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CRISPR/Cas9 Genome Editing in Bread Wheat (Triticum aestivum L.) Genetic Improvement

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Abstract

Bread wheat (Triticum aestivum L.) is the most important staple crop worldwide. Wheat has a large and allohexaploid genome with more than 107 thousand gene models that expand over 21 chromosomes with 3 replicates. The high complexity of the wheat genome has restricted the success of conventional breeding programs. Wheat genome modification by biotechnological methods has been hindered due to the current methods limitations and safety issues over genetically-modified crops. CRISPR/Cas9 is an emerging biotechnological tool that holds promises for multiplexed, sequence-specific, efficient and rapid manipulation of large genomes such as that of wheat. The CRISPR/Cas9 system introduces sequence-specific double-strand breaks (DSBs) in DNA by synthetic nucleases. The targeted genomic loci are then fixed by DNA repair mechanisms such as non-homologous end-joining (NHEJ) or homology-directed repair (HDR). The system and its improved sub-techniques have achieved significant successes in addressing biosafety and legal concerns over genetically-modified plant production. In this chapter, the history, potentials and the latest results of CRISPR/Cas9-based genetic manipulations in bread wheat is reviewed.

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References

  • Al-Attar S, Westra ER, van der Oost J et al (2011) Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem 392:277–289

    Article  CAS  PubMed  Google Scholar 

  • Appels R, Eversole K, Feuillet C et al (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361(6403). https://doi.org/10.1126/science.aar7191

  • Araki M, Ishii T (2015) Towards social acceptance of plant breeding by genome editing. Trends Plant Sci 20:145–149

    Article  CAS  PubMed  Google Scholar 

  • Barrangou R, Fremaux C, Deveau H et al (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712

    Article  CAS  PubMed  Google Scholar 

  • Belhaj K, Chaparro-Garcia A, Kamoun S et al (2015) Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol 32:76–84

    Article  CAS  PubMed  Google Scholar 

  • Bhowmik P, Ellison E, Polley B et al (2018) Targeted mutagenesis in wheat microspores using CRISPR/Cas9. Sci Rep 8:6502. https://www.nature.com/articles/s41598-018-24690-8

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bortesi L, Fischer R (2015) The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 33:41–52

    Article  CAS  PubMed  Google Scholar 

  • Carroll D, Morton JJ, Beumer KJ et al (2006) Design, construction and in vitro testing of zinc finger nucleases. Nat Protoc 1:1329–1341

    Article  CAS  PubMed  Google Scholar 

  • Čermák T, Baltes NJ, Čegan R et al (2015) High-frequency, precise modification of the tomato genome. Genome Biol 16:232. https://doi.org/10.1186/s13059-015-0796-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christian M, Cermak T, Doyle EL et al (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong L, Wang F, Liu T et al (2014) Natural variation of TaGASR7-A1 affects grain length in common wheat under multiple cultivation conditions. Mol Breed 34:937–947

    Article  CAS  Google Scholar 

  • Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862–1866

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dvorak J (2001) Triticum species (Wheat). In: Brenner S, Miller JH (eds) Encyclopedia of genetics. Academic, New York, pp 2060–2068. https://doi.org/10.1006/rwgn.2001.1672

    Chapter  Google Scholar 

  • Dvořák J (2009) Triticeae genome structure and evolution. In: Muehlbauer G, Feuillet C (eds) Genetics and genomics of the Triticeae. Springer, New York, pp 685–711

    Chapter  Google Scholar 

  • Endo M, Mikami M, Toki S (2015) Multigene knockout utilizing off-target mutations of the CRISPR/Cas9 system in rice. Plant Cell Physiol 56:41–47

    Article  CAS  PubMed  Google Scholar 

  • Feng B, Dong Z, Xu Z et al (2010) Molecular analysis of lipoxygenase (LOX) genes in common wheat and phylogenetic investigation of LOX proteins from model and crop plants. J Cereal Sci 52:387–394

    Article  CAS  Google Scholar 

  • Feng Z, Mao Y, Xu N et al (2014) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci 111:4632–4637

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Freiermuth JL, Powell Castilla IJ, Gallicano GI (2018) Toward a CRISPR picture: use of CRISPR/Cas9 to model diseases in human stem cells in vitro. J Cell Biochem 119:62–68

    Article  CAS  PubMed  Google Scholar 

  • Fu Y, Foden JA, Khayter C et al (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Nanotechnol 31:822–826

    CAS  Google Scholar 

  • Gaj T, Gersbach CA, Barbas CF III (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao J, Wang G, Ma S et al (2015) CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol Biol 87:99–110

    Article  CAS  PubMed  Google Scholar 

  • Gapinske M, Luu A, Winter J et al (2018) CRISPR-SKIP: programmable gene splicing with single base editors. Genome Biol 19:1–11

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Godfray HCJ, Beddington JR, Crute IR et al (2010) Food security: the challenge of feeding 9 billion people. Science 327:812–818

    Article  CAS  PubMed  Google Scholar 

  • Haque E, Taniguchi H, Hassan MM et al (2018) Application of CRISPR/Cas9 genome editing technology for the improvement of crops cultivated in tropical climates: recent progress, prospects, and challenges. Front Plant Sci 9:1–12

    Article  CAS  Google Scholar 

  • Hyun Y, Kim J, Cho SW et al (2015) Site-directed mutagenesis in Arabidopsis thaliana using dividing tissue-targeted RGEN of the CRISPR/Cas system to generate heritable null alleles. Planta 241:271–284

    Article  CAS  PubMed  Google Scholar 

  • Jansen R, van Embden JD, Gaastra W et al (2002) Identification of a novel family of sequence repeats among prokaryotes. OMICS 6:23–33

    Article  CAS  PubMed  Google Scholar 

  • 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:e188. https://doi.org/10.1093/nar/gkt780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jones HD (2015) Regulatory uncertainty over genome editing. Nat Plants 1:14011. https://www.nature.com/articles/nplants201411

    Article  PubMed  Google Scholar 

  • Jordan KW, Wang S, Lun Y et al (2015) A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 16:1–18

    Article  Google Scholar 

  • Joung JK, Sander JD (2013) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14:49–55

    Article  CAS  PubMed  Google Scholar 

  • Kamburova VS, Nikitina EV, Shermatov SE et al (2017) Genome editing in plants: an overview of tools and applications. Int J Agron 2017:1–15

    Article  CAS  Google Scholar 

  • Kanchiswamy CN, Malnoy M, Velasco R et al (2015) Non-GMO genetically edited crop plants. Trends Biotechnol 33:489–491

    Article  CAS  PubMed  Google Scholar 

  • Kim D, Alptekin B, Budak H (2018) CRISPR/Cas9 genome editing in wheat. Funct Integr Genomics 18:31–41

    Article  CAS  PubMed  Google Scholar 

  • Krasileva KV, Vasquez-Gross HA, Howell T et al (2017) Uncovering hidden variation in polyploid wheat. Proc Natl Acad Sci 114:E913–E921. https://doi.org/10.1073/pnas.1619268114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kusch S, Pesch L, Panstruga R (2016) Comprehensive phylogenetic analysis sheds light on the diversity and origin of the MLO family of integral membrane proteins. Genome Biol Evol 8:878–895

    Article  PubMed  PubMed Central  Google Scholar 

  • Lawrenson T, Shorinola O, Stacey N et al (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease. Genome Biol 16:258. https://doi.org/10.1186/s13059-015-0826-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li J-F, Norville JE, Aach J et al (2013) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Nanotechnol 31:688–691. https://www.nature.com/articles/nbt.2654

    CAS  Google Scholar 

  • Li Z, Liu Z-B, Xing A et al (2015) Cas9-guide RNA directed genome editing in soybean. Plant Physiol 169:960–970

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liang Z, Chen K, Li T et al (2017) Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat Commun 8:14261. https://doi.org/10.1038/ncomms14261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liang Z, Chen K, Zhang Y et al (2018) Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins. Nat Protoc 13(3):413–430. https://doi.org/10.1038/nprot

    Article  CAS  PubMed  Google Scholar 

  • Ling H-Q, Zhao S, Liu D et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90

