References
-
Li, B., Sun, C., Li, J. & Gao, C. Targeted genome-modification tools and their advanced applications in crop breeding. Nat. Rev. Genet. 25, 603–622 (2024).
-
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).
-
Chen, P. J. & Liu, D. R. Prime editing for precise and highly versatile genome manipulation. Nat. Rev. Genet. 24, 161–177 (2023).
-
Vu, T. V., Nguyen, N. T., Kim, J., Hong, J. C. & Kim, J. Y. Prime editing: mechanism insight and recent applications in plants. Plant Biotechnol. J. 22, 19–36 (2024).
-
Zong, Y. et al. An engineered prime editor with enhanced editing efficiency in plants. Nat. Biotechnol. 40, 1394–1402 (2022).
-
Lin, Q. et al. Prime genome editing in rice and wheat. Nat. Biotechnol. 38, 582–585 (2020).
-
Jin, S., Lin, Q., Gao, Q. & Gao, C. Optimized prime editing in monocot plants using PlantPegDesigner and engineered plant prime editors (ePPEs). Nat. Protoc. 18, 831–853 (2023).
-
Ni, P. et al. Efficient and versatile multiplex prime editing in hexaploid wheat. Genome Biol. 24, 156 (2023).
-
Cao, Z. et al. PE6c greatly enhances prime editing in transgenic rice plants. J. Integr. Plant Biol. 66, 1864–1870 (2024).
-
Jiang, Y. et al. Optimized prime editing efficiently generates glyphosate-resistant rice plants carrying homozygous TAP-IVS mutation in EPSPS. Mol. Plant 15, 1646–1649 (2022).
-
Jiang, Y. Y. et al. Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize. Genome Biol. 21, 257 (2020).
-
Li, J. et al. Development of a highly efficient prime editor 2 system in plants. Genome Biol. 23, 161 (2022).
-
Zhong, Z. et al. An improved plant prime editor for efficient generation of multiple-nucleotide variations and structural variations in rice. Plant Commun. 5, 100976 (2024).
-
Zou, J. et al. Improving the efficiency of prime editing with epegRNAs and high-temperature treatment in rice. Sci. China Life Sci. 65, 2328–2331 (2022).
-
Qiao, D. et al. Optimized prime editing efficiently generates heritable mutations in maize. J. Integr. Plant Biol. 65, 900–906 (2023).
-
Liu, X. et al. Conditional knockdown of OsMLH1 to improve plant prime editing systems without disturbing fertility in rice. Genome Biol. 25, 131 (2024).
-
Lu, Y. et al. One-step generation of prime-edited transgene-free rice. Plant Commun. 6, 101227 (2024).
-
Zhang, J. et al. Developing an efficient and visible prime editing system to restore tobacco 8-hydroxy-copalyl diphosphate gene for labdane diterpene Z-abienol biosynthesis. Sci. China Life Sci. 66, 2910–2921 (2023).
-
Li, H. et al. Multiplex precision gene editing by a surrogate prime editor in rice. Mol. Plant 15, 1077–1080 (2022).
-
Bai, M. et al. Expressing a human RNA demethylase as an assister improves gene-editing efficiency in plants. Mol. Plant 17, 363–366 (2024).
-
Xu, W. et al. A design optimized prime editor with expanded scope and capability in plants. Nat. Plants 8, 45–52 (2022).
-
Liang, Z., Wu, Y., Guo, Y. & Wei, S. Addition of the T5 exonuclease increases the prime editing efficiency in plants. J. Genet. Genom. 50, 582–588 (2023).
-
Choi, J. et al. Precise genomic deletions using paired prime editing. Nat. Biotechnol. 40, 218–226 (2022).
-
Li, X. et al. Efficient in situ epitope tagging of rice genes by nuclease-mediated prime editing. Plant Cell 37, koae316 (2025).
-
Zhao, Y. et al. Precise deletion, replacement and inversion of large DNA fragments in plants using dual prime editing. Nat. Plants 11, 191–205 (2025).
-
Sun, C. et al. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nat. Biotechnol. 42, 316–327 (2024).
-
Lu, Y. et al. Precise genome modification in tomato using an improved prime editing system. Plant Biotechnol. J. 19, 415–417 (2021).
-
Perroud, P. F. et al. Prime editing in the model plant Physcomitrium patens and its potential in the tetraploid potato. Plant Sci. 316, 111162 (2022).
