# A long journey towards genome editing technologies in plants: a technical and critical review of genome editing technologies

**Authors:** Dylan Gallo, Anne-Cécile Meunier, Christophe Périn

PMC · DOI: 10.3389/fgeed.2025.1663352 · Frontiers in Genome Editing · 2025-11-11

## TL;DR

This paper reviews recent advances in plant genome editing technologies, focusing on CRISPR/Cas9, base editing, and prime editing to improve crops for global warming challenges.

## Contribution

The paper critically analyzes recent innovations in SpCas9-based tools and methodological advancements in prime editing for precise plant genome modifications.

## Key findings

- Dual pegRNA strategies and site-specific integrases enhance prime editing for precise gene insertions.
- SpCas9-based tools have seen improvements in editing efficiency and specificity.
- Insights into DNA repair mechanisms guide future genome editing applications in plant breeding.

## Abstract

Advancements in genome editing technologies, notably CRISPR/Cas9, base editing (BE), and prime editing (PE), have revolutionized plant biotechnology, offering unprecedented precision in crop improvement to address the ongoing global warming challenge. This review provides a critical analysis of recent developments in SpCas9-based editing tools, emphasizing enhancements in editing efficiency and specificity and follow the chronological development of editing tools. We explore methodological innovations, including dual pegRNA strategies and site-specific integrases, that have expanded the potential of PE for precise gene insertions. By integrating insights into DNA repair mechanisms and leveraging SpCas9 enhancements, we outline future directions for the application of genome editing in plant breeding.

## Full-text entities

- **Genes:** tRNA [NCBI Gene 29141390], CCR5 (C-C motif chemokine receptor 5) [NCBI Gene 1234] {aka CC-CKR-5, CCCKR5, CCR-5, CD195, CKR-5, CKR5}, RAD1 (RAD1 checkpoint DNA exonuclease) [NCBI Gene 5810] {aka HRAD1, REC1}, CAS9 [NCBI Gene 46806597]
- **Diseases:** PE (MESH:C566449), GRAND (MESH:D042822), cNHEJ (MESH:D003643), bacterial blast (MESH:D001753)
- **Chemicals:** oleic acid (MESH:D019301), TOPO (MESH:C044965), PE3s (MESH:C015467), U (MESH:D014501), BE4max (-), GABA (MESH:D005680), Adenine (MESH:D000225), Cytosine (MESH:D003596), TA (MESH:D013635), uracil (MESH:D014498), Nitrogen (MESH:D009584), thymine (MESH:D013941), guanine (MESH:D006147), C (MESH:D002244), inosine (MESH:D007288), T (MESH:D014316)
- **Species:** Streptococcus thermophilus (species) [taxon 1308], Agrobacterium tumefaciens (species) [taxon 358], Triticum aestivum (bread wheat, species) [taxon 4565], Nicotiana benthamiana (species) [taxon 4100], Oryza sativa (Asian cultivated rice, species) [taxon 4530], Moloney murine leukemia virus (no rank) [taxon 11801], Zea mays (maize, species) [taxon 4577], Rattus norvegicus (brown rat, species) [taxon 10116], Cauliflower mosaic virus (no rank) [taxon 10641], Homo sapiens (human, species) [taxon 9606], Streptococcus canis (species) [taxon 1329], Solanum lycopersicum (tomato, species) [taxon 4081], Streptococcus macacae (species) [taxon 1339], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Populus trichocarpa (black cottonwood, species) [taxon 3694], Neisseria meningitidis (species) [taxon 487], Streptococcus pyogenes (species) [taxon 1314], Tequintavirus T5 (species) [taxon 10726], Mus musculus (house mouse, species) [taxon 10090], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Zygnema sp. 'M' (species) [taxon 2494501], Glycine max (soybean, species) [taxon 3847]
- **Mutations:** E543D, W596R, R105H, N863A, N260D, N394K, V223Y, D200N, K133A, N968K, E782K, S593Q, cytosine (C) to an uracil (U), D10A, R221K, T1337R, R1335Q, L603W, G to G, A-to-G, uracil is converted to thymine, W313F, E1219V, E1007L, C-to-T, T128N, N854A, D1135V, G1218R, R1335E, T330P, H840A, V223A, N200C, T to G, G to T, C-to-G, E480K, D1135E, T306K
- **Cell lines:** nCas9 — Homo sapiens (Human), Induced pluripotent stem cell (CVCL_RG56), HEK3 — Homo sapiens (Human), Transformed cell line (CVCL_VP06), SaCas9 — Homo sapiens (Human), Transformed cell line (CVCL_UR28)

## Full text

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## Figures

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## References

203 references — full list in the complete paper: https://tomesphere.com/paper/PMC12643982/full.md

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Source: https://tomesphere.com/paper/PMC12643982