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CRISPR–Cas9-mediated 75.5-Mb inversion in maize

Nature Plants volume 6, pages 1427–1431 (2020)Cite this article

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Abstract

CRISPR–Cas is a powerful double-strand-break technology with wide-ranging applications from gene discovery to commercial product development. Thus far, this tool has been almost exclusively used for gene knockouts and deletions, with a few examples of gene edits and targeted gene insertions. Here, we demonstrate the application of CRISPR–Cas9 technology to mediate targeted 75.5-Mb pericentric inversion in chromosome 2 in one of the elite maize inbred lines from Corteva Agriscience. This inversion unlocks a large chromosomal region containing substantial genetic variance for recombination, thus providing opportunities for the development of new maize varieties with improved phenotypes.

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Fig. 1: Chromosome 2 pan-genome assembly comparison in 66 maize lines.
Fig. 2: Schematic illustration of the hypothetical mechanism of pericentric inversion.
Fig. 3: T0 plant analysis.

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Data availability

The authors declare that the data supporting the findings are available within the paper or are available from the corresponding author upon reasonable request. Corteva Agriscience will provide plasmids to academic investigators for non-commