Chen, R. Z. et al. Rice functional genomics: decades’ efforts and roads ahead. Sci. China Life Sci. 65, 33–92 (2022).
Google Scholar
Li, B. S., Sun, C., Li, J. Y. & Gao, C. X. Targeted genome-modification tools and their advanced applications in crop breeding. Nat. Rev. Genet. 25, 603–622 (2024).
Google Scholar
Wallace, J. G., Rodgers-Melnick, E. & Buckler, E. S. On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics. Annu. Rev. Genet. 52, 421–444 (2018).
Google Scholar
Shan, Q. et al. Targeted genome modification of crop plants using a CRISPR–Cas system. Nat. Biotechnol. 31, 686–688 (2013).
Google Scholar
Li, S. N. et al. Genome-edited powdery mildew resistance in wheat without growth penalties. Nature 602, 455–460 (2022).
Google Scholar
Huang, J. et al. Discovery of deaminase functions by structure-based protein clustering. Cell 186, 3182–3195 (2023).
Google Scholar
Kuroiwa, K. et al. An iterative gene-editing strategy broadens eIF4E1 genetic diversity in Solanum lycopersicum and generates resistance to multiple potyvirus isolates. Plant Biotechnol. J. 21, 918–930 (2023).
Google Scholar
Li, C. et al. SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds. Genome Biol. 21, 141 (2020).
Google Scholar
Cowan, Q. T. et al. Development of multiplexed orthogonal base editor (MOBE) systems. Nat. Biotechnol. 43, 593–607 (2025).
Google Scholar
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).
Google Scholar
Lin, Q. P. et al. High-efficiency prime editing with optimized, paired pegRNAs in plants. Nat. Biotechnol. 39, 923–927 (2021).
Google Scholar
Zheng, C. W. et al. Template-jumping prime editing enables large insertion and exon rewriting in vivo. Nat. Commun. 14, 3369 (2023).
Google Scholar
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).
Google Scholar
Choi, J. H. et al. Precise genomic deletions using paired prime editing. Nat. Biotechnol. 40, 218–226 (2022).
Google Scholar
Jiang, T. T., Zhang, X. O., Weng, Z. P. & Xue, W. Deletion and replacement of long genomic sequences using prime editing. Nat. Biotechnol. 40, 227–234 (2022).
Google Scholar
Wang, J. L. et al. Efficient targeted insertion of large DNA fragments without DNA donors. Nat. Methods 19, 331–340 (2022).
Google Scholar
Yarnall, M. T. N. et al. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat. Biotechnol. 41, 500–512 (2023).
Google Scholar
Pandey, S. et al. Efficient site-specific integration of large genes in mammalian cells via continuously evolved recombinases and prime editing. Nat. Biomed. Eng. 9, 22–39 (2025).
Google Scholar
Sun, C. et al. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nat. Biotechnol. 42, 316–327 (2024).
Google Scholar
Sun, C. et al. Iterative recombinase technologies for efficient and precise genome engineering across kilobase to megabase scales. Cell 188, 4693–4710 (2025).
Google Scholar
Zou, J. P. et al. Cas9-PE: a robust multiplex gene editing tool for simultaneous precise editing and site-specific random mutation in rice. Trends Biotechnol. 43, 433–446 (2025).
Google Scholar
Zhang, Y. Q. et al. Readthrough events in plants reveal plasticity of stop codons. Cell Rep. 43, 113723 (2024).
Google Scholar
Yu, G. et al. Prediction of efficiencies for diverse prime editing systems in multiple cell types. Cell 186, 2256–2272 (2023).
Google Scholar
Koeppel, J. et al. Prediction of prime editing insertion efficiencies using sequence features and DNA repair determinants. Nat. Biotechnol. 41, 1446–1456 (2023).
Google Scholar
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).
Google Scholar
Li, H. C. et al. Maize plant architecture is regulated by the ethylene biosynthetic gene ZmACS7. Plant Physiol. 183, 1184–1199 (2020).
Google Scholar
Ni, P. et al. Efficient and versatile multiplex prime editing in hexaploid wheat. Genome Biol. 24, 156 (2023).
Google Scholar
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).
Google Scholar
Kweon, J. et al. Targeted genomic translocations and inversions generated using a paired prime editing strategy. Mol. Ther. 31, 249–259 (2023).
Google Scholar
Zhang, R. et al. Amplification editing enables efficient and precise duplication of DNA from short sequence to megabase and chromosomal scale. Cell 187, 3936–3952 (2024).
Google Scholar
Fei, H. et al. Advancing protein evolution with inverse folding models integrating structural and evolutionary constraints. Cell 188, 4674–4692 (2025).
Google Scholar
Varshney, R. K. et al. Fast-forward breeding for a food-secure world. Trends Genet. 37, 1124–1136 (2021).
Google Scholar
Sha, G. et al. Genome editing of a rice CDP-DAG synthase confers multipathogen resistance. Nature 618, 1017–1023 (2023).
Google Scholar
Song, X. et al. Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size. Nat. Biotechnol. 40, 1403–1411 (2022).
Google Scholar
Meng, X. et al. Construction of a genome-wide mutant library in rice using CRISPR–Cas9. Mol. Plant 10, 1238–1241 (2017).
Google Scholar
Gupta, A., Liu, B., Raza, S., Chen, Q.-J. & Yang, B. Modularly assembled multiplex prime editors for simultaneous editing of agronomically important genes in rice. Plant Commun. 5, 100741 (2024).
Google Scholar
Chauhan, V. P., Sharp, P. A. & Langer, R. Engineered prime editors with minimal genomic errors. Nature 646, 1254–1260 (2025).
Google Scholar
Dong, Y. et al. A rice endogenous small RNA-binding protein improves prime editing for precise sequence insertion and replacement. Plant Biotechnol. J. 24, 2315–2317 (2025).
Google Scholar
Li, H. et al. Multiplex precision gene editing by a surrogate prime editor in rice. Mol. Plant 15, 1077–1080 (2022).
Google Scholar
Lu, P. Repeated high-temperature treatment can increase prime editing efficiency in dicot model species. ACS Agric. Sci. Technol. 4, 1179–1183 (2024).
Google Scholar
Vu, T. V. et al. Optimized dicot prime editing enables heritable desired edits in tomato and Arabidopsis. Nat. Plants 10, 1502–1513 (2024).
Google Scholar
Jin, S. et al. Functional RNA splitting drove the evolutionary emergence of type V CRISPR–Cas systems from transposons. Cell 188, 6283–6300 (2025).
Google Scholar
Zhu, H. et al. Engineered geminivirus replicons enable rapid in planta directed evolution. Science 390, eady2167 (2025).
Google Scholar
Chen, Y. et al. Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application. Signal Transduct. Target. Ther. 9, 340 (2025).
Google Scholar
Foster, M. P., Benedek, M. J., Billings, T. D. & Montgomery, J. S. Dynamics in Cre-loxP site-specific recombination. Curr. Opin. Struct. Biol. 88, 102878 (2024).
Google Scholar
Liu, G. W., Yin, K. Q., Zhang, Q. W., Gao, C. X. & Qiu, J. L. Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo. Genome Biol. 20, 145 (2019).
Google Scholar
Xie, X. R. et al. CRISPR-GE: a convenient software toolkit for CRISPR-based genome editing. Mol. Plant 10, 1246–1249 (2017).
Google Scholar
Liang, Z., Zong, Y. & Gao, C. An efficient targeted mutagenesis system using CRISPR/Cas in monocotyledons. Curr. Protoc. Plant Biol. 1, 329–344 (2016).
Google Scholar
Zhang, Y., Li, J. & Gao, C. Generation of stable transgenic rice (Oryza sativa L.) by Agrobacterium-mediated transformation. Curr. Protoc. Plant Biol. 1, 235–246 (2016).
Google Scholar
Zhang, Y. et al. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat. Commun. 7, 12617 (2016).
Google Scholar
Kumar, R. et al. Optimization of Agrobacterium-mediated transformation in spring bread wheat using mature and immature embryos. Mol. Biol. Rep. 46, 1845–1853 (2019).
Google Scholar
Shi, X. xs787xlshi/CRISPRDataCraft: next-generation sequencing data analysis. Zenodo https://doi.org/10.5281/zenodo.15846650 (2025).