agriculture’ project and support from the Director, NRRI. S.S. is a Foundation for Food & Agriculture Research Fellow, with matching funds provided by Inari Agriculture. The content of this publication is solely the responsibility of the authors and does not necessarily represent the official views of these funding agencies. Figures were created using the BioRender tool.

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Y.Q. led the project planning. K.A.M., S.S., K.C.B. and Y.Q. wrote the manuscript. K.A.M. and S.S. prepared the figures and tables. All of the authors read and approved the final manuscript.

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Correspondence to Kutubuddin A. Molla or Yiping Qi.

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Y.Q. is a consultant for Inari Agriculture and CTC Genomics, companies that use genome editing tools in plants. The other authors declare no competing interests.

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Peer review information Nature Plants thanks Paul Hooykaas, Pengcheng Wei and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Molla, K.A., Sretenovic, S., Bansal, K.C. et al. Precise plant genome editing using base editors and prime editors. Nat. Plants 7, 1166–1187 (2021). https://doi.org/10.1038/s41477-021-00991-1

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