Skip to main content

CRISPR/Cas9-Based Gene Editing in Soybean

  • Protocol
  • First Online:
Legume Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2107))

Abstract

CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR associated Cas9)-based gene editing is a robust tool for functional genomics research and breeding programs in various crops. In soybean, a number of laboratories have obtained mutants by CRISPR/Cas9 system; however, there has been not yet a detailed method for the CRISPR/Cas9-based gene editing in soybean. Here, we describe the procedures for constructing the CRISPR/Cas9 plasmid suitable for soybean gene editing and the modified protocols for Agrobacterium-mediated soybean transformation and regeneration from cotyledonary node explants containing the Cas9/sgRNA (single guide RNA) transgenes.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Hartman GL, West ED, Herman TK (2011) Crops that feed the world 2. Soybean-worldwide production, use, and constraints caused by pathogens and pests. Food Security 3(1):5–17

    Article  Google Scholar 

  2. Homrich MS, Wiebke-Strohm B, Weber RLM, Bodanese-Zanettini MH (2012) Soybean genetic transformation: a valuable tool for the functional study of genes and the production of agronomically improved plants. Genet Mol Biol 35(4):998–1010

    Article  CAS  Google Scholar 

  3. Li S, Cong Y, Liu Y, Wang T, Shuai Q, Chen N, Gai J, Li Y (2017) Optimization of Agrobacterium-mediated transformation in soybean. Front Plant Sci 8:246

    PubMed  PubMed Central  Google Scholar 

  4. Gregory P (2012) Gene overexpression: uses, mechanisms, and interpretation. Genetics 190(3):841–854

    Article  Google Scholar 

  5. Krysan PJ, Young JC, Sussman MR (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11(12):2283–2290

    Article  CAS  Google Scholar 

  6. Kusaba M (2004) RNA interference in crop plants. Curr Opin Biotechnol 15(2):139–143

    Article  CAS  Google Scholar 

  7. Ma X, Zhu Q, Chen Y, Liu Y-G (2016) CRISPR/Cas9 platforms for genome editing in plants: developments and applications. Mol Plant 9:961–974

    Article  CAS  Google Scholar 

  8. Abdelrahman M, Al-Sadi AM, Pour-Aboughadareh A, Burritt DJ, Tran LSP (2018) Genome editing using CRISPR/Cas9–targeted mutagenesis: an opportunity for yield improvements of crop plants grown under environmental stresses. Plant physiology. Biochemistry 131:31–36

    CAS  Google Scholar 

  9. Bao A, Burritt DJ, Chen H, Zhou X, Cao D, Tran LSP (2019) The CRISPR/Cas9 system and its applications in crop genome editing. Crit Rev Biotechnol 39(3):321–336

    Article  CAS  Google Scholar 

  10. Gao X, Chen J, Dai X, Zhang D, Zhao Y (2016) An effective strategy for reliably isolating heritable and Cas9-free Arabidopsis mutants generated by CRISPR/Cas9-mediated genome editing. Plant Physiol 171(3):1794

    Article  Google Scholar 

  11. Woo JW, Kim J, SIl K, Corvalán C, Cho SW, Kim H, Kim SG, Kim ST, Choe S, Kim JS (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat Biotechnol 33(11):1162–1164

    Article  CAS  Google Scholar 

  12. Liang Z, Chen K, Zhang Y, Liu J, Yin K, Qiu JL, Gao C (2018) Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins. Nat Protoc 13(3):413–430

    Article  CAS  Google Scholar 

  13. Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, Kim JS, Velasco R, Kanchiswamy CN (2016) DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Front Plant Sci 7(e188):1904

    PubMed  PubMed Central  Google Scholar 

  14. Cai Y, Chen L, Liu X, Sun S, Wu C, Jiang B, Han T, Hou W (2015) CRISPR/Cas9-mediated genome editing in soybean hairy roots. PLoS One 10(8):e0136064

    Article  Google Scholar 

  15. Jacobs TB, Lafayette PR, Schmitz RJ, Parrott WA (2015) Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnol 15:16

    Article  Google Scholar 

  16. Michno JM, Wang X, Liu J, Curtin SJ, Kono TJ, Stupar RM (2015) CRISPR/Cas mutagenesis of soybean and Medicago truncatula using a new web-tool and a modified Cas9 enzyme. GM Crops Food 6(4):243–252