-
Biswas, S., Bridgeland, A., Irum, S., Thomson, M. J. & Septiningsih, E. M. Optimization of prime editing in rice, peanut, chickpea, and cowpea protoplasts by restoration of GFP activity. Int. J. Mol. Sci. 23, 9809 (2022).
-
Vu, T. V. et al. Optimized dicot prime editing enables heritable desired edits in tomato and Arabidopsis. Nat. Plants 10, 1502–1513 (2024).
-
Lou, H. et al. Engineering source-sink relations by prime editing confers heat-stress resilience in tomato and rice. Cell 188, 530–549 (2025).
-
Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652 (2021).
-
Zou, J., Li, Y., Wang, K., Wang, C. & Zhuo, R. Prime editing enables precise genome modification of a Populus hybrid. aBIOTECH 5, 497–501 (2024).
-
Bai, M. et al. Generation of a multiplex mutagenesis population via pooled CRISPR-Cas9 in soya bean. Plant Biotechnol. J. 18, 721–731 (2020).
-
Liu, Q. et al. Hi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems. Sci. China Life Sci. 62, 1–7 (2019).
-
Perotti, V. E. et al. A novel triple amino acid substitution in the EPSPS found in a high-level glyphosate-resistant Amaranthus hybridus population from Argentina. Pest Manag. Sci. 75, 1242–1251 (2019).
-
Butt, H. et al. Engineering herbicide resistance via prime editing in rice. Plant Biotechnol. J. 18, 2370–2372 (2020).
-
Xu, R. et al. Development of plant prime-editing systems for precise genome editing. Plant Commun. 1, 100043 (2020).
-
Tang, X. et al. Plant prime editors enable precise gene editing in rice cells. Mol. Plant 13, 667–670 (2020).
-
Ferreira da Silva, J. et al. Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair. Nat. Commun. 13, 760 (2022).
-
Anzalone, A. V. et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat. Biotechnol. 40, 731–740 (2022).
-
Wang, J. et al. Efficient targeted insertion of large DNA fragments without DNA donors. Nat. Methods 19, 331–340 (2022).
-
Zhuang, Y. et al. Increasing the efficiency and precision of prime editing with guide RNA pairs. Nat. Chem. Biol. 18, 29–37 (2022).
-
Tao, R. et al. Bi-PE: bi-directional priming improves CRISPR/Cas9 prime editing in mammalian cells. Nucleic Acids Res. 50, 6423–6434 (2022).
-
Lin, Q. et al. High-efficiency prime editing with optimized, paired pegRNAs in plants. Nat. Biotechnol. 39, 923–927 (2021).
-
Xiong, Y. et al. EXPERT expands prime editing efficiency and range of large fragment edits. Nat. Commun. 16, 1592 (2025).
-
Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 186, 3983–4002 (2023).
-
Yan, J. et al. Improving prime editing with an endogenous small RNA-binding protein. Nature 628, 639–647 (2024).
-
Gao, C. Genome engineering for crop improvement and future agriculture. Cell 184, 1621–1635 (2021).
-
Huang, J. et al. Discovery of deaminase functions by structure-based protein clustering. Cell 186, 3182–3195 (2023).
-
Li, X. et al. Chromatin context-dependent regulation and epigenetic manipulation of prime editing. Cell 187, 2411–2427 (2024).
-
Han, X. et al. Enhancing prime editing efficiency through modulation of methylation on the newly synthesized DNA strand and prolonged expression. Adv. Sci. 12, 2417790 (2025).
-
Adikusuma, F. et al. Optimized nickase- and nuclease-based prime editing in human and mouse cells. Nucleic Acids Res. 49, 10785–10795 (2021).
-
Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. 40, 402–410 (2022).
-
Bai, M. et al. Development of PmCDA1-based high-efficiency cytidine base editors (ChyCBEs) incorporating a GmRad51 DNA-binding domain in soybean. N. Crops 1, 100001 (2024).
-
Fan, Y. L. et al. One-step generation of composite soybean plants with transgenic roots by Agrobacterium rhizogenes-mediated transformation. BMC Plant Biol. 20, 208 (2020).
-
Song, S. et al. Soybean seeds expressing feedback-insensitive cystathionine gamma-synthase exhibit a higher content of methionine. J. Exp. Bot. 64, 1917–1926 (2013).
-
Horsch, R. et al. A simple and general method for transferring genes into plants. Science 227, 1229–1231 (1985).
-
Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
-
Xie, X. et al. CRISPR-GE: a convenient software toolkit for CRISPR-based genome editing. Mol. Plant 10, 1246–1249 (2017).
