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Sequence modification on demand: search and replace tools for precise gene editing in plants

  • GENOME EDITING IN PLANTS
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Abstract

Until recently, our ability to generate allelic diversity in plants was limited to introduction of variants from domesticated and wild species by breeding via uncontrolled recombination or the use of chemical and physical mutagens—processes that are lengthy and costly or lack specificity, respectively. Gene editing provides a faster and more precise way to create new variation, although its application in plants has been dominated by the creation of short insertion and deletion mutations leading to loss of gene function, mostly due to the dependence of editing outcomes on DNA repair pathway choices intrinsic to higher eukaryotes. Other types of edits such as point mutations and precise and pre-designed targeted sequence insertions have rarely been implemented, despite providing means to modulate the expression of target genes or to engineer the function and stability of their protein products. Several advancements have been developed in recent years to facilitate custom editing by regulation of repair pathway choices or by taking advantage of alternative types of DNA repair. We have seen the advent of novel gene editing tools that are independent of DNA double-strand break repair, and methods completely independent of host DNA repair processes are being increasingly explored. With the aim to provide a comprehensive review of the state-of-the-art methodology for allele replacement in plants, I discuss the adoption of these improvements for plant genome engineering.

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Acknowledgements

I thank members of the Inari science team for their assistance with completing this review. I particularly thank Asa Budnick for help with the figures and literature compilation, Thomas DuBois and Ryan Shepard for literature review, and Mike Nuccio, Orlando Gonzalez, Neena Pyzocha and John Paul Issa for providing critical feedback. I also thank Holger Puchta (Karlsruhe Institute of Technology) for helpful discussions and insights.

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Correspondence to Tomáš Čermák.

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The author is an employee of Inari Agriculture, Inc., an agricultural biotechnology company that uses gene editing to develop next-generation seeds.

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Čermák, T. Sequence modification on demand: search and replace tools for precise gene editing in plants. Transgenic Res 30, 353–379 (2021). https://doi.org/10.1007/s11248-021-00253-y

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  • DOI: https://doi.org/10.1007/s11248-021-00253-y

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