CRISPR/LbCas12a-Mediated Genome Editing in Soybean

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Plant Genome Engineering

Abstract

Currently methods for generating soybean edited lines are time-consuming, inefficient, and limited to certain genotypes. Here we describe a fast and highly efficient genome editing method based on CRISPR-Cas12a nuclease system in soybean. The method uses Agrobacterium-mediated transformation to deliver editing constructs and uses aadA or ALS genes as selectable marker. It only takes about 45 days to obtain greenhouse-ready edited plants at higher than 30% transformation efficiency and 50% editing rate. The method is applicable to other selectable markers including EPSPS and has low transgene chimera rate. The method is also genotype-flexible and has been applied to genome editing of several elite soybean varieties.

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References

  1. Lee G-J, Wu XJ, Shannon G, Sleper DA, Nguyen HT (2007) Soybean. In: Kole C (ed) Genome map** and molecular breeding in plants, Oilseeds, vol 2. Springer-Verlag, Berlin/Heidelberg

    Google Scholar 

  2. USDA Foreign Agricultural Service, Circular Series WAP 12-21, World Agricultural Production, December 2021, https://apps.fas.usda.gov/psdonline/circulars/production.pdf

  3. Homrich MS, Wiebke-Strohm B, Weber RL, 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 suppl):998–1010. https://doi.org/10.1590/S1415-47572012000600015

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Lusser M, Parisi C, Plan D, Rodriguez-Cerezo E (2012) Deployment of new biotechnologies in plant breeding. Nat Biotechnol 30:231

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Brookes G, Barfoot P (2016) Global income and production impacts of using GM crop technology 1996–2014. GM Crops Food 7:38–77. https://doi.org/10.1080/21645698.2016.1176817

    Article  PubMed Central  PubMed  Google Scholar 

  6. Xu H, Zhang L, Zhang K, Ran Y (2020) Progresses, challenges, and prospects of genome editing in soybean (Glycine max). Front Plant Sci 11:571138. https://doi.org/10.3389/fpls.2020.571138

    Article  PubMed Central  PubMed  Google Scholar 

  7. Que Q, Chilton M-D, de Fontes C, He C, Nuccio M, Zhu T, Wu Y, Chen J, Shi L (2010) Trait stacking in transgenic crops: challenges and opportunities. GM Crops 1:220–229

    Article  PubMed  Google Scholar 

  8. Cohen J (2005) Poorer nations turn to publicly developed GM crops. Nat Biotechnol 23:27–33

    Article  CAS  PubMed  Google Scholar 

  9. Wilke C (2019) Gene-edited soybean oil makes restaurant debut. The Scientist. https://www.the-scientist.com/news-opinion/gene-edited-soybean-oil-makes-restaurant-debut-65590

  10. Patil GB, Stupar RM, Zhang F (2022) Protoplast isolation, transfection, and gene editing for soybean (Glycine max). In: Wang K, Zhang F (eds) Protoplast technology, Methods in molecular biology, vol 2464. Humana, New York. https://doi.org/10.1007/978-1-0716-2164-6_13

    Chapter  Google Scholar 

  11. Hinchee MA, Connor-Ward DV, Newell CA, McDonell RE, Sato SJ, Gasser CS, Fishhoff DA, Re DB, Fraley RT, Horsch RB (1988) Production of transgenic soybean plants using Agrobacterium-mediated DNA transfer. Bio/Technol 6:915–922

    CAS  Google Scholar 

  12. Martinell B, Julson LS, Emler CA, Huang Y, McCabe DE, Williams EJ (2002) Soybean Agrobacterium transformation method. US Patent number 6,384,301

    Google Scholar 

  13. Paz MM, Shou H, Guo Z, Zhang Z, Banergee AK, Wang K (2004) Assessment of conditions affecting Agrobacterium mediated soybean transformation using the cotyledonary node explants. Euphytica 136:167–179

    Article  CAS  Google Scholar 

  14. 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 25:206–213

    Article  CAS  PubMed  Google Scholar 

  15. Ye X, Williams EJ, Shen J, Esser JA, Nichols AM, Petersen MW, Gilbertson LA (2008) Plant development inhibitory genes in binary vector backbone improve quality event efficiency in soybean transformation. Transgenic Res 17:827–838

