Abstract
CRISPR/Cas system has been widely used for genome editing in the past few years. Even though it has been performed in many polyploid species to date, its efficient accomplishment in these organisms is still a challenge. The presence of multiple homoeologous genes as targets for their editing requires more rigorous work and specific needs to assess successful genome editing. Here, we describe a general stepwise protocol to select target sites, design sgRNAs, indicate vector requirements, and screen CRISPR/Cas9-mediated genome editing in polyploid species.
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References
Songstad DD, Petolino JF, Voytas DF, Reichert NA (2017) Genome editing of plants. CRC Crit Rev Plant Sci 36:1–23. https://doi.org/10.1080/07352689.2017.1281663
Zhu H, Li C, Gao C (2020) Applications of CRISPR–Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol 21:661–677. https://doi.org/10.1038/s41580-020-00288-9
Gaj T, Gersbach CA, Barbas CF III (2013) ZFN, TALEN and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405. https://doi.org/10.1016/j.tibtech.2013.04.004.ZFN
Cong L, Ran FA, Cox D et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823. https://doi.org/10.1126/science.1231143.Multiplex
Mojica FJM, Díez-Villaseñor C, García-Martínez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60:174–182. https://doi.org/10.1007/s00239-004-0046-3
Sorek R, Kunin V, Hugenholtz P (2008) CRISPR – A widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 6:181–186. https://doi.org/10.1038/nrmicro1793
**ek M, Chylinski K, Fonfara I et al (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (80-) 337:816–821. https://doi.org/10.1126/science.1225829
Feng Z, Zhang B, Ding W et al (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23:1229–1232. https://doi.org/10.1038/cr.2013.114
Mao Y, Zhang H, Xu N et al (2013) Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol Plant 6:2008–2011. https://doi.org/10.1093/mp/sst121
Jiang W, Zhou H, Bi H et al (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41:1–12. https://doi.org/10.1093/nar/gkt780
Woodhouse M, Burkart-Waco D, Comai L (2009) Polyploidy Nat Educ 2:1
Soppa J (2014) Polyploidy in archaea and bacteria: about desiccation resistance, giant cell size, long-term survival, enforcement by a eukaryotic host and additional aspects. J Mol Microbiol Biotechnol 24:409–419. https://doi.org/10.1159/000368855
Baatout S (1999) Molecular basis to understand polyploidy. Hematol Cell Ther 41:169–170. https://doi.org/10.1007/s00282-999-0169-5
Yin F, Liu W, Chai J et al (2018) CRISPR/Cas9 application for gene copy fate survey of polyploid vertebrates. Front Genet 9:1–7. https://doi.org/10.3389/fgene.2018.00260
Fang Z, Morrell PL (2016) Polyploidy boosts domestication. Nat Plants 2:1–2. https://doi.org/10.1038/NPLANTS.2016.116
Zaman QU, Li C, Cheng H, Hu Q (2019) Genome editing opens a new era of genetic improvement in polyploid crops. Crop J 7:141–150. https://doi.org/10.1016/j.cj.2018.07.004
Shan Q, Wang Y, Li J et al (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:684–686. https://doi.org/10.1038/nbt.2652
Kaur N, Alok A, Shivani et al (2020) CRISPR/Cas9 directed editing of lycopene epsilon-cyclase modulates metabolic flux for β-carotene biosynthesis in banana fruit. Metab Eng 59:76–86. https://doi.org/10.1016/j.ymben.2020.01.008
Sun X, Hu Z, Chen R et al (2015) Targeted mutagenesis in soybean using the CRISPR-Cas9 system. Sci Rep 5:1–10. https://doi.org/10.1038/srep10342
Gao J, Wang G, Ma S et al (2015) CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol Biol 87:99–110. https://doi.org/10.1007/s11103-014-0263-0
Andersson M, Turesson H, Nicolia A et al (2017) Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. Plant Cell Rep 36:117–128. https://doi.org/10.1007/s00299-016-2062-3
Li C, Unver T, Zhang B (2017) A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.). Sci Rep 7:1–10. https://doi.org/10.1038/srep43902
Braatz J, Harloff HJ, Mascher M et al (2017) CRISPR-Cas9 targeted mutagenesis leads to simultaneous modification of different homoeologous gene copies in polyploid oilseed rape (Brassica napus). Plant Physiol 174:935–942. https://doi.org/10.1104/pp.17.00426
Park JJ, Yoo CG, Flanagan A et al (2017) Defined tetra-allelic gene disruption of the 4-coumarate:coenzyme A ligase 1 (Pv4CL1) gene by CRISPR/Cas9 in switchgrass results in lignin reduction and improved sugar release Mike Himmel. Biotechnol Biofuels 10:1–11. https://doi.org/10.1186/s13068-017-0972-0
Shan S, Mavrodiev EV, Li R et al (2018) Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy. Mol Ecol Resour 18:1427–1443. https://doi.org/10.1111/1755-0998.12935
Morineau C, Bellec Y, Tellier F et al (2017) Selective gene dosage by CRISPR-Cas9 genome editing in hexaploid Camelina sativa. Plant Biotechnol J 15:729–739. https://doi.org/10.1111/pbi.12671
Martín-Pizarro C, Triviño JC, Posé D (2019) Functional analysis of the TM6 MADS-box gene in the octoploid strawberry by CRISPR/Cas9-directed mutagenesis. J Exp Bot 70:949–961. https://doi.org/10.1093/jxb/ery400
Eid A, Mohan C, Sanchez S et al (2021) Multiallelic, targeted mutagenesis of magnesium chelatase with CRISPR/Cas9 provides a rapidly scorable phenotype in highly polyploid sugarcane. Front Genome Ed 3. https://doi.org/10.3389/fgeed.2021.654996
Hsu PD, Scott DA, Weinstein JA et al (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31:827–832. https://doi.org/10.1038/nbt.2647
Moreno-Mateos MA, Vejnar CE, Beaudoin JD et al (2015) CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods 12:982–988. https://doi.org/10.1038/nmeth.3543
Xu H, **ao T, Chen CH et al (2015) Sequence determinants of improved CRISPR sgRNA design. Genome Res 25:1147–1157. https://doi.org/10.1101/gr.191452.115
Liu H, Ding Y, Zhou Y et al (2017) CRISPR-P 2.0: an improved CRISPR-Cas9 tool for genome editing in plants. Mol Plant 10:530–532. https://doi.org/10.1016/j.molp.2017.01.003
Concordet JP, Haeussler M (2018) CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res 46:W242–W245. https://doi.org/10.1093/nar/gky354
Labun K, Montague TG, Krause M et al (2019) CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res 47:W171–W174. https://doi.org/10.1093/nar/gkz365
Prykhozhij SV, Rajan V, Gaston D, Berman JN (2015) CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One 10:1–18. https://doi.org/10.1371/journal.pone.0119372
Bae S, Park J, Kim JS (2014) Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30:1473–1475. https://doi.org/10.1093/bioinformatics/btu048
Feng C, Su H, Bai H et al (2018) High-efficiency genome editing using a dmc1 promoter-controlled CRISPR/Cas9 system in maize. Plant Biotechnol J 16:1848–1857. https://doi.org/10.1111/pbi.12920
Qi X, Dong L, Liu C et al (2018) Systematic identification of endogenous RNA polymerase III promoters for efficient RNA guide-based genome editing technologies in maize. Crop J 6:314–320. https://doi.org/10.1016/j.cj.2018.02.005
Miyagishi M, Taira K (2002) U6 promoter-driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells. Nat Biotechnol 20:497–500. https://doi.org/10.1038/nbt0502-497
**a XG, Zhou H, Ding H et al (2003) An enhanced U6 promoter for synthesis of short hairpin RNA. Nucleic Acids Res 31:e100. https://doi.org/10.1093/nar/gng098
Zhou J, Wang G, Liu Z (2018) Efficient genome editing of wild strawberry genes, vector development and validation. Plant Biotechnol J 16:1868–1877. https://doi.org/10.1111/pbi.12922
Long L, Guo DD, Gao W et al (2018) Optimization of CRISPR/Cas9 genome editing in cotton by improved sgRNA expression. Plant Methods 14:1–9. https://doi.org/10.1186/s13007-018-0353-0
Johansen IE, Liu Y, Jørgensen B et al (2019) High efficacy full allelic CRISPR/Cas9 gene editing in tetraploid potato. Sci Rep 9:1–7. https://doi.org/10.1038/s41598-019-54126-w
Gil-Humanes J, Wang Y, Liang Z et al (2017) High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant J 89:1251–1262. https://doi.org/10.1111/tpj.13446
Wolabu TW, Cong L, Park J et al (2020) Development of a highly efficient multiplex genome editing system in outcrossing tetraploid alfalfa (Medicago sativa). Front Plant Sci 11:1–9. https://doi.org/10.3389/fpls.2020.01063
Yan L, Wei S, Wu Y et al (2015) High-efficiency genome editing in arabidopsis using YAO promoter-driven CRISPR/Cas9 system. Mol Plant 8:1820–1823. https://doi.org/10.1016/j.molp.2015.10.004
Zhang F, LeBlanc C, Irish VF, Jacob Y (2017) Rapid and efficient CRISPR/Cas9 gene editing in Citrus using the YAO promoter. Plant Cell Rep 36:1883–1887. https://doi.org/10.1007/s00299-017-2202-4
Liu W, ** of targeted mutations. Mol Plant 8:1431–1433. https://doi.org/10.1016/j.molp.2015.05.009
Güell M, Yang L, Church GM (2014) Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 30:2968–2970. https://doi.org/10.1093/bioinformatics/btu427
Park J, Lim K, Kim JS, Bae S (2017) Cas-analyzer: an online tool for assessing genome editing results using NGS data. Bioinformatics 33:286–288. https://doi.org/10.1093/bioinformatics/btw561
Ledda M, Cobo N, Lorant A, et al (2019) PolyOligo: a bioinformatic platform for identifying target DNA sequences for the development of sub-genome specific DNA markers in polyploid/complex genomes
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 1–13. https://doi.org/10.1093/molbev/msab120
Doench JG, Fusi N, Sullender M et al (2016) Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 34:184–191. https://doi.org/10.1038/nbt.3437
Belhaj K, Chaparro-Garcia A, Kamoun S, Nekrasov V (2013) Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9:1–10. https://doi.org/10.1186/1746-4811-9-39
Tycko J, Wainberg M, Marinov GK et al (2019) Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nat Commun 10:1–14. https://doi.org/10.1038/s41467-019-11955-7
Acknowledgments
CSG was supported by a grant from the Spanish Ministries of Science and Innovation (MICINN, RTI2018-09309-A-I00). CMP was supported by a grant from the European Research Council (ERC-2014-StG 638134).
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Sánchez-Gómez, C., Posé, D., Martín-Pizarro, C. (2023). Genome Editing by CRISPR/Cas9 in Polyploids. In: Van de Peer, Y. (eds) Polyploidy. Methods in Molecular Biology, vol 2545. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2561-3_24
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DOI: https://doi.org/10.1007/978-1-0716-2561-3_24
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