    Article  Google Scholar 

  17. Sun X, Hu Z, Chen R, Jiang Q, Song G, Zhang H, Xi Y (2015) Targeted mutagenesis in soybean using the CRISPR-Cas9 system. Sci Rep 5:10342

    Article  Google Scholar 

  18. Li Z, Liu Z, Xing A, Moon BP, Koellhoffer JP, Huang L, Timothy Ward R, Clifton E, Carl Falco S, Mark Cigan A (2015) Cas9-guide RNA directed genome editing in soybean. Plant Physiol 169(2):960–970

    Article  Google Scholar 

  19. Du H, Zeng X, Zhao M, Cui X, Wang Q, Yang H, Cheng H, Yu D (2016) Efficient targeted mutagenesis in soybean by TALENs and CRISPR/Cas9. J Biotechnol 217:90–97

    Article  CAS  Google Scholar 

  20. Kanazashi Y, Hirose A, Takahashi I, Mikami M, Endo M, Hirose S, Toki S, Kaga A, Naito K, Ishimoto M (2018) Simultaneous site-directed mutagenesis of duplicated loci in soybean using a single guide RNA. Plant Cell Rep 37(3):553–563

    Article  CAS  Google Scholar 

  21. Cai Y, Chen L, Liu X, Guo C, Sun S, Wu C, Jiang B, Han T, Hou W (2018) CRISPR/Cas9-mediated targeted mutagenesis of GmFT2a delays flowering time in soya bean. Plant Biotechnol J 16(1):176–185

    Article  CAS  Google Scholar 

  22. Cai Y, Chen L, Sun S, Wu C, Yao W, Jiang B, Han T, Hou W (2018) CRISPR/Cas9-mediated deletion of large genomic fragments in soybean. Int J Mol Sci 19:3835. https://doi.org/10.3390/ijms19123835

    Article  CAS  PubMed Central  Google Scholar 

  23. Ma X, Liu Y-G (2016) CRISPR/Cas9-based multiplex genome editing in monocot and dicot plants. Curr Protoc Mol Biol 115:31.6.1–31.6.21

    Article  Google Scholar 

  24. Ma X, Zhang Q, Zhu Q, Wei L, Yan C, Rong Q, Wang B, Yang Z, Li H, Lin Y (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8(8):1274–1284

    Article  CAS  Google Scholar 

  25. Xie X, Ma X, Zhu Q, Zeng D, Li G, Liu Y-G (2017) CRISPR-GE: a convenient software toolkit for CRISPR-based genome editing. Mol Plant 10(9):1246–1249

    Article  CAS  Google Scholar 

  26. Carola E, Romy K, Sylvestre M (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS One 3(11):e3647

    Article  Google Scholar 

  27. Chen L, Cai Y, Liu X, Yao W, Guo C, Sun S, Wu C, Jiang B, Han T, Hou W (2018) Improvement of soybean Agrobacterium-mediated transformation efficiency by adding glutamine and asparagine into the culture media. Int J Mol Sci 19(10):E3039. https://doi.org/10.3390/ijms19103039

    Article  CAS  PubMed  Google Scholar 

  28. Paz MM, Martinez JC, Kalvig AB, Fonger TM, Wang K (2006) Improved cotyledonary node method using an alternative explant derived from mature seed for efficient Agrobacterium-mediated soybean transformation. Plant Cell Rep 25(3):248–248

    Article  CAS  Google Scholar 

  29. Paz MM, Shou H, Guo Z, Zhang Z, Banerjee A, Wang K (2004) Assessment of conditions affecting Agrobacteriummediated soybean transformation using the cotyledonary node explant. Euphytica 136:167–179

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors are thankful to Professor Yaoguang Liu from South China Agricultural University for providing the vectors pYLsgRNA-AtU3d/LacZ, pYLsgRNA-AtU3b, pYLsgRNA-AtU6-1, pYLsgRNA-AtU6-29, and pYLCRISPR/Cas9P35S-B.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Lam-Son Phan Tran or Dong Cao .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Bao, A., Tran, LS.P., Cao, D. (2020). CRISPR/Cas9-Based Gene Editing in Soybean. In: Jain, M., Garg, R. (eds) Legume Genomics. Methods in Molecular Biology, vol 2107. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0235-5_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0235-5_19

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0234-8

  • Online ISBN: 978-1-0716-0235-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics