Puchta H, Fauser F. Gene targeting in plants: 25 years later. Int J Dev Biol. 2013;57:629–37.
Article
CAS
PubMed
Google Scholar
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A. 2012;109:E2579–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339:823–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cho SW, Kim S, Kim JM, Kim J-S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol. 2013;31:230–2.
Article
CAS
PubMed
Google Scholar
Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. RNA-programmed genome editing in human cells. Elife. 2013;2:e00471.
Article
PubMed
PubMed Central
Google Scholar
Puchta H. The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. J Exp Bot. 2005;56:1–14.
Article
CAS
PubMed
Google Scholar
Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol. 2013;31:686–8.
Article
CAS
PubMed
Google Scholar
Feng Z, Zhang B, Ding W, Liu X, Yang D-L, Wei P, et al. Efficient genome editing in plants using a CRISPR/Cas system. Cell Res. 2013;23:1229–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mao Y, Zhang H, Xu N, Zhang B, Gou F, Zhu J-K. Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol Plant. 2013;6:2008–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang D-L, et al. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci U S A. 2014;111:4632–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li J, Norville JE, Aach J, McCormack M, Zhang D, Bush J, et al. Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol. 2013;31:688–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baltes NJ, Gil-Humanes J, Cermak T, Atkins PA, Voytas DF. DNA replicons for plant genome engineering. Plant Cell. 2014;26:151–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 2015;169:931–45.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li Z, Liu Z-B, Xing A, Moon BP, Koellhoffer JP, Huang L, et al. Cas9-guide RNA directed genome editing in soybean. Plant Physiol. 2015;169:960–70.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sun Y, Zhang X, Wu C, He Y, Ma Y, Hou H, et al. Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol Plant. 2016;9:628–31.
Article
CAS
PubMed
Google Scholar
Endo M, Mikami M, Toki S. Biallelic gene targeting in rice. Plant Physiol. 2016;170:667–77.
Article
CAS
PubMed
Google Scholar
Nakade S, Tsubota T, Sakane Y, Kume S, Sakamoto N, Obara M, et al. Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9. Nat Commun. 2014;5:5560.
Article
CAS
PubMed
Google Scholar
Zhang Y, Liang Z, Zong Y, Wang Y, Liu J, Chen K, et al. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat Commun. 2016;7:12617.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andersson M, Turesson H, Nicolia A, Fält AS, Samuelsson M, Hofvander P. Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. Plant Cell Rep. 2017;36:117–28.
Article
CAS
PubMed
Google Scholar
Ryder P, McHale M, Fort A, Spillane C. Generation of stable nulliplex autopolyploid lines of Arabidopsis thaliana using CRISPR/Cas9 genome editing. Plant Cell Rep. 2017;36:1005–8.
Article
CAS
PubMed
Google Scholar
Baltes NJ, Gil-Humanes J, Voytas DF. Genome engineering and agriculture: opportunities and challenges. Prog Mol Biol Transl Sci. 2017;149:1–26.
Article
PubMed
PubMed Central
Google Scholar
Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2014;24:132–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lawrenson T, Shorinola O, Stacey N, Li C, Østergaard L, Patron N, et al. Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease. Genome Res. 2015;16:258.
Google Scholar
Wolt JD, Wang K, Sashital D, Lawrence-Dill CJ. Achieving plant CRISPR targeting that limits off-target effects. Plant Genome. 2016;9. https://doi.org/10.3835/plantgenome2016.05.0047.
Article
CAS
Google Scholar
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31:827–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014;507:62–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014;32:670–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
O’Geen H, Henry IM, Bhakta MS, Meckler JF, Segal DJ. A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res. 2015;43:3389–404.
Article
PubMed
PubMed Central
CAS
Google Scholar
Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, et al. Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation. Nat Biotechnol. 2014;32:1262–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wong N, Liu W, Wang X. WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol. 2015;16:218.
Article
PubMed
PubMed Central
CAS
Google Scholar
Graham DB, Root DE. Resources for the design of CRISPR gene editing experiments. Genome Biol. 2015;16:260.
Article
PubMed
PubMed Central
CAS
Google Scholar
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016;34:184–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oliveros JC, Franch M, Tabas-Madrid D, San-León D, Montoliu L, Cubas P, et al. Breaking-Cas—interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. Nucleic Acids Res. 2016;44:W267–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu H, Ding Y, Zhou Y, Jin W, Xie K, Chen L-L. CRISPR-P 2.0: an improved CRISPR-Cas9 tool for genome editing in plants. Mol Plant. 2017;10:530–2.
Article
CAS
PubMed
Google Scholar
Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud J-B, et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016;17:148.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sammons RD, Gaines TA. Glyphosate resistance: state of knowledge. Pest Manag Sci. 2014;70:1367–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu Q, Jalaludin A, Han H, Chen M, Sammons RD, Powles SB. Evolution of a double amino acid substitution in the 5-enolpyruvylshikimate-3-phosphate synthase in Eleusine indica conferring high-level glyphosate resistance. Plant Physiol. 2015;167:1440–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li J, Meng X, Zong Y, Chen K, Zhang H, Liu J, et al. Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9. Nat Plants. 2016;2:16139.
Article
CAS
PubMed
Google Scholar
Zhang HH, Zhang J, Wei P, Zhang B, Gou F, Feng Z, et al. The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J. 2014;12:797–807.
Article
CAS
PubMed
Google Scholar
Brinkman EK, Chen T, Amendola M, van Steensel B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 2014;42:e168.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, et al. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol. 2016;34:695–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, et al. Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnol J. 2015;13:97–104.
Article
CAS
PubMed
Google Scholar
Aramrak A, Kidwell KK, Steber CM, Burke IC. Molecular and phylogenetic characterization of the homoeologous EPSP synthase genes of allohexaploid wheat, Triticum aestivum (L.). BMC Genomics. 2015;16:844.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhou M, Xu H, Wei X, Ye Z, Wei L, Gong W, et al. Identification of a glyphosate-resistant mutant of rice 5-enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol. 2006;140:184–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shan Q, Wang Y, Li J, Gao C. Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc. 2014;9:2395–410.
Article
CAS
PubMed
Google Scholar
Zhou H, Arrowsmith JW, Fromm ME, Hironaka CM, Taylor ML, Rodriguez D, et al. Glyphosate-tolerant CP4 and GOX genes as a selectable marker in wheat transformation. Plant Cell Rep. 1995;15:159–63.
Article
CAS
PubMed
Google Scholar
Hu T, Metz S, Chay C, Zhou HP, Biest N, Chen G, et al. Agrobacterium-mediated large-scale transformation of wheat (Triticum aestivum L.) using glyphosate selection. Plant Cell Rep. 2003;21:1010–9.
Article
CAS
PubMed
Google Scholar
Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol. 2014;32:947–51.
Article
CAS
PubMed
Google Scholar
Liang Z, Chen K, Li T, Zhang Y, Wang Y, Zhao Q, et al. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat Commun. 2017;8:14261.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim D, Alptekin B, Budak H. CRISPR/Cas9 genome editing in wheat. Funct Integr Genomics. 2018;18:31–41.
Article
CAS
PubMed
Google Scholar
Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol. 2014;32:279–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, et al. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature. 2016;529:490–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paquet D, Kwart D, Chen A, Sproul A, Jacob S, Teo S, et al. Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9. Nature. 2016;533:125–9.
Article
CAS
PubMed
Google Scholar
Kim J, Kim J-S. Bypassing GMO regulations with CRISPR gene editing. Nat Biotechnol. 2016;34:1014–5.
Article
CAS
PubMed
Google Scholar
Vu GTH, Cao HX, Reiss B, Schubert I. Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage. New Phytol. 2017;214:1712–21.
Article
CAS
PubMed
Google Scholar
Woo JW, Kim J, Kwon SI, Corvalán C, Cho SW, Kim H, et al. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat Biotechnol. 2015;33:1162–4.
Article
CAS
PubMed
Google Scholar
Svitashev S, Schwartz C, Lenderts B, Young JK, Cigan AM. Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes. Nat Commun. 2016;7:13274.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zischewski J, Fischer R, Bortesi L. Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases. Biotechnol Adv. 2017;35:95–104.
Article
CAS
PubMed
Google Scholar
Bae S, Kweon J, Kim HS, Kim J-S. Microhomology-based choice of Cas9 nuclease target sites. Nat Methods. 2014;11:705–6.
Article
CAS
PubMed
Google Scholar
Vu GTH, Cao HX, Fauser F, Reiss B, Puchta H, Schubert I. Endogenous sequence patterns predispose the repair modes of CRISPR/Cas9-induced DNA double strand breaks in Arabidopsis thaliana. Plant J. 2017;92:57–67.
Article
CAS
PubMed
Google Scholar
Yang Z, Steentoft C, Hauge C, Hansen L, Thomsen AL, Niola F, et al. Fast and sensitive detection of indels induced by precise gene targeting. Nucleic Acids Res. 2015;43:e59.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mock U, Hauber I, Fehse B. Digital PCR to assess gene-editing frequencies (GEF-dPCR) mediated by designer nucleases. Nat Protoc. 2016;11:598–615.
Article
CAS
PubMed
Google Scholar
Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol. 2014;32:347–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
sgRNA Designer. https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design. Accessed 16 Feb 2017.
WU-CRISPR. http://crispr.wustl.edu/. Accessed 16 Feb 2017.
Christensen AH, Sharrock RA, Quail PH. Maize polyubiquitin genes: structure, thermal perturbation of expression and transcript splicing, and promoter activity following transfer to protoplasts by electroporation. Plant Mol Biol. 1992;18:675–89.
Article
CAS
PubMed
Google Scholar
Christensen AH, Quail PH. Ubiquitin promoter-based vectors for high-level expression of selectable and/or screenable marker genes in monocotyledonous plants. Transgenic Res. 1996;5:213–8.
Article
CAS
PubMed
Google Scholar
Sasanuma T. Characterization of the rbcS multigene family in wheat: subfamily classification, determination of chromosomal location and evolutionary analysis. Mol Gen Genomics. 2001;265:161–71.
Article
CAS
Google Scholar
Yoo S-D, Cho Y-H, Sheen J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc. 2007;2:1565–72.
Article
CAS
PubMed
Google Scholar
Langmead B, Salzberg S. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar