Skip to main content
SpringerLink
Log in

Challenges in wide implementation of genome editing for crop improvement

  • Research Article
  • Published:
Journal of Crop Science and Biotechnology Aims and scope Submit manuscript

Abstract

Genome editing technologies using customizable sequence specific nucleases (SSNs) enables precise genome modification in plants, which has revolutionized functional genomics research as well as crop improvement. Applicability of SSN-mediated genome editing ranges from targeted gene knockout and single base modification to multiple gene stacking into desired genomic sites. However, there are still considerable challenges in implementing genome editing technologies for practical crop improvement. Here, we briefly discuss the technological challenges, especially those associated with the delivery of SSNs and with homologous recombination-mediated genome editing, and address some promising solutions to overcome the issues.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Altpeter F, Springer NM, Bartley LE, Blechl AE, Brutnell TP Citovsky V, Conrad L, Gelvin SB, Jackson D, Kausch AP, Lemaux PG, Medford JI, Orozo-Cardenas M, Tricoli D, VanEck J, Voytas DF, Walbot V, Wang K, Zhang ZJ, Stewart CN. 2016. Advancing crop transformation in the era of genome editing. Plant Cell 28(7): 1510–1520

    CAS  PubMed  PubMed Central  Google Scholar 

  • Baltes NJ, Gil-Humanes J, Cermak T, Atkins PA, Voytas DF. 2014. DNA replicons for plant genome engineering. Plant Cell 26(1): 151–163

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bartlett JG, Alves SC, Smedley M, Snape JW, Harwood WA. 2008. High-throughput Agrobacterium-mediated barley transformation. Plant Methods 4(1): 22

    Article  PubMed  PubMed Central  Google Scholar 

  • Bastaki NK, Cullis CA. 2014. Floral-Dip Transformation of flax (Linum usitatissimum) to generate transgenic progenies with a high transformation rate. JoVE 94: 52189

    Google Scholar 

  • Bortesi L, Fischer R. 2015. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol. Adv. 33(1): 41–52

    Article  CAS  PubMed  Google Scholar 

  • Cermák T, Baltes NJ, Cegan R, Zhang Y, Voytas DF. 2015. High-frequency, precise modification of the tomato genome. Genome Biol. 16(1): 232

    Article  PubMed  PubMed Central  Google Scholar 

  • Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186(2): 757–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clough SJ, Bent AF. 1998. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16(6): 735–743

    Article  CAS  PubMed  Google Scholar 

  • Curtis IS, Nam HG. 2001. Transgenic radish (Raphanus sativusL.longipinnatus Bailey) by floral-dip method–plant development and surfactant are important in optimizing transformation efficiency. Transgenic Res. 10(4): 363–371

    Article  CAS  PubMed  Google Scholar 

  • Ding Y, Li H, Chen L-L, Xie K. 2016. Recent advances in genome editing using CRISPR/Cas9. Front. Plant Sci. 7: 703

    PubMed  PubMed Central  Google Scholar 

  • Elmayan T, Vaucheret H. 1996. Expression of single copies of a strongly expressed 35S transgene can be silenced post-transcriptionally. Plant J. 9(6): 787–797

    Article  CAS  Google Scholar 

  • Endo M, Mikami M, Toki S. 2016. Biallelic gene targeting in rice. Plant Physiol. 170(2): 667–677

    Article  CAS  PubMed  Google Scholar 

  • Even-Faitelson L, Samach A, Melamed-Bessudo C, Avivi-Ragolsky N, Levy AA. 2011. Localized egg-cell expression of effector proteins for targeted modification of the Arabidopsis genome. Plant J. 68(5): 929–937

    Article  CAS  PubMed  Google Scholar 

  • Hilscher J, Bürstmayr H, Stoger E. 2016. Targeted modification of plant genomes for precision crop breeding. Biotechnol. J. 12: 1600173

    Article  Google Scholar 

  • Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096): 816–821

    Article  CAS  PubMed  Google Scholar 

  • Kaeppler SM, Kaeppler HF, Rhee Y. 2000. Epigenetic aspects of somaclonal variation in plants. Plant Mol. Biol. 43(2): 179–188

    Article  CAS  PubMed  Google Scholar 

  • Kim YG, Cha J, Chandrasegaran S. 1996. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl. Acad. Sci. USA 93(3): 1156–1160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kwon Y-I, Abe K, Osakabe K, Endo M, Nishizawa-Yokoi A, Saika H, Shimada H, Toki S. 2012. Overexpression of OsRecQl4 and/or OsExo1 enhances DSB-induced homologous recombination in rice. Plant Cell Physiol. 53(12): 2142–2152

    Article  CAS  PubMed  Google Scholar 

  • Li J, Tan X, Zhu F, Guo J. 2010. A rapid and simple method for Brassica napus floral-dip transformation and selection of transgenic plantlets. Int. J. Biol. 2(1): 127–131

    CAS  Google Scholar 

  • Liang Z, Chen K, Li T, Zhang Y, Wang Y, Zhao Q, Liu J, Zhang H, Liu C, Ran Y, Gao C. 2017. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nature Comm. 8: 14261

    Article  CAS  Google Scholar 

  • Lu C, Kang J. 2008. Generation of transgenic plants of a potential oilseed crop Camelina sativa by Agrobacterium-mediated transformation. Plant Cell Rep. 27(2): 273–278

    Article  CAS  PubMed  Google Scholar 

  • Luo S, Li J, Stoddard Thomas J, Baltes Nicholas J, Demorest Zachary L, Clasen Benjamin M, Coffman A, Retterath A, Mathis L, Voytas Daniel F, Zhang F. 2015. Non-transgenic plant genome editing using purified sequence-specific nucleases. Mol. Plant 8(9): 1425–1427

    Article  CAS  PubMed  Google Scholar 

  • Malyska A, Bolla R, Twardowski T. 2016. The role of public opinion in shaping trajectories of agricultural biotechnology. Trends Biotechnol. 34(7): 530–534

    Article  CAS  PubMed  Google Scholar 

  • Martin-Ortigosa S, Peterson DJ, Valenstein JS, Lin VS-Y, Trewyn BG, Lyznik LA, Wang K. 2014. Mesoporous silica nanoparticle-mediated intracellular Cre protein delivery for maize genome editing via loxP Site excision. Plant Physiol. 164(2): 537–547

    Article  CAS  PubMed  Google Scholar 

  • Martin-Ortigosa S, Wang K. 2014. Proteolistics: a biolistic method for intracellular delivery of proteins. Transgenic Res. 23(5): 743–756

    Article  CAS  PubMed  Google Scholar 

  • Martins PK, Nakayama TJ, Ribeiro AP, Cunha BADBd, Nepomuceno AL, Harmon FG, Kobayashi AK, Molinari HBC. 2015. Setaria viridis floral-dip: A simple and rapid Agrobacterium-mediated transformation method. Biotechnol. Rep. 6: 61–63

    Article  Google Scholar 

  • Matzke AJM, Matzke MA. 1998. Position effects and epigenetic silencing of plant transgenes. Curr. Opin. Plant Biol. 1(2): 142–148

    Article  CAS  PubMed  Google Scholar 

  • Morbitzer R, Römer P, Boch J, Lahaye T. 2010. Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors. Proc. Natl. Acad. Sci. USA 107(50): 21617–21622

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mu G, Chang N, Xiang K, Sheng Y, Zhang Z, Pan G. 2012. Genetic transformation of maize female inflorescence following floral dip method mediated by Agrobacterium. Biotechnol. Adv. 11(3): 178–183

    CAS  Google Scholar 

  • Nishizawa-Yokoi A, Nonaka S, Osakabe K, Saika H, Toki S. 2015. A universal positive-negative selection system for gene targeting in plants combining an antibiotic resistance gene and its antisense RNA. Plant Physiol. 169(1): 362–370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pellegrineschi A, Noguera LM, Skovmand B, Brito RM, Velazquez L, Salgado MM, Hernandez R, Warburton M, Hoisington D. 2002. Identification of highly transformable wheat genotypes for mass production of fertile transgenic plants. Genome 45(2): 421–430

    Article  CAS  PubMed  Google Scholar 

  • Pitzschke A, Hirt H. 2010. New insights into an old story: Agrobacterium-induced tumour formation in plants by plant transformation. EMBO J. 29(6): 1021–1032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Popat A, Hartono SB, Stahr F, Liu J, Qiao SZ, Qing Lu G. 2011. Mesoporous silica nanoparticles for bioadsorption, enzyme immobilisation, and delivery carriers. Nanoscale 3(7): 2801–2818

    Article  CAS  PubMed  Google Scholar 

  • Puchta H. 2005. The repair of double-strand breaks in plants: Mechanisms and consequences for genome evolution. J. Exp. Bot. 56(409): 1–14

    CAS  PubMed  Google Scholar 

  • Puchta H. 2017. Applying CRISPR/Cas for genome engineering in plants: the best is yet to come. Curr. Opin. Plant Biol. 36: 1–8

    Article  CAS  PubMed  Google Scholar 

  • Reiss B, Schubert I, Köpchen K, Wendeler E, Schell J, Puchta H. 2000. RecA stimulates sister chromatid exchange and the fidelity of double-strand break repair, but not gene targeting, in plants transformed by Agrobacterium. Proc. Natl. Acad. Sci. USA 97(7): 3358–3363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rod-in W, Sujipuli K, Ratanasut K. 2014. The floral-dip method for rice (Oryza sativa) transformation. J. Agri. Technol. 10(2): 467–474

    CAS  Google Scholar 

  • Sarmast MK. 2016. Genetic transformation and somaclonal variation in conifers. Plant Biotechnol. Rep. 10(6): 309–325

    Article  Google Scholar 

  • Sauer NJ, Narváez-Vásquez J, Mozoruk J, Miller RB, Warburg ZJ Woodward MJ, Mihiret YA, Lincoln TA, Segami RE, Sanders SL, Walker KA, Beetham PR, Schöpke CR, Gocal GF. 2016. Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants. Plant Physiol. 170(4): 1917–1928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shimatani Z, Nishizawa-Yokoi A, Endo M, Toki S, Terada R. 2015. Positive–negative-selection-mediated gene targeting in rice. Front. Plant Sci. 5: 748

    Article  PubMed  PubMed Central  Google Scholar 

  • Smith J, Grizot S, Arnould S, Duclert A, Epinat J-C Chames P, Prieto J, Redondo P, Blanco FJ, Bravo J, Montoya G, Pâques F, Duchateau P. 2006. A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res. 34(22): e149

    Article  PubMed  PubMed Central  Google Scholar 

  • Steinert J, Schiml S, Puchta H. 2016. Homology-based doublestrand break-induced genome engineering in plants. Plant Cell Rep. 35(7): 1429–1438

    Article  CAS  PubMed  Google Scholar 

  • Stoddard TJ, Clasen BM, Baltes NJ, Demorest ZL, Voytas DF, Zhang F, Luo S. 2016. Targeted mutagenesis in plant cells through transformation of sequence-specific nuclease mRNA. PLOS One 5: e0154634

    Article  Google Scholar 

  • Subburaj S, Chung SJ, Lee C, Ryu S-M, Kim DH, Kim J-S, Bae S, Lee G-J. 2016. Site-directed mutagenesis in Petunia × hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins. Plant Cell Rep. 35(7): 1535–1544

    Article  CAS  PubMed  Google Scholar 

  • Sun Y, Li J, Xia L. 2016a. Precise genome modification via sequence-specific nucleases-mediated gene targeting for crop improvement. Front. Plant Sci. 7: 1928

    PubMed  PubMed Central  Google Scholar 

  • Sun Y, Zhang X, Wu C, He Y, Ma Y, Hou H, Guo X, Du W, Zhao Y, Xia L. 2016b. Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol. Plant 9(4): 628–631

    Article  CAS  PubMed  Google Scholar 

  • Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM. 2015. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 169(2): 931–945

    Article  PubMed  PubMed Central  Google Scholar 

  • Terada R, Urawa H, Inagaki Y, Tsugane K, Iida S. 2002. Efficient gene targeting by homologous recombination in rice. Nat. Biotech. 20(10): 1030–1034

    Article  CAS  Google Scholar 

  • Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF. 2009. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459(7245): 442–445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trieu AT, Burleigh SH, Kardailsky IV, Maldonado-Mendoza IE, Versaw WK Blaylock LA, Shin H, Chiou TJ, Katagi H, Dewbre GR, Weigel D, Harrison MJ. 2000. Transformation of Medicago truncatula via infiltration of seedlings or flowering plants with Agrobacterium. Plant J. 22(6): 531–541

    Article  CAS  PubMed  Google Scholar 

  • Voytas DF. 2013. Plant genome engineering with sequence-specific nucleases. Annu. Rev. Plant Biol. 64(1): 327–350

    Article  CAS  PubMed  Google Scholar 

  • Waterworth WM, Drury GE, Bray CM, West CE. 2011. Repairing breaks in the plant genome: the importance of keeping it together. New Phytol. 192(4): 805–822

    Article  CAS  PubMed  Google Scholar 

  • Woo JW, Kim J, Kwon SI, Corvalan C, Cho SW, Kim H, Kim S-G, Kim S-T, Choe S, Kim J-S. 2015. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat. Biotech. 33(11): 1162–1164

    Article  CAS  Google Scholar 

  • Wright DA, Townsend JA, Winfrey RJ, Irwin PA, Rajagopal J, Lonosky PM, Hall BD, Jondle MD, Voytas DF. 2005. Highfrequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J. 44(4): 693–705

    Article  CAS  PubMed  Google Scholar 

  • Zale JM, Agarwal S, Loar S, Steber CM. 2009. Evidence for stable transformation of wheat by floral dip in Agrobacterium tumefaciens. Plant Cell Rep. 28(6): 903–913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Center for Natural Products Convergence Research, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea

    Je Hyeong Jung

  2. Division of Biotechnology, Korea University, Seoul, Republic of Korea

    Yong Weon Seo

Authors
  1. Je Hyeong Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yong Weon Seo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yong Weon Seo.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jung, J.H., Seo, Y.W. Challenges in wide implementation of genome editing for crop improvement. J. Crop Sci. Biotechnol. 20, 129–135 (2017). https://doi.org/10.1007/s12892-017-0019-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12892-017-0019-0

Key words

Search

Navigation