A CRISPR/Cas9 toolkit for multiplex genome editing in plants
Open accessAbstract
BACKGROUND: To accelerate the application of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9) system to a variety of plant species, a toolkit with additional plant selectable markers, more gRNA modules, and easier methods for the assembly of one or more gRNA expression cassettes is required. RESULTS: We developed a CRISPR/Cas9 binary vector set based on the pGreen or pCAMBIA backbone, as well as a gRNA (guide RNA) module vector set, as a toolkit for multiplex genome editing in plants. This toolkit requires no restriction enzymes besides BsaI to generate final constructs harboring maize-codon optimized Cas9 and one or more gRNAs with high efficiency in as little as one cloning step. The toolkit was validated using maize protoplasts, transgenic maize lines, and transgenic Arabidopsis lines and was shown to exhibit high efficiency and specificity. More importantly, using this toolkit, targeted mutations of three Arabidopsis genes were detected in transgenic seedlings of the T1 generation. Moreover, the multiple-gene mutations could be inherited by the next generation. CONCLUSIONS: We developed a toolkit that facilitates transient or stable expression of the CRISPR/Cas9 system in a variety of plant species, which will facilitate plant research, as it enables high efficiency generation of mutants bearing multiple gene mutations.
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Advancement of the technique to multiplex gene editing allows the simultaneous editing of several targets in a single genome.
“Advancement of the technique to multiplex gene editing allows the simultaneous editing of several targets in a single genome (Xing et al., 2014).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Xing et al., 2014
Multiplex gene editing can solve the problem of traits controlled by a few QTL by facilitating the simultaneous editing of two or more genes, or multiple loci of the same gene.
“Multiplex gene editing can solve this problem by facilitating the simultaneous editing of two or more genes, or multiple loci of the same gene (Xing et al., 2014).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Xing et al., 2014
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Cites
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116 · see citing works
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339 · see citing works
Enzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 9,742 · see citing works
RNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210 · see citing works
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 6,304 · see citing works
DNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741 · see citing works
ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
Gaj, T., Gersbach, C. A., & Barbas, C. F. (2013) · Trends in Biotechnology · doi:10.1016/j.tibtech.2013.04.004 · Cited by 3,820 · see citing works
Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.04.025 · Cited by 3,495 · see citing works
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937 · see citing works
A Gateway Cloning Vector Set for High-Throughput Functional Analysis of Genes in Planta
Curtis, M. D., & Grossniklaus, U. (2003) · PLANT PHYSIOLOGY · doi:10.1104/pp.103.027979 · Cited by 2,752 · see citing works
CRISPR/Cas, the Immune System of Bacteria and Archaea
Horvath, P., & Barrangou, R. (2010) · Science · doi:10.1126/science.1179555 · Cited by 2,471 · see citing works
A One Pot, One Step, Precision Cloning Method with High Throughput Capability
Engler, C., Kandzia, R., & Marillonnet, S. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003647 · Cited by 2,398 · see citing works
Crystal structure of Cas9 in complex with guide RNA and target DNA
Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306 · see citing works
Targeted genome modification of crop plants using a CRISPR-Cas system
Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., Zhang, K., Liu, J., Xi, J., Qiu, J., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2650 · Cited by 1,965 · see citing works
Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
Cho, S. W., Kim, S., Kim, J. M., & Kim, J.-S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2507 · Cited by 1,863 · see citing works
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
Sternberg, S. H., Redding, S., Jínek, M., Greene, E. C., & Doudna, J. A. (2014) · Nature · doi:10.1038/nature13011 · Cited by 1,775 · see citing works
Yang, H., Wang, H., Shivalila, C. S., Cheng, A. W., Shi, L., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.08.022 · Cited by 1,596 · see citing works
pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation
Hellens, R. P., Edwards, E. A., Leyland, N., Bean, S., & Mullineaux, P. M. (2000) · Plant Molecular Biology · doi:10.1023/a:1006496308160 · Cited by 1,568 · see citing works
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
DiCarlo, J. E., Norville, J. E., Mali, P., Rios, X., Aach, J., & Church, G. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt135 · Cited by 1,566 · see citing works
The small, versatilepPZP family ofAgrobacterium binary vectors for plant transformation
Hajdukiewicz, P. T. J., Sváb, Z., & Maliga, P. (1994) · Plant Molecular Biology · doi:10.1007/bf00014672 · Cited by 1,536 · see citing works
Li, J., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G. M., & Sheen, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2654 · Cited by 1,499 · see citing works
A Modular Cloning System for Standardized Assembly of Multigene Constructs
Weber, E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016765 · Cited by 1,385 · see citing works
Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system
Jao, L.-E., Wente, S. R., & Chen, W. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1308335110 · Cited by 1,261 · see citing works
Jiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B., & Weeks, D. P. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt780 · Cited by 1,250 · see citing works
Structures of Cas9 endonucleases reveal RNA-mediated conformational activation
Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., et al. (2014) · Science · doi:10.1126/science.1247997 · Cited by 1,230 · see citing works
Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease
Nekrasov, V., Staskawicz, B. J., Weigel, D., Jones, J. D. G., & Kamoun, S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2655 · Cited by 1,123 · see citing works
Efficient genome editing in plants using a CRISPR/Cas system
Feng, Z., Zhang, B., Ding, W., Liu, X., Yang, D., Wei, P., Cao, F., Zhu, S., Zhang, F., Mao, Y., et al. (2013) · Cell Research · doi:10.1038/cr.2013.114 · Cited by 1,070 · see citing works
Niu, Y., Shen, B., Cui, Y., Chen, Y., Wang, J., Wang, L., Kang, Y., Zhao, X., Si, W., Li, W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.01.027 · Cited by 1,033 · see citing works
Zhang, Y., Su, J., Duan, S., Ao, Y., Dai, J., Liu, J., Wang, P., Li, Y., Liu, B., Feng, D., et al. (2011) · Plant Methods · doi:10.1186/1746-4811-7-30 · Cited by 1,010 · see citing works
Self-citationTargeted mutagenesis in rice using CRISPR-Cas system
Miao, J., Guo, D., Zhang, J., Huang, Q., Qin, G., Zhang, X., Wan, J., Gu, H., & Qu, L. (2013) · Cell Research · doi:10.1038/cr.2013.123 · Cited by 908 · see citing works
Heritable genome editing in C. elegans via a CRISPR-Cas9 system
Friedland, A. E., Tzur, Y. B., Esvelt, K. M., Colaiácovo, M. P., Church, G. M., & Calarco, J. A. (2013) · Nature Methods · doi:10.1038/nmeth.2532 · Cited by 899 · see citing works
RNA-Guided Genome Editing in Plants Using a CRISPR–Cas System
Xie, K., & Yang, Y. (2013) · Molecular Plant · doi:10.1093/mp/sst119 · Cited by 806 · see citing works
Zhang, H., Zhang, J., Wei, P., Zhang, B., Gou, F., Feng, Z., Mao, Y., Yang, L., Zhang, H., Xu, N., et al. (2014) · Plant Biotechnology Journal · doi:10.1111/pbi.12200 · Cited by 799 · see citing works
Self-citationT‐DNA insertional mutagenesis for functional genomics in rice
Jeon, J., Lee, S., Jung, K., et al. (2000) · The Plant Journal · doi:10.1046/j.1365-313x.2000.00767.x · Cited by 723 · see citing works
T-DNA as an Insertional Mutagen in Arabidopsis
Krysan, P. J., Young, J. C., & Sussman, M. R. (1999) · The Plant Cell · doi:10.1105/tpc.11.12.2283 · Cited by 722 · see citing works
Fauser, F., Schiml, S., & Puchta, H. (2014) · The Plant Journal · doi:10.1111/tpj.12554 · Cited by 704 · see citing works
Feng, Z., Mao, Y., Xu, N., Zhang, B., Wei, P., Yang, D., Wang, Z., Zhang, Z., Zheng, R., Yang, L., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400822111 · Cited by 657 · see citing works
Self-citationHeritable gene targeting in the mouse and rat using a CRISPR-Cas system
Li, D., Qiu, Z., Shao, Y., Chen, Y., Guan, Y., Liu, M., Li, Y., Wang, L., Wang, L., Lu, X., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2661 · Cited by 639 · see citing works
Belhaj, K., Chaparro‐Garcia, A., Kamoun, S., & Nekrasov, V. (2013) · Plant Methods · doi:10.1186/1746-4811-9-39 · Cited by 582 · see citing works
Application of the CRISPR–Cas System for Efficient Genome Engineering in Plants
Mao, Y., Zhang, H., Xu, N., Zhang, B., Gou, F., & Zhu, J. (2013) · Molecular Plant · doi:10.1093/mp/sst121 · Cited by 576 · see citing works
Self-citationGeneration of gene-modified mice via Cas9/RNA-mediated gene targeting
Shen, B., Zhang, J., Wu, H., Wang, J., Ma, K., Li, Z., Zhang, X., Zhang, P., & Huang, X. (2013) · Cell Research · doi:10.1038/cr.2013.46 · Cited by 556 · see citing works
Targeted Genome Editing of Sweet Orange Using Cas9/sgRNA
Jia, H., & Wang, N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093806 · Cited by 487 · see citing works
Li, W., Teng, F., Li, T., & Zhou, Q. (2013) · Nature Biotechnology · doi:10.1038/nbt.2652 · Cited by 422 · see citing works
Pennisi, E. (2013) · Science · doi:10.1126/science.341.6148.833 · Cited by 334 · see citing works
Xie, K., Zhang, J., & Yang, Y. (2014) · Molecular Plant · doi:10.1093/mp/ssu009 · Cited by 325 · see citing works
T-DNA Binary Vectors and Systems
Lee, L., & Gelvin, S. B. (2008) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.113001 · Cited by 253 · see citing works
Kirik, V., Simon, M. K., Wester, K., Schiefelbein, J., & Hülskamp, M. (2004) · Plant Molecular Biology · doi:10.1007/s11103-004-0893-8 · Cited by 213 · see citing works
Jiang, W., Yang, B., & Weeks, D. P. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099225 · Cited by 163 · see citing works
Arabidopsis CHLI2 Can Substitute for CHLI1
Huang, Y.-S., & Li, H. (2009) · PLANT PHYSIOLOGY · doi:10.1104/pp.109.135368 · Cited by 102 · see citing works
Bacteria herald a new era of gene editing
Segal, D. J. (2013) · eLife · doi:10.7554/elife.00563 · Cited by 18 · see citing works
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Lin, Q., Zong, Y., Xue, C., Wang, S., Jin, S., Zhu, Z., Wang, Y., Anzalone, A. V., Raguram, A., Doman, J. L., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0455-x · Cited by 873 · see citing works
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- Authors
- Xing, H.-L., Dong, L., Wang, Z.-P., Zhang, H.-Y., Han, C.-Y., Liu, B., Wang, X.-C., & Chen, Q.-J.
- Affiliations
- State Key Laboratory of Plant Physiology and Biochemistry (CN)
- Corresponding author
- Chen, Qi-Jun
- Venue
- BMC Plant Biology
- Published
- 2014-11-29
- Volume
- 14
- Issue
- 1
- Pages
- 327-327
- ISSN
- 1471-2229 (ISSN-L)
- PMC
- PMC4262988
- OpenAlex
- W2165016943
- Cited by
- 1,684
- References
- 50
- Citations by year
- 2026: 162 · 2025: 214 · 2024: 214 · 2023: 197 · 2022: 211 · 2021: 174 · 2020: 159 · 2019: 113 · 2018: 89 · 2017: 64 · 2016: 56 · 2015: 31
- FWCI
- 20.62
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Plant Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (31070329)
- National Key Research and Development Program of China (2012CB114200)
- National Transgenic Science and Technology Program (2011ZX08009)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Transgenic Plants and Applications
- Keywords
- CRISPR/Cas9, multiplex genome editing, binary vectors, transgenic plants, Arabidopsis mutants, selectable marker
- MeSH terms
- Base Sequence, Zea mays, Genetic Engineering, Genetic Vectors, Protoplasts, Sequence Alignment, Arabidopsis, Genome, Plant, Plants, Genetically Modified, Agrobacterium, CRISPR-Cas Systems
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