    Article  CAS  PubMed  Google Scholar 

  • Lombardo A, Cesana D, Genovese P et al (2011) Site-specific integration and tailoring of cassette design for sustainable gene transfer. Nat Methods 8:861–869

    Article  CAS  PubMed  Google Scholar 

  • Malnoy M, Viola R, Jung M-H et al (2016) DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Front Plant Sci 7:1–9

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Minkenberg B, Wheatley M, Yang Y (2017) CRISPR/Cas9-enabled multiplex genome editing and its application. In: Weeks DP, Yang B (eds) Progress in molecular biology and translational science, vol 149. Academic, Netherlands, pp 111–132

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Platt RJ, Chen S, Zhou Y et al (2014) CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159:440–455

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rath D, Amlinger L, Rath A et al (2015) The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie 117:119–128

    Article  CAS  PubMed  Google Scholar 

  • Richardson CD, Ray GJ, DeWitt MA et al (2016) Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Nanotechnol 34:339–344

    CAS  Google Scholar 

  • Sánchez-León S, Gil-Humanes J, Ozuna CV et al (2018) Low-gluten, nontransgenic wheat engineered with CRISPR/Cas9. Plant Biotechnol J 16:902–910

    Article  PubMed  CAS  Google Scholar 

  • Schenkwein D, Ylä-Herttuala S (2018) Gene editing of human embryos with CRISPR/Cas9: great promise coupled with important caveats. Mol Ther 26:659–660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shan Q, Wang Y, Li J et al (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Nanotechnol 31:686–688

    CAS  Google Scholar 

  • Shan Q, Wang Y, Li J et al (2014) Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc 9:2395–2410. https://www.nature.com/articles/nprot.2014.157

    Article  CAS  PubMed  Google Scholar 

  • Singh M, Kumar M, Albertsen MC et al (2018) Concurrent modifications in the three homeologs of Ms45 gene with CRISPR-Cas9 lead to rapid generation of male sterile bread wheat (Triticum aestivum L.). Plant Mol Biol 97:371–383

    Article  CAS  PubMed  Google Scholar 

  • Smulders MR, Jouanin A, Gilissen LJ (2017) Gene editing using CRISPR/Cas9 to modify or remove gliadins from wheat and produce coeliac disease epitope-free wheat. In: Koehler P (ed) Proceedings of the 31st meeting of the working group on Prolamin analysis and toxicity, Minden, pp 63–68

    Google Scholar 

  • Svitashev S, Schwartz C, Lenderts B et al (2016) Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nat Commun 7:13274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Symington LS, Gautier J (2011) Double-strand break end resection and repair pathway choice. Annu Rev Genet 45:247–271

    Article  CAS  PubMed  Google Scholar 

  • Thurtle-Schmidt DM, Lo TW (2018) Molecular biology at the cutting edge: a review on CRISPR/CAS9 gene editing for undergraduates. Biochem Mol Biol Educ 46:195–205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uauy C, Wulff BB, Dubcovsky J (2017) Combining traditional mutagenesis with new high-throughput sequencing and genome editing to reveal hidden variation in polyploid wheat. Annu Rev Genet 51:435–454

    Article  CAS  PubMed  Google Scholar 

  • Upadhyay SK, Kumar J, Alok A et al (2013) RNA–guided genome editing for target gene mutations in wheat. G3. Genes Genomes Genet 3:2233–2238

    CAS  Google Scholar 

  • Wang S, Wong D, Forrest K et al (2014a) Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Cheng X, Shan Q et al (2014b) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Nanotechnol 32:947–951

    CAS  Google Scholar 

  • Wang W, Akhunova A, Chao S et al (2016) Optimizing multiplex CRISPR/Cas9-based genome editing for wheat. BioRxiv. https://doi.org/10.1101/051342

  • Wang W, Pan Q, He F et al (2018) Transgenerational CRISPR–Cas9 activity facilitates multiplex gene editing in allopolyploid wheat. CRISPR J 1:65–74

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weinthal DM, Gürel F (2016) Plant genome editing and its applications in cereals. In: Manohar R (ed) Genetic engineering: an insight into the strategies and applications. InTech, UK, pp 63–73

    Google Scholar 

  • Wolt JD (2017) Safety, security, and policy considerations for plant genome editing. In: Weeks DP, Yang B (eds) Progress in molecular biology and translational science, vol 149. Elsevier, Amsterdam, pp 215–241

    Google Scholar 

  • Xu R-F, Li H, Qin R-Y et al (2015) Generation of inheritable and “transgene clean” targeted genome-modified rice in later generations using the CRISPR/Cas9 system. Sci Rep 5:11491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Z, Bai Z, Li X et al (2012) SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight. Theor Appl Genet 125:1057–1068

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Liang Z, Zong Y et al (2016a) Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat Commun 7:12617. https://www.nature.com/articles/ncomms12617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Mao Y, Ha S et al (2016b) A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant Cell Rep 35:1519–1533

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Bai Y, Wu G et al (2017) Simultaneous modification of three homoeologs of ta EDR1 by genome editing enhances powdery mildew resistance in wheat. Plant J 91:714–724

    Article  CAS  PubMed  Google Scholar 

  • Zong Y, Wang Y, Li C et al (2017) Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat Nanotechnol 35:438–440

    CAS  Google Scholar 

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Authors and Affiliations

Authors

Corresponding author

Correspondence to Mohammad R. Sabzalian .

Editor information

Editors and Affiliations

Appendix I: Research Institutes Relevant to Wheat Biotechnology

Appendix I: Research Institutes Relevant to Wheat Biotechnology

Institution

Specialization and research activities

Website

International Maize and Wheat Improvement Center (CIMMYT), Mexico

The development of improved varieties of wheat and maize

www.cimmyt.org/

The Nottingham/BBSRC Wheat Research Centre (WISP), UK

Creating genetic variation for agronomically and scientifically important traits from wild and distantly related species into wheat

http://www.wheatisp.org/

Wheat initiative institutions, Berlin, Germany

International collaboration for wheat breeding

http://www.wheatinitiative.org/about-us/countries-international-research-centres

Institute of Agrobiological Sciences, NARO, Japan

Understanding the biological phenomena of wheat transformation

ww.naro.affrc.go.jp

Institute of Molecular Plant Biology, ETH, Zurich

Improving wheat nutritional qualities as well as understanding the molecular processes that play a key role in protecting the crop against biotic and abiotic stresses

http://www.impb.ethz.ch

The International Service for the Acquisition of Agri-Biotech Applications (ISAAA)

To share the benefits of crop biotechnology to various stakeholders, particularly resource-poor farmers in developing countries, through knowledge sharing initiatives and the transfer and delivery of proprietary biotechnology applications

http://www.isaaa.org

BASF Plant Science, USA

Wheat genetic engineering

https://agriculture.basf.com

John Innes Centre, UK

To develop new wheat germplasm containing the next generation of key traits

https://www.jic.ac.uk

Rothamsted Research (RRES), UK

Improving the environmental resilience of the wheat crop through genetics and targeted traits analysis

https://www.rothamsted.ac.uk

National Institute of Agricultural Botany (NIAB)

Functional analysis of wheat genes for breeding new traits for commercial exploitation through traditional breeding techniques

http://www.niab.com

Earlham Institute (EI), UK

Genetic diversity in wheat and Sequencing the wheat genome

http://www.earlham.ac.uk

European Bioinformatics Institute (EBI)

Analysis of the bread wheat genome

https://www.ebi.ac.uk

International Wheat Genome Sequencing Consortium, IWGSC

To establish a high quality reference sequence of the wheat genome anchored to the genetic/phenotypic maps

http://www.wheatgenome.org/

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Dayani, S., Sabzalian, M.R., Mazaheri-Tirani, M. (2019). CRISPR/Cas9 Genome Editing in Bread Wheat (Triticum aestivum L.) Genetic Improvement. In: Al-Khayri, J., Jain, S., Johnson, D. (eds) Advances in Plant Breeding Strategies: Cereals. Springer, Cham. https://doi.org/10.1007/978-3-030-23108-8_12

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