    Article  CAS  PubMed  Google Scholar 

  16. Christou P, Swain WF, Yang NS, McCabe DE (1989) Inheritance and expression of foreign genes in transgenic soybean plants. Genetics 88:7500–7504

    Google Scholar 

  17. Aragão FJL, Sarokin L, Vianna GR, Rech EL (2000) Selection of transgenic meristematic cells utilizing a herbicidal molecule results in the recovery of fertile transgenic soybean [Glycine max (L) Merrill] plants at a high frequency. Theor Appl Genet 101:1–6

    Article  Google Scholar 

  18. Vianna GR, Aragão FJL, Rech EL (2011) A minimal DNA cassette as a vector for genetic transformation of soybean (Glycine max). Genet Mol Res 10:382–390

    Article  CAS  PubMed  Google Scholar 

  19. Miki B, McHugh S (2004) Selectable marker genes in transgenic plants: applications, alternatives and biosafety. J Biotechnol 107:193–232

    Article  CAS  PubMed  Google Scholar 

  20. Ye X, Williams EJ, Shen J et al (2011) Enhanced production of single copy backbone-free transgenic plants in multiple crop species using binary vectors with a pRi replication origin in Agrobacterium tumefaciens. Transgenic Res 20:773–786. https://doi.org/10.1007/s11248-010-9458-6

    Article  CAS  PubMed  Google Scholar 

  21. Liu J, Gunapati S, Mihelich NT, Stec AO, Michno JM, Stupar RM (2019) Genome editing in soybean with CRISPR/Cas9. In: Qi Y (ed) Plant genome editing with CRISPR systems, Methods in molecular biology, vol 1917. Humana Press, New York. https://doi.org/10.1007/978-1-4939-8991-1_16

    Chapter  Google Scholar 

  22. Olhoft P, Somers D (2001) L-cysteine increases Agrobacterium -mediated T-DNA delivery into soybean cotyledonary-node cells. Plant Cell Rep 20:706–711. https://doi.org/10.1007/s002990100379

    Article  CAS  Google Scholar 

  23. Wang G, Wang P, Lin Y, Zhang L, Wu Y (2002) The studies of sensitivity of genotypes in soybean to lines of Agrobacterium tumefaciens. Heresitas 24:297–300. https://doi.org/10.16288/j.yczz.2002.03.018

    Article  Google Scholar 

  24. Khan R (2004) Method of transforming soybean. World Intellectual Property Organization, International Publication Number WO2004000006, December 31, 2003

    Google Scholar 

  25. Li W, Li W, Lv W, Ning H (2008) Breakthrough of two questions on the Agrobacterium-mediated soybean cotyledonary node systems. Soybean Sci 27:173–175. https://doi.org/10.11861/j.issn.1000-9841.2008.01.0173

    Article  Google Scholar 

  26. Que Q, Dawson J, Sigareva M (2008) Transformation of immature soybean seeds through organogenesis. World Intellectual Property Organization, International Publication Number WO2008112267, September 18, 2008

    Google Scholar 

  27. Li S, Cong Y, Liu Y, Li S, Cong Y, Liu Y, Wang T, Shuai Q, Che N, Gai J, Li Y (2017) Optimization of Agrobacterium-mediated transformation in soybean. Front Plant Sci 8:246. https://doi.org/10.3389/fpls.2017.00246

    Article  PubMed Central  PubMed  Google Scholar 

  28. Li W, Ning H, Lv W, Li W (2008b) Optimization of the Agrobacterium mediated transformation systems of soybean cotyledonary node. Sci Agric Sin 41:971–977. https://doi.org/10.3864/j.issn.0578-1752.2008.04.005

    Article  CAS  Google Scholar 

  29. Cho HJ, Moy Y, Rudnick NA, Klein TM, Yin J, Bolar J et al (2022) Development of an efficient marker-free soybean transformation method using the novel bacterium Ochrobactrum haywardense H1. Plant Biotechnol J 20:977–990. https://doi.org/10.1111/pbi.13777

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Article  PubMed Central  PubMed  Google Scholar 

  31. Cai Y, Chen L, Liu X, Guo C, Sun S, Wu C et al (2018b) CRISPR/Cas9-mediated targeted mutagenesis of GmFT2a delays flowering time in soya bean. Plant Biotechnol J 16:176–185. https://doi.org/10.1111/pbi.12758

    Article  CAS  PubMed  Google Scholar 

  32. Bao A, Zhang C, Huang Y, Chen H, Zhou X, Cao D (2020) Genome editing technology and application in soybean improvement. Oil Crop Sci 5:31–40. https://doi.org/10.1016/j.ocsci.2020.03.001

    Article  Google Scholar 

  33. Li Z, **ng A, Moon BP, McCardell RP, Mills K, Falco SC (2009) Site-specific integration of transgenes in soybean via recombinase-mediated DNA cassette exchange. Plant Physiol 151:1087–1095. https://doi.org/10.1104/pp.109.137612

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  34. Kumar S, Liu Z-B, Sanour-Doyel N, Lenderts B, Worden A, Anand A, Cho H-J, Bolar J, Harris C, Huang L, **ng A, Richardson A (2022) Efficient gene targeting in soybean using O. haywardense-mediated delivery of a marker-free donor template. Plant Physiol 189(2):585–594. https://doi.org/10.1093/plphys/kiac075

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  35. Kim H, Kim ST, Ryu J, Kang BC, Kim JS, Kim SG (2017) CRISPR/Cpf1- mediated DNA-free plant genome editing. Nat Commun 8:14406. https://doi.org/10.1038/ncomms14406

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  36. Duan K, Cheng Y, Ji J, Wang C, Wei Y, Wang Y (2021) Large chromosomal segment deletions by CRISPR/LbCpf1-mediated multiplex gene editing in soybean. J Integr Plant Biol 63:1620–1631

    Article  CAS  PubMed  Google Scholar 

  37. Kim H, Choi J (2021) A robust and practical CRISPR/crRNA screening system for soybean cultivar editing using LbCpf1 ribonucleoproteins. Plant Cell Rep 40:1059–1070. https://doi.org/10.1007/s00299-020-02597-x

    Article  CAS  PubMed  Google Scholar 

  38. Hood EE, Helmer GL, Fraley RT, Chilton MD (1986) The hypervirulence of Agrobacterium tumefaciens A281 is encoded in a region of pTiBo542 outside of T-DNA. J Bacteriol 168:1283–1290

    Google Scholar 

  39. Chen ZY, Que Q, Rose MS, Zhong H, Chilton M-D, Levy E, Qin YL (2021) Novel Agrobacterium strains. World Intellectual Property Organization, International Publication Number WO2019027790, February 7, 2019

    Google Scholar 

  40. Schindele P, Puchta H (2020) Engineering CRISPR/LbCas12a for highly efficient, temperature-tolerant plant gene editing. Plant Biotechnol J 18:1118–1120. https://doi.org/10.1111/pbi.13275

    Article  PubMed  Google Scholar 

  41. Xu J, Li J (2021) Methods and compositions for DNA base editing. World Intellectual Property Organization (WIPO) International Publication Number WO 2021/056302, April 1, 2021

    Google Scholar 

  42. Lee KY, Townsend J, Tepperman J, Black M, Chui CF, Mazur B, Dunsmuir P, Bedbrook J (1988) The molecular basis of sulfonylurea herbicide resistance in tobacco. EMBO J 7:1241–1248

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Tang X, Lowder L, Zhang T, Malzahn AA, Zheng X et al (2017) A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants 3:17018. https://doi.org/10.1038/nplants.2017.18

    Article  CAS  PubMed  Google Scholar 

  44. Ingham DJ, Beer S, Money S, Hansen G (2001) Quantitative real-time PCR assay for determining transgene copy number in transformed plants. BioTechniques 31:132–140

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank our transformation, plant analysis, and greenhouse colleagues Juan Wei, ** Jiang, Wenling Wang, Cheng** Zhang, Ling Zhu, Sabrina Patton, ** Xu, Lizhao Geng, Chunxia Liu, Huaibing ** & Yang Gao

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    Correspondence to Dawei Liang or Qiudeng Que .

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    Liang, D. et al. (2023). CRISPR/LbCas12a-Mediated Genome Editing in Soybean. In: Yang, B., Harwood, W., Que, Q. (eds) Plant Genome Engineering. Methods in Molecular Biology, vol 2653. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3131-7_3

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    • DOI: https://doi.org/10.1007/978-1-0716-3131-7_3

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    • Publisher Name: Humana, New York, NY

    • Print ISBN: 978-1-0716-3130-0

    • Online ISBN: 978-1-0716-3131-7

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