Improved plant cytosine base editors with high editing activity, purity, and specificity

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

Integrative genomics viewer

Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390 · see citing works

Circos: An information aesthetic for comparative genomicsPreprint

Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,838 · see citing works

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,283 · see citing works

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016) · Nature · doi:10.1038/nature17946 · Cited by 5,437 · see citing works

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingPreprint

Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., Miller, C. A., Mardis, E. R., Ding, L., & Wilson, R. K. (2012) · Genome Research · doi:10.1101/gr.129684.111 · Cited by 4,822 · see citing works

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825 · cited 1× · see citing works

Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

Bae, S., Park, J., & Kim, J.-S. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu048 · Cited by 2,339 · see citing works

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Kawahara, Y., de la Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., Zhou, S., et al. (2013) · Rice · doi:10.1186/1939-8433-6-4 · Cited by 2,237 · see citing works

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0561-9 · Cited by 2,237 · see citing works

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

Ye, K., Schulz, M. H., Long, Q., Apweiler, R., & Ning, Z. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp394 · Cited by 1,978 · see citing works

Cytokinin Oxidase Regulates Rice Grain Production

Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E. R., Qian, Q., Kitano, H., & Matsuoka, M. (2005) · Science · doi:10.1126/science.1113373 · Cited by 1,908 · see citing works

Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice

Jiao, Y., Wang, Y., Xue, D., Wang, J., Yan, M., Liu, G., Dong, G., Zeng, D., Lu, Z., Zhu, X., et al. (2010) · Nature Genetics · doi:10.1038/ng.591 · Cited by 1,528 · see citing works

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

Jiang, H., Lei, R., Ding, S., & Zhu, S. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-182 · Cited by 1,525 · see citing works

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K. Y., et al. (2016) · Science · doi:10.1126/science.aaf8729 · Cited by 1,349 · see citing works

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

Wilm, A., Aw, P. P. K., Bertrand, D., Yeo, G. H. T., Ong, S. H., Wong, C. H., Khor, C. C., Petric, R., Hibberd, M. L., & Nagarajan, N. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks918 · Cited by 1,338 · see citing works

Control of grain size, shape and quality by OsSPL16 in rice

Wang, S., Wu, K., Yuan, Q., Liu, X., Liu, Z., Lin, X., Zeng, R., Zhu, H., Dong, G., Qian, Q., et al. (2012) · Nature Genetics · doi:10.1038/ng.2327 · Cited by 1,191 · see citing works

Engineered CRISPR-Cas9 nuclease with expanded targeting space

Nishimasu, H., Shi, X., Ishiguro, S., Gao, L., Hirano, S., Okazaki, S., Noda, T., Abudayyeh, O. O., Gootenberg, J. S., Mori, H., et al. (2018) · Science · doi:10.1126/science.aas9129 · Cited by 1,100 · see citing works

Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion

Zong, Y., Wang, Y., Li, C., Zhang, R., Chen, K., Ran, Y., Qiu, J., Wang, D., & Gao, C. (2017) · Nature Biotechnology · doi:10.1038/nbt.3811 · Cited by 875 · see citing works

Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion

Shimatani, Z., Kashojiya, S., Takayama, M., Terada, R., Arazoe, T., Ishii, H., Teramura, H., Yamamoto, T., Komatsu, H., Miura, K., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3833 · Cited by 812 · see citing works

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

Zuo, E., Sun, Y., Wei, W., Yuan, T., Ying, W., Sun, H., Yuan, L., Steinmetz, L. M., Li, Y., & Yang, H. (2019) · Science · doi:10.1126/science.aav9973 · Cited by 782 · see citing works

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

Komor, A. C., Zhao, K. T., Packer, M. S., Gaudelli, N. M., Waterbury, A. L., Koblan, L. W., Kim, Y. B., Badran, A. H., & Liu, D. R. (2017) · Science Advances · doi:10.1126/sciadv.aao4774 · Cited by 766 · see citing works

Calling Somatic SNVs and Indels with Mutect2Preprint

Benjamin, D. I., Sato, T., Cibulskis, K., Getz, G. A., Stewart, C., & Lichtenstein, L. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/861054 · Cited by 722 · see citing works

A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation

Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., Voytas, D. F., Hsieh, T.-F., Zhang, Y., & Qi, Y. (2015) · Plant Physiology · doi:10.1104/pp.15.00636 · Cited by 707 · see citing works

Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice

Jin, S., Zong, Y., Gao, Q., Zhu, Z., Wang, Y., Qin, P., Liang, C., Wang, D., Qiu, J.-L., Zhang, F., et al. (2019) · Science · doi:10.1126/science.aaw7166 · Cited by 665 · see citing works

A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants

Tang, X. D., Lowder, L. G., Zhang, T., Malzahn, A. A., Zheng, X., Voytas, D. F., Zhong, Z., Chen, Y., Ren, Q., Li, Q., et al. (2017) · Nature Plants · doi:10.1038/nplants.2017.18 · Cited by 619 · see citing works

Resistance to AHAS inhibitor herbicides: current understanding

Yu, Q. P., & Powles, S. B. (2013) · Pest Management Science · doi:10.1002/ps.3710 · Cited by 503 · see citing works

Transcription Activator-Like Effector Nucleases Enable Efficient Plant Genome Engineering

Zhang, Y., Zhang, F., Li, X., Baller, J. A., Qi, Y., Starker, C. G., Bogdanove, A. J., & Voytas, D. F. (2012) · PLANT PHYSIOLOGY · doi:10.1104/pp.112.205179 · Cited by 487 · see citing works

Glyphosate resistance: state of knowledge

Sammons, R. D., & Gaines, T. A. (2014) · Pest Management Science · doi:10.1002/ps.3743 · Cited by 476 · see citing works

Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors

Doman, J. L., Raguram, A., Newby, G. A., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0414-6 · Cited by 473 · see citing works

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities

Gehrke, J. M., Cervantes, O., Clement, K., Wu, Y., Zeng, J., Bauer, D. E., Pinello, L., & Joung, J. K. (2018) · Nature Biotechnology · doi:10.1038/nbt.4199 · Cited by 433 · see citing works

Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A

Zong, Y., Song, Q., Li, C., Jin, S., Zhang, D., Wang, Y., Qiu, J., & Gao, C. (2018) · Nature Biotechnology · doi:10.1038/nbt.4261 · Cited by 433 · see citing works

Precise Editing of a Target Base in the Rice Genome Using a Modified CRISPR/Cas9 System

Lu, Y., & Zhu, J. (2016) · Molecular Plant · doi:10.1016/j.molp.2016.11.013 · Cited by 423 · see citing works

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors

Li, C., Zhang, R., Meng, X., Chen, S., Zong, Y., Lu, C., Qiu, J., Chen, Y., Li, J., & Gao, C. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0393-7 · Cited by 410 · see citing works

The emerging and uncultivated potential of CRISPR technology in plant science

Zhang, Y., Malzahn, A. A., Sretenovic, S., & Qi, Y. (2019) · Nature Plants · doi:10.1038/s41477-019-0461-5 · Cited by 404 · see citing works

Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing

Zhang, R., Liu, J., Chai, Z., Chen, S., Bai, Y., Zong, Y., Chen, K., Li, J., Jiang, L., & Gao, C. (2019) · Nature Plants · doi:10.1038/s41477-019-0405-0 · Cited by 340 · see citing works

CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications

Molla, K. A., & Yang, Y. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.03.008 · Cited by 336 · see citing works

A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice

Tang, X. D., Liu, G., Zhou, J., Ren, Q., You, Q., Tian, L., Xin, X., Zhong, Z., Liu, B., Zheng, X., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1458-5 · Cited by 305 · see citing works

Generation of Targeted Point Mutations in Rice by a Modified CRISPR/Cas9 System

Li, J., Sun, Y., Du, J., Zhao, Y., & Xia, L. (2016) · Molecular Plant · doi:10.1016/j.molp.2016.12.001 · Cited by 304 · see citing works

Dual base editor catalyzes both cytosine and adenine base conversions in human cells

Zhang, X., Zhu, B., Chen, L., Xie, L., Yu, W., Wang, Y., Li, L., Yin, S., Yang, L., Hu, H., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0527-y · Cited by 270 · see citing works

Base-Editing-Mediated Artificial Evolution of OsALS1 In Planta to Develop Novel Herbicide-Tolerant Rice Germplasms

Kuang, Y., Li, S., Ren, B., Yan, F., Spetz, C., Li, X., Zhou, X., & Zhou, H. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.01.010 · Cited by 268 · see citing works

Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion

Wang, X., Li, J., Wang, Y., Yang, B., Wei, J., Wu, J., Wang, R., Huang, X., Chen, J., & Yang, L. C. (2018) · Nature Biotechnology · doi:10.1038/nbt.4198 · Cited by 264 · see citing works

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

Shi, K., Carpenter, M. A., Banerjee, S., Shaban, N. M., Kurahashi, K., Salamango, D. J., McCann, J. L., Starrett, G. J., Duffy, J. V., Demir, Ö., et al. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3344 · Cited by 254 · see citing works

A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing

Grünewald, J., Zhou, R., Lareau, C. A., Garcia, S. P., Iyer, S., Miller, B. R., Langner, L. M., Hsu, J. Y., Aryee, M. J., & Joung, J. K. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0535-y · Cited by 242 · see citing works

PAM-less plant genome editing using a CRISPR–SpRY toolbox

Ren, Q., Sretenovic, S., Liu, S., Tang, X. D., Huang, L., He, Y., Liu, L., Guo, Y., Zhong, Z., Liu, G., et al. (2021) · Nature Plants · doi:10.1038/s41477-020-00827-4 · Cited by 237 · see citing works

Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems

Lowder, L. G., Zhou, J., Zhang, Y., Malzahn, A., Zhong, Z., Hsieh, T.-F., Voytas, D. F., Zhang, Y., & Qi, Y. (2018) · Molecular Plant · doi:10.1016/j.molp.2017.11.010 · Cited by 232 · see citing works

Improved Base Editor for Efficiently Inducing Genetic Variations in Rice with CRISPR/Cas9-Guided Hyperactive hAID Mutant

Ren, B., Yan, F., Kuang, Y., Li, N., Zhang, D., Zhou, X., Lin, H., & Zhou, H. (2018) · Molecular Plant · doi:10.1016/j.molp.2018.01.005 · Cited by 230 · see citing works

CRISPR-Cas9 Based Genome Editing Reveals New Insights into MicroRNA Function and Regulation in Rice

Zhou, J., Deng, K., Cheng, Y., Zhong, Z., Tian, L., Tang, X. D., Tang, A., Zheng, X., Zhang, T., Qi, Y., et al. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.01598 · Cited by 204 · see citing works

Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG

Zhong, Z., Sretenovic, S., Ren, Q., Yang, L., Bao, Y., Qi, C., Yuan, M., He, Y., Liu, S., Liu, X., et al. (2019) · Molecular Plant · doi:10.1016/j.molp.2019.03.011 · Cited by 198 · see citing works

Multiplex QTL editing of grain-related genes improves yield in elite rice varieties

Zhou, J., Xin, X., He, Y., Chen, H., Li, Q., Tang, X. D., Zhong, Z., Deng, K., Zheng, X., Akher, S. A., et al. (2018) · Plant Cell Reports · doi:10.1007/s00299-018-2340-3 · Cited by 192 · see citing works

Base editors for simultaneous introduction of C-to-T and A-to-G mutations

Sakata, R. C., Ishiguro, S., Mori, H., Tanaka, M., Tatsuno, K., Ueda, H., Yamamoto, S., Seki, M., Masuyama, N., Nishida, K., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0509-0 · Cited by 192 · see citing works

A Single Transcript CRISPR-Cas9 System for Efficient Genome Editing in Plants

Tang, X. D., Zheng, X., Qi, Y., Zhang, D., Cheng, Y., Tang, A., Voytas, D. F., & Zhang, Y. (2016) · Molecular Plant · doi:10.1016/j.molp.2016.05.001 · Cited by 184 · see citing works

Fine-tuning sugar content in strawberry

Xing, S., Chen, K., Zhu, H., Zhang, R., Zhang, H., Li, B., & Gao, C. (2020) · Genome biology · doi:10.1186/s13059-020-02146-5 · Cited by 178 · see citing works

Plant Genome Editing Using FnCpf1 and LbCpf1 Nucleases at Redefined and Altered PAM Sites

Zhong, Z., Zhang, Y., You, Q., Tang, X. D., Ren, Q., Liu, S., Yang, L., Wang, Y., Liu, X., Liu, B., et al. (2018) · Molecular Plant · doi:10.1016/j.molp.2018.03.008 · Cited by 173 · see citing works

A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects

Zuo, E., Sun, Y., Yuan, T., He, B., Zhou, C., Ying, W., Liu, J., Wu, W., Zeng, R., Li, Y., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0832-x · Cited by 164 · see citing works

Rationally designed APOBEC3B cytosine base editors with improved specificity

Jin, S., Fei, H., Zhu, Z., Luo, Y., Liu, J., Gao, S., Zhang, F., Chen, Y.-H., Wang, Y., & Gao, C. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.07.005 · Cited by 159 · see citing works

Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing

Tang, X. D., Ren, Q., Yang, L., Bao, Y., Zhong, Z., He, Y., Liu, S., Qi, C., Liu, B., Wang, Y., et al. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.13068 · Cited by 156 · see citing works

Targeted Mutagenesis of NAC Transcription Factor Gene, OsNAC041, Leading to Salt Sensitivity in Rice

Wang, B., Zhong, Z., Huanhuan, Z., Wang, X., Binglin, L., Lijia, Y., Xiangyan, H., Yu, D., Xuelian, Z., Wang, C., et al. (2019) · Rice Science · doi:10.1016/j.rsci.2018.12.005 · Cited by 150 · see citing works

Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor

Wang, L., Xue, W., Yan, L., Li, X., Wei, J., Chen, M., Wu, J., Yang, B., Yang, L. C., & Chen, J. (2017) · Cell Research · doi:10.1038/cr.2017.111 · Cited by 136 · see citing works

A Cas9 with PAM recognition for adenine dinucleotides

Chatterjee, P., Lee, J., Nip, L., Koseki, S., Tysinger, E., Sontheimer, E. J., Jacobson, J. M., & Jakimo, N. (2020) · Nature Communications · doi:10.1038/s41467-020-16117-8 · Cited by 121 · see citing works

SpRY greatly expands the genome editing scope in rice with highly flexible PAM recognition

Xu, Z., Kuang, Y., Ren, B., Yan, D., Yan, F., Spetz, C., Sun, W., Wang, G., Zhou, X., & Zhou, H. (2021) · Genome biology · doi:10.1186/s13059-020-02231-9 · Cited by 114 · see citing works

Genome editing mediated by SpCas9 variants with broad non-canonical PAM compatibility in plants

Li, J., Xu, R., Qin, R., Liu, X., Kong, F., & Wei, P. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.12.017 · Cited by 99 · see citing works

Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism

Zheng, X., Yang, S., Zhang, D., Zhong, Z., Tang, X. D., Deng, K., Zhou, J., Qi, Y., & Zhang, Y. (2016) · Plant Cell Reports · doi:10.1007/s00299-016-1967-1 · Cited by 86 · see citing works

Base editing with high efficiency in allotetraploid oilseed rape by A3A‐PBE system

Cheng, H., Hao, M., Ding, B., Mei, D., Wang, W., Wang, H., Zhou, R., Liu, J., Li, C., & Hu, Q. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13444 · Cited by 83 · see citing works

Expanding the genome-targeting scope and the site selectivity of high-precision base editors

Tan, J., Zhang, F., Karcher, D., & Bock, R. (2020) · Nature Communications · doi:10.1038/s41467-020-14465-z · Cited by 78 · see citing works

Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects

Lee, S., Ding, N., Sun, Y., Yuan, T., Li, J., Yuan, Q., Liu, L., Yang, J., Wang, Q., Kolomeisky, A. B., et al. (2020) · Science Advances · doi:10.1126/sciadv.aba1773 · Cited by 76 · see citing works

CRISPRMatch: An Automatic Calculation and Visualization Tool for High-throughput CRISPR Genome-editing Data Analysis

You, Q., Zhong, Z., Ren, Q., Hassan, F., Zhang, Y., & Zhang, T. (2018) · International Journal of Biological Sciences · doi:10.7150/ijbs.24581 · Cited by 72 · see citing works

Developing a highly efficient and wildly adaptive CRISPR ‐SaCas9 toolset for plant genome editing

Qin, R., Li, J., Li, H., Zhang, Y., Liu, X., Miao, Y., Zhang, X., & Wei, P. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.13047 · Cited by 65 · see citing works

Bidirectional Promoter-Based CRISPR-Cas9 Systems for Plant Genome Editing

Ren, Q., Zhong, Z., Wang, Y., You, Q., Li, Q., Yuan, M., He, Y., Qi, C., Tang, X. D., Zheng, X., et al. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.01173 · Cited by 60 · see citing works

Expanding plant genome-editing scope by an engineered iSpyMacCas9 system that targets A-rich PAM sequences

Sretenovic, S., Yin, D., Levav, A., Selengut, J., Mount, S. M., & Qi, Y. (2020) · Plant Communications · doi:10.1016/j.xplc.2020.100101 · Cited by 52 · see citing works

CRISPR-Cas nucleases and base editors for plant genome editing

Gürel, F., Zhang, Y., Sretenovic, S., & Qi, Y. (2019) · aBIOTECH · doi:10.1007/s42994-019-00010-0 · Cited by 31 · see citing works

Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing

Zhong, Z., Liu, S., Liu, X., Liu, B., Tang, X. D., Ren, Q., Zhou, J., Zheng, X., Qi, Y., & Zhang, Y. (2020) · Rice · doi:10.1186/s12284-020-0369-8 · Cited by 28 · see citing works

Expanding the scope of genome editing with SpG and SpRY variants in rice

Ren, J., Meng, X., Hu, F., Liu, Q., Cao, Y., Li, H., Yan, C., Li, J., Wang, K., Yu, H. J., et al. (2021) · Science China Life Sciences · doi:10.1007/s11427-020-1883-5 · Cited by 27 · see citing works

CRISPR enables directed evolution in plants

Zhang, Y., & Qi, Y. (2019) · Genome Biology · doi:10.1186/s13059-019-1693-4 · Cited by 25 · see citing works

Precise plant genome editing using base editors and prime editors

Molla, K. A., Sretenovic, S., Bansal, K. C., & Qi, Y. (2021) · Nature Plants · doi:10.1038/s41477-021-00991-1 · Cited by 387 · see citing works

An efficient CRISPR–Cas12a promoter editing system for crop improvement

Zhou, J., Liu, G., Zhao, Y., Zhang, R., Tang, X. D., Li, L., Jia, X., Guo, Y., Wu, Y., Han, Y., et al. (2023) · Nature Plants · doi:10.1038/s41477-023-01384-2 · Cited by 170 · see citing works

Boosting plant genome editing with a versatile CRISPR-Combo system

Pan, C., Li, G., Malzahn, A. A., Cheng, Y., Leyson, B., Sretenovic, S., Gürel, F., Coleman, G. D., & Qi, Y. (2022) · Nature Plants · doi:10.1038/s41477-022-01151-9 · Cited by 167 · see citing works

Construct design for CRISPR/Cas-based genome editing in plants

Hassan, M. M., Zhang, Y., Yuan, G., De, K., Chen, J., Muchero, W., Tuskan, G. A., Qi, Y., & Yang, X. (2021) · Trends in Plant Science · doi:10.1016/j.tplants.2021.06.015 · Cited by 136 · see citing works

CRISPR–Cas applications in agriculture and plant research

Tuncel, A., Pan, C., Clem, J. S., Liu, D., & Qi, Y. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00834-3 · Cited by 139 · see citing works

Beyond knockouts: fine‐tuning regulation of gene expression in plants with CRISPR‐Cas ‐based promoter editing

Tang, X., & Zhang, Y. (2023) · New Phytologist · doi:10.1111/nph.19020 · Cited by 85 · see citing works

A detailed landscape of CRISPR-Cas-mediated plant disease and pest management

Karmakar, S., Das, P., Panda, D., Xie, K., Baig, M. J., & Molla, K. A. (2022) · Plant Science · doi:10.1016/j.plantsci.2022.111376 · Cited by 83 · see citing works

Systematic optimization of Cas12a base editors in wheat and maize using the ITER platform

Gaillochet, C., Fernández, A. P., Goossens, V., D’Halluin, K., Drozdzecki, A., Shafie, M., Duyse, J. V., Isterdael, G. V., Gonzalez, C., Vermeersch, M., et al. (2023) · Genome biology · doi:10.1186/s13059-022-02836-2 · Cited by 73 · see citing works

Development of an efficient and precise adenine base editor (ABE) with expanded target range in allotetraploid cotton (Gossypium hirsutum)

Wang, G., Xu, Z., Wang, F., Huang, Y., Xin, Y., Liang, S., Li, B., Si, H., Sun, L., Wang, Q., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01232-3 · Cited by 71 · see citing works

Exploring C-To-G Base Editing in Rice, Tomato, and Poplar

Sretenovic, S., Liu, S., Li, G., Cheng, Y., Fan, T., Xu, Y., Zhou, J., Zheng, X., Coleman, G. D., Zhang, Y., et al. (2021) · Frontiers in Genome Editing · doi:10.3389/fgeed.2021.756766 · Cited by 63 · see citing works

Efficient C‐to‐G editing in rice using an optimized base editor

Tian, Y., Shen, R., Li, Z., Yao, Q., Zhang, X., Zhong, D., Tan, X., Song, M., Han, H., Zhu, J., et al. (2022) · Plant Biotechnology Journal · doi:10.1111/pbi.13841 · Cited by 59 · see citing works

Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice

Wu, Y., Ren, Q., Zhong, Z., Liu, G., Han, Y., Bao, Y., Liu, L., Xiang, S., Liu, S., Tang, X., et al. (2022) · Plant Biotechnology Journal · doi:10.1111/pbi.13838 · Cited by 56 · see citing works

Improvement of base editors and prime editors advances precision genome engineering in plants

Hua, K., Han, P., & Zhu, J. (2021) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiab591 · Cited by 61 · see citing works

High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants

Fan, T., Cheng, Y., Wu, Y., Liu, S., Tang, X. D., He, Y., Liao, S., Zheng, X., Zhang, T., Qi, Y., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49473-w · Cited by 56 · see citing works

Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system

Zhong, Z., Liu, G., Tang, Z., Xiang, S., Yang, L., Huang, L., He, Y., Fan, T., Liu, S., Zheng, X., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41802-9 · Cited by 54 · see citing works

Heritable base-editing in Arabidopsis using RNA viral vectors

Liu, D., Xuan, S., Prichard, L. E., Donahue, L. I., Pan, C., Nagalakshmi, U., Ellison, E. E., Starker, C. G., Dinesh‐Kumar, S. P., Qi, Y., et al. (2022) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiac206 · Cited by 49 · see citing works

Large-scale genome editing in plants: approaches, applications, and future perspectives

Liu, T., Zhang, X., Li, K., Yao, Q., Zhong, D., Deng, Q., & Lu, Y. (2023) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2022.102875 · Cited by 46 · see citing works

CRISPR‐BETS: a base‐editing design tool for generating stop codons

Wu, Y., He, Y., Sretenovic, S., Liu, S., Cheng, Y., Han, Y., Liu, G., Bao, Y., Fang, Q., Zheng, X., et al. (2021) · Plant Biotechnology Journal · doi:10.1111/pbi.13732 · Cited by 45 · see citing works

Emerging applications of gene editing technologies for the development of climate-resilient crops

Chavhan, R. L., Jaybhaye, S. G., Hinge, V. R., Deshmukh, A. S., Shaikh, U. S., Jadhav, P. K., Kadam, U. S., & Hong, J. C. (2025) · Frontiers in Genome Editing · doi:10.3389/fgeed.2025.1524767 · Cited by 43 · see citing works

CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding

Pan, C., & Qi, Y. (2023) · Nature Protocols · doi:10.1038/s41596-023-00823-w · Cited by 41 · see citing works

Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding

Li, Y., Liang, J. Y., Deng, B., Jiang, Y., Zhu, J., Chen, L., Li, M., & Li, J. (2023) · Current Issues in Molecular Biology · doi:10.3390/cimb45020059 · Cited by 41 · see citing works

CRISPR–Cas12a base editors confer efficient multiplexed genome editing in rice

Cheng, Y., Zhang, Y., Li, G., Fang, H., Sretenovic, S., Fan, A., Li, J., Xu, J., Que, Q., & Qi, Y. (2023) · Plant Communications · doi:10.1016/j.xplc.2023.100601 · Cited by 36 · see citing works

A large-scale genome and transcriptome sequencing analysis reveals the mutation landscapes induced by high-activity adenine base editors in plants

Li, S., Liu, L., Sun, W., Zhou, X., & Zhou, H. (2022) · Genome biology · doi:10.1186/s13059-022-02618-w · Cited by 35 · see citing works

Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops

Zaman, Q. U., Raza, A., Lozano‐Juste, J., Li, C., Jones, M. G. K., Wang, H., & Varshney, R. K. (2023) · Trends in biotechnology · doi:10.1016/j.tibtech.2023.10.007 · Cited by 35 · see citing works

CRISPR/Cas genome editing in soybean: challenges and new insights to overcome existing bottlenecks

Alves, N. S. F., Pinto, C. E. M., Távora, F. T. P. K., de Melo, B. P., Arraes, F. B. M., Lourenço‐Tessutti, I. T., de Moura, S. M., de Oliveira, A. C., Morgante, C. V., Qi, Y., et al. (2024) · Journal of Advanced Research · doi:10.1016/j.jare.2024.08.024 · Cited by 35 · see citing works

Highly efficient CRISPR systems for loss-of-function and gain-of-function research in pear calli

Ming, M., Long, H., Ye, Z., Pan, C., Chen, J., Tian, R., Sun, C., Xue, Y., Zhang, Y., Li, J., et al. (2022) · Horticulture Research · doi:10.1093/hr/uhac148 · Cited by 33 · see citing works

Improved Dual Base Editor Systems (iACBEs) for Simultaneous Conversion of Adenine and Cytosine in the Bacterium Escherichia coli

Shelake, R. M., Pramanik, D., & Kim, J. (2023) · mBio · doi:10.1128/mbio.02296-22 · Cited by 33 · see citing works

Directed evolution rice genes with randomly multiplexed sgRNAs assembly of base editors

Zhang, A., Shan, T., Sun, Y., Chen, Z., Hu, J., Hu, Z., Ming, Z., Zhu, Z., Li, X., He, J., et al. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14156 · Cited by 32 · see citing works

Split complementation of base editors to minimize off-target edits

Xiong, X., Liu, K., Li, Z., Xia, F., Ruan, X.-M., He, X., & Li, J. (2023) · Nature Plants · doi:10.1038/s41477-023-01540-8 · Cited by 32 · see citing works

RNAi and genome editing of sugarcane: Progress and prospects

Brant, E. J., Zuniga‐Soto, E., & Altpeter, F. (2025) · The Plant Journal · doi:10.1111/tpj.70048 · Cited by 31 · see citing works

Genome editing with type II‐C CRISPR‐Cas9 systems from Neisseria meningitidis in rice

Xu, R., Qin, R., Xie, H., Li, J., Liu, X., Zhu, M., Sun, Y., Yu, Y., Lu, P., & Wei, P. (2021) · Plant Biotechnology Journal · doi:10.1111/pbi.13716 · Cited by 28 · see citing works

Guide RNA library-based CRISPR screens in plants: opportunities and challenges

Pan, C., Li, G., Bandyopadhyay, A., & Qi, Y. (2023) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2022.102883 · Cited by 29 · see citing works

Expanding plant genome editing scope and profiles with CRISPR‐FrCas9 systems targeting palindromic TA sites

He, Y., Han, Y., Ma, Y., Liu, S., Fan, T., Liang, Y., Tang, X., Zheng, X., Wu, Y., Zhang, T., et al. (2024) · Plant Biotechnology Journal · doi:10.1111/pbi.14363 · Cited by 29 · see citing works

PhieDBEs : a DBD ‐containing, PAM ‐flexible, high‐efficiency dual base editor toolbox with wide targeting scope for use in plants

Zheng, Z., Liu, T., Chai, N., Zeng, D., Zhang, R., Wu, Y., Hang, J. X., Liu, Y., Deng, Q., Tan, J., et al. (2024) · Plant Biotechnology Journal · doi:10.1111/pbi.14438 · Cited by 28 · see citing works

Breeding herbicide-resistant rice using CRISPR-Cas gene editing and other technologies

Luo, Q., & Liu, Y. (2024) · Plant Communications · doi:10.1016/j.xplc.2024.101172 · Cited by 27 · see citing works

Plant genome editing: CRISPR, base editing, prime editing, and beyond

Xie, Y., Haq, S. I. U., Jiang, X., Zheng, D., Feng, N., Wang, W., He, J., & Qiu, Q. (2022) · Grassland Research · doi:10.1002/glr2.12034 · Cited by 27 · see citing works

PAM‐relaxed and temperature‐tolerant CRISPR‐Mb3Cas12a single transcript unit systems for efficient singular and multiplexed genome editing in rice, maize, and tomato

Liu, S., He, Y., Fan, T., Zhu, M., Qi, C., Ma, Y., Yang, M., Yang, L., Tang, X., Zhou, J., et al. (2024) · Plant Biotechnology Journal · doi:10.1111/pbi.14486 · Cited by 25 · see citing works

An efficient CRISPR ‐Cas12a‐mediated MicroRNA knockout strategy in plants

Zheng, X., Tang, X., Wu, Y., Zheng, X., Zhou, J., Han, Q., Tang, Y., Fu, X., Deng, J., Wang, Y., et al. (2024) · Plant Biotechnology Journal · doi:10.1111/pbi.14484 · Cited by 25 · see citing works

Directional improvement of agronomic traits in salt‐tolerant rice by multiplex‐genome‐editing

Hao, Y., Xu, B., Zong, W., Li, S., Du, D., Chen, M., Xiao, D., Song, Y., Guo, X., Li, W., et al. (2025) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13926 · Cited by 25 · see citing works

Efficient and heritable A-to-K base editing in rice and tomato

Li, X., Xie, J., Dong, C., Zheng, Z. S., Shen, R., Cao, X., Chen, X., Wang, M., Zhu, J., & Tian, Y. (2023) · Horticulture Research · doi:10.1093/hr/uhad250 · Cited by 25 · see citing works

CRISPR for accelerating genetic gains in under-utilized crops of the drylands: progress and prospects

Sharma, K. K., Palakolanu, S. R., Bhattacharya, J., Shankhapal, A. R., & Bhatnagar-Mathur, P. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.999207 · Cited by 24 · see citing works

Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat

Singh, C., Kumar, R., Sehgal, H., Bhati, S., Singhal, T., Gayacharan, Nimmy, M. S., Yadav, R., Gupta, S. K., Abdallah, N. A., et al. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1085024 · Cited by 26 · see citing works

Transgene‐free genome editing in poplar

Hoengenaert, L., Anders, C., Doorsselaere, J. V., Vanholme, R., & Boerjan, W. (2025) · New Phytologist · doi:10.1111/nph.20415 · Cited by 23 · see citing works

CRISPR/Cas mediated genome editing in potato: Past achievements and future directions

Tuncel, A., & Qi, Y. (2022) · Plant Science · doi:10.1016/j.plantsci.2022.111474 · Cited by 23 · see citing works

Genome-edited trees for high-performance engineered wood

Liu, Y., Li, G., Mao, Y., Gao, Y., Zhao, M., Brozena, A. H., Wang, D., von Keitz, S., Meng, T., Kim, H., et al. (2024) · Matter · doi:10.1016/j.matt.2024.07.003 · Cited by 20 · see citing works

Genome- and transcriptome-wide off-target analyses of a high-efficiency adenine base editor in tomato

Sretenovic, S., Green, Y., Wu, Y., Cheng, Y., Zhang, T., Eck, J. M. V., & Qi, Y. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad347 · Cited by 20 · see citing works

Targeted A‐to‐T and A‐to‐C base replacement in maize using an optimized adenine base editor

Zhong, D., Pan, H., Li, K., Zhou, Y., Zhao, F., Ye, L., Ruan, S., Deng, Q., Xu, J., & Lu, Y. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14256 · Cited by 20 · see citing works

CRISPR towards a Sustainable Agriculture

Camerlengo, F., Frittelli, A., & Pagliarello, R. (2022) · Encyclopedia · doi:10.3390/encyclopedia2010036 · Cited by 20 · see citing works

Recent trends and advances in chloroplast engineering and transformation methods

Narra, M., Nakazato, I., Polley, B., Arimura, S., Woronuk, G. N., & Bhowmik, P. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2025.1526578 · Cited by 19 · see citing works

Dissecting Plant Gene Functions Using CRISPR Toolsets for Crop Improvement

Zhang, R., Li, B., Yang, Z.-G., Huang, J., Sun, W.-H., Bhanbhro, N., Liu, W., & Chen, K. (2022) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.2c01754 · Cited by 19 · see citing works

Development of TALE‐adenine base editors in plants

Zhang, D., & Boch, J. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14246 · Cited by 19 · see citing works

On- and Off-Target Analyses of CRISPR-Cas12b Genome Editing Systems in Rice

Gürel, F., Wu, Y., Pan, C., Cheng, Y., Li, G., Zhang, T., & Qi, Y. (2022) · The CRISPR Journal · doi:10.1089/crispr.2022.0072 · Cited by 18 · see citing works

Cytosine base editing in cyanobacteria by repressing archaic Type <scp>IV uracil‐DNA</scp> glycosylase

Lee, M., Heo, Y. B., & Woo, H. M. (2023) · The Plant Journal · doi:10.1111/tpj.16074 · Cited by 15 · see citing works

Genome editing for plant synthetic metabolic engineering and developmental regulation

Tan, J., Shen, M., Chai, N., Liu, Q., Liu, Y., & Zhu, Q. (2023) · Journal of Plant Physiology · doi:10.1016/j.jplph.2023.154141 · Cited by 16 · see citing works

Improving plant C-to-G base editors with a cold-adapted glycosylase and TadA-8e variants

Jiang, Y., Xiao, Z., Luo, Z., Zhou, S., Tong, C., Jin, S., Liu, X., Qin, R., Xu, R., Pan, L., et al. (2025) · Trends in biotechnology · doi:10.1016/j.tibtech.2025.03.001 · Cited by 15 · see citing works

Broad range plastid genome editing with monomeric TALE ‐linked cytosine and dual base editors

Wang, X., Fang, T., Lu, J., Tripathi, L., & Qi, Y. (2024) · Plant Biotechnology Journal · doi:10.1111/pbi.14358 · Cited by 15 · see citing works

Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis

Adeyinka, O. S., Tabassum, B., Landry, K. B., & Ogungbe, I. V. (2023) · Planta · doi:10.1007/s00425-023-04110-6 · Cited by 14 · see citing works

Protoplast technology enables the identification of efficient multiplex genome editing tools in Phalaenopsis

Xia, K., Zhang, D., Xu, X., Liu, G., Yong, Y., Chen, Z., Wang, X., Zhang, G., Sun, H., & Gu, Y. (2022) · Plant Science · doi:10.1016/j.plantsci.2022.111368 · Cited by 13 · see citing works

Development of plant cytosine base editors with the Cas12a system

Wang, H., Liang, J., Chen, L., Deng, B., Gu, D., Liu, X., Jin, S., Xu, R., Qin, R., Zhu, Y., et al. (2023) · The Crop Journal · doi:10.1016/j.cj.2023.03.002 · Cited by 13 · see citing works

Boosting genome editing in plants with single transcript unit surrogate reporter systems

Tang, X., Ren, Q., Yan, X., Zhang, R., Liu, L., Han, Q., Zheng, X., Qi, Y., Song, H., & Zhang, Y. (2024) · Plant Communications · doi:10.1016/j.xplc.2024.100921 · Cited by 14 · see citing works

Genome editing in angiosperm chloroplasts: targeted DNA double‐strand break and base editing

Nakazato, I., & Arimura, S. (2024) · The Plant Journal · doi:10.1111/tpj.17027 · Cited by 13 · see citing works

Creating large-scale genetic diversity in Arabidopsis via base editing-mediated deep artificial evolution

Wang, X., Pan, W., Sun, C., Yang, H., Cheng, Z., Yan, F., Ma, G., Shang, Y., Zhang, R., Gao, C., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03358-9 · Cited by 12 · see citing works

Cytosine base editors (CBEs) for inducing targeted DNA base editing in Nicotiana benthamiana

Luo, J., Abid, M., Tu, J., Cai, X., Zhang, Y., Gao, P., Wang, Z., & Huang, H. (2023) · BMC Plant Biology · doi:10.1186/s12870-023-04322-8 · Cited by 11 · see citing works

Directed mutagenesis in plants through genome editing using guide RNA library

Dutta, S., Paul, D., Das, A., Kumar, S., Roy, A., Barua, A., & Chinnusamy, V. (2024) · The Nucleus · doi:10.1007/s13237-024-00481-7 · Cited by 11 · see citing works

An Agrobacterium‐mediated base editing approach generates transgene‐free edited banana

den Broeck, S. V., Ngapout, Y., Panis, B., & Vanderschuren, H. (2025) · New Phytologist · doi:10.1111/nph.70044 · Cited by 11 · see citing works

Transgene-free genome editing in citrus and poplar trees using positive and negative selection markers

Rocha, D. C., Omoregbee, M. O., Contiliani, D. F., Mandlik, R., Li, G., Mascoveto, J., Coleman, G. D., Culver, J. N., Rodríguez-Leal, D., de Souza, A. A., et al. (2025) · Plant Cell Reports · doi:10.1007/s00299-025-03627-2 · Cited by 10 · see citing works

Versatile plant genome engineering using anti-CRISPR-Cas12a systems

He, Y., Liu, S., Chen, L., Pu, D., Zhong, Z., Xu, T., Ren, Q., Dong, C., Wang, Y., Wang, D., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2704-7 · Cited by 10 · see citing works

Harnessing novel cytidine deaminases from the animal kingdom for robust multiplexed base editing in rice

Contiliani, D. F., Sretenovic, S., Dailey, M., Zhou, M., Cheng, Y., Creste, S., Xiao, S., & Qi, Y. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.70000 · Cited by 10 · see citing works

Fusion of a rice endogenous N-methylpurine DNA glycosylase to a plant adenine base transition editor ABE8e enables A-to-K base editing in rice plants

Li, Y., Li, S., Li, C., Zhang, C., Yan, L., Li, J., He, Y., Guo, Y. J., & Xia, L. (2024) · aBIOTECH · doi:10.1007/s42994-024-00138-8 · Cited by 9 · see citing works

Development of PmCDA1-based high-efficiency cytidine base editors (ChyCBEs) incorporating a GmRad51 DNA-binding domain in soybean

Bai, M., Hu, X., Lin, W., Peng, C., Kuang, H., Zhong, X., Li, Y., Chen, B., Wang, J., Li, H., et al. (2023) · New Crops · doi:10.1016/j.ncrops.2023.07.001 · Cited by 8 · see citing works

Advances in the use of morphogenic regulators and peptide regenerating factors for boosting plant transformation and genome editing

Achary, V. M. M., Syombua, E. D., Kaur, S., Cindhuri, K. S., Zou, D., Hearne, S., & Bandyopadhyay, A. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2026.1699984 · Cited by 8 · see citing works

A comprehensive all-in-one CRISPR toolbox for large-scale screens in plants

Cheng, Y., Li, G., Qi, A., Mandlik, R., Pan, C., Wang, D., Ge, S., & Qi, Y. (2025) · The Plant Cell · doi:10.1093/plcell/koaf081 · Cited by 9 · see citing works

Epigenome editing strategies for plants: a mini review

Subramanian, A. T., Roy, P., Aravind, B., Kumar, A. P., & Mohannath, G. (2024) · The Nucleus · doi:10.1007/s13237-024-00483-5 · Cited by 7 · see citing works

An insight into the journey of CRISPR-CAS9 and its application in crop improvement

Sharma, U., Nisha, N., & Ray, A. (2025) · Discover Plants. · doi:10.1007/s44372-025-00343-9 · Cited by 7 · see citing works

Orthogonal genome editing and transcriptional activation in tomato using CRISPR-Combo systems

Byiringiro, I., Pan, C., & Qi, Y. (2024) · Plant Cell Reports · doi:10.1007/s00299-024-03316-6 · Cited by 6 · see citing works

CRISPR/Cas genome editing and applications in forest tree breeding

Cao, H. X., Vu, G. T. H., & Gailing, O. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-18444-4.00001-6 · Cited by 6 · see citing works

Development and optimization of base editors and its application in crops

Jiang, C., Li, Y., Wang, R., Sun, X., Zhang, Y., & Zhang, Q. (2024) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2024.150942 · Cited by 6 · see citing works

The Continuous Improvement of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)–CRISPR-Associated Protein System Has Led to Its Highly Efficient Application in Plants

Tan, W. Z., Wang, Z., & Liu, L. (2024) · Agriculture · doi:10.3390/agriculture15010029 · Cited by 5 · see citing works

Identification of optimal adenine and cytosine base editors for genome editing in Arabidopsis and soybean

Jeong, Y. Y., Han, J. H., Yu, J., Bae, S., & Seo, P. J. (2025) · BMB Reports · doi:10.5483/bmbrep.2024-0102 · Cited by 4 · see citing works

Enhanced exonuclease–Cas9 systems promote multiple nucleotide deletions with higher efficiency and broader targeting scope in plants

Zhang, R., Tang, X., He, Y., Wang, W., Ren, Q., Qi, Y., & Zhang, Y. (2026) · Journal of Integrative Plant Biology · doi:10.1111/jipb.70155 · Cited by 4 · see citing works

Coupling of both a transactivation module and a double‐stranded DNA‐binding domain boosts Cas12i3 variant‐based cytosine and adenine editing in plants

Zhang, C., Li, J., Li, Y., Yan, L., Yong, C. S. Y., Li, S., He, Y., & Xia, L. (2026) · Journal of Integrative Plant Biology · doi:10.1111/jipb.70154 · Cited by 4 · see citing works

Emerging trends in the development of efficient CAS nucleases for meticulous gene editing in plants

Gujjar, R. S., Sherin, S., Batra, S., Mahto, A., Goswami, S. K., KUMAR, R. R., Tiwari, R. K., Singh, A., & Kumari, M. (2025) · Plant Science · doi:10.1016/j.plantsci.2025.112820 · Cited by 4 · see citing works

Enhancements of the CRISPR-Cas System in the Silkworm Bombyx mori

Tsubota, T., Takasu, Y., Yonemura, N., & Sezutsu, H. (2025) · The CRISPR Journal · doi:10.1089/crispr.2024.0089 · Cited by 4 · see citing works

Synergistic optimization enhancing the precision and efficiency of cytosine base editors in poplar

Liu, H., Zhang, M., Sun, L., Peng, Y., Sun, Y., Fan, Y., Li, H., Liu, D., & Lu, H. (2025) · Communications Biology · doi:10.1038/s42003-025-08308-0 · Cited by 4 · see citing works

Systematic optimization of Cas12a base editors in wheat and maize using the ITER platformPreprint

Gaillochet, C., Fernández, A. P., Goossens, V., D’Halluin, K., Drozdzecki, A., Shafie, M., Duyse, J. V., Isterdael, G. V., Gonzalez, C., Vermeersch, M., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.11.491340 · Cited by 4 · see citing works

Precise Genome Editing of Plants Through Base and Prime Editor

Alharbi, S., Al‐Dakhil, M., & Alotaibi, F. S. (2024) · doi:10.1002/9781394209156.ch14 · Cited by 4 · see citing works

TALE-based C-to-T base editor for multiple homologous genes with flexible precision

Hosoda, A., Nakazato, I., Okuno, M., Itoh, T., Takanashi, H., Tsutsumi, N., & Arimura, S. (2024) · Plant Biotechnology · doi:10.5511/plantbiotechnology.24.0510a · Cited by 3 · see citing works

Floral stage optimization and immune evasion enhance Agrobacterium ‐mediated genome editing in Arabidopsis

Liu, M., Huang, T., Wang, Y., Wang, S., Wu, C., Kuo, C., & Lai, E. (2025) · New Phytologist · doi:10.1111/nph.70795 · Cited by 3 · see citing works

Enhancing CRISPR‐Cas12a base editing in plants with LbCas12a variants and introns

Cheng, Y., Li, G., Zhou, M., Mandlik, R., Wang, D., & Qi, Y. (2026) · Journal of Integrative Plant Biology · doi:10.1111/jipb.70249 · Cited by 3 · see citing works

Charcoal rot in sesame: infection biology, host resistance mechanism, and genomic-enabled strategies for durable resistance breeding

Ali, A., Nadeem, M. A., Ölmez, F., Kurt, C., & Baloch, F. S. (2026) · Theoretical and Applied Genetics · doi:10.1007/s00122-026-05241-6 · Cited by 3 · see citing works

Boosting genome editing of non-coding sequences in plants with glycosylase-mediated multi-nucleotide deletion editors

Liao, S., He, Y., Liu, G., Li, Y., Tang, X., Zheng, X., Qi, Y., Zhang, T., & Zhang, Y. (2026) · 中国科学通报：英文版 · doi:10.1016/j.scib.2026.05.046 · Cited by 3 · see citing works

If Mendel Was Using CRISPR: Genome Editing Meets Non‐Mendelian Inheritance

Hudzieczek, V., Hobza, R., Cápal, P., Šafář, J., & Doležel, J. (2022) · Advanced Functional Materials · doi:10.1002/adfm.202202585 · Cited by 3 · see citing works

Genome editing interventions to combat rice blast disease

Khanale, V., Bhattacharya, A., Prashar, M., & Char, B. R. (2022) · Plant Biotechnology Reports · doi:10.1007/s11816-022-00749-x · Cited by 3 · see citing works

Seeing is believing: Genome editing made easy with RUBY for educational purposes

Sexton, W. K., Cheng, Y., Yang, B., Ullah, H., Qi, Y., & Xiao, S. (2025) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiaf265 · Cited by 2 · see citing works

CRISPR/Cas-mediated genome editing: playing a versatile role in mitigating the challenges of sustainable rice improvement

Dash, B., Bhuyan, S. S., Sahoo, R. K., Swain, N., Jeughale, K., Sarkar, S., Verma, R., Parameswaran, C., Devanna, B. N., & Samantaray, S. (2025) · 3 Biotech · doi:10.1007/s13205-025-04494-0 · Cited by 3 · see citing works

Identification of multiple miRNA-encoded peptide reveals OsmiPEP162a putatively stabilizes OsMIR162 in rice

Zhou, J., Zhang, R., Han, Q., Yang, H., Wang, W. J., Wang, Y., Zheng, X., Luo, F., Cai, G., & Zhang, Y. (2024) · Plant Cell Reports · doi:10.1007/s00299-024-03380-y · Cited by 2 · see citing works

One-step generation of sh2isu1 sweet maize via CRISPR/Cas9 cytosine base editor (CBE)

Zhang, L., Wang, Y., Liu, M., Song, Z., Li, X., Fu, Y., Wang, P., Liu, Y., Wang, R., & Zhao, J. (2025) · Journal of Integrative Agriculture · doi:10.1016/j.jia.2025.11.031 · Cited by 1 · see citing works

Precise Generation of High‐β‐Carotene Watermelon via Visualised Base Editing

Tian, S., Zhang, X., Wang, J., Guo, S., Zhang, H., Gong, G., Ren, Y., Li, M., Yu, Y., Liao, S., et al. (2026) · Plant Biotechnology Journal · doi:10.1111/pbi.70520 · Cited by 1 · see citing works

Mining and effect evaluation and prediction of natural allele combinations of rice grain-size regulating genes

Zhang, S., Zhang, J., Zhang, Y., Ling, Y., Luo, H., Liu, H., & Yang, G. (2023) · Euphytica · doi:10.1007/s10681-023-03254-6 · Cited by 1 · see citing works

Application of an efficient adenine base editing system in developing Danshen (Salvia miltiorrhiza) dinitroaniline-resistant germplasm

Han, H., Wu, Z., Zhang, Z., Qu, Y., Wang, Y., Wang, P., & Ma, C. (2024) · Horticultural Plant Journal · doi:10.1016/j.hpj.2024.08.007 · Cited by 1 · see citing works

Genome- and transcriptome-wide off-target analyses of an improved cytosine base editor

Randall, L. B., Sretenovic, S., Wu, Y., Yin, D., Zhang, T., Eck, J. M. V., & Qi, Y. (2021) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiab264 · Cited by 51 · see citing works

Harnessing novel cytidine deaminases from the animal kingdom for robust multiplexed base editing in rice

Contiliani, D. F., Sretenovic, S., Dailey, M., Zhou, M., Cheng, Y., Creste, S., Xiao, S., & Qi, Y. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.70000 · Cited by 10 · see citing works

High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants

Fan, T., Cheng, Y., Wu, Y., Liu, S., Tang, X. D., He, Y., Liao, S., Zheng, X., Zhang, T., Qi, Y., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49473-w · Cited by 56 · see citing works

Exploring C-to-G and A-to-Y Base Editing in Rice by Using New Vector Tools

Zeng, D., Zheng, Z., Liu, Y., Liu, T., Li, T., Liu, J., Luo, Q., Xue, Y., Li, S., Chai, N., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23147990 · Cited by 25 · see citing works

Increasing fidelity and efficiency by modifying cytidine base-editing systems in rice

Qin, R., Liao, S., Li, J., Li, H., Liu, X., Yang, J., & Wei, P. (2019) · The Crop Journal · doi:10.1016/j.cj.2019.04.007 · Cited by 25 · see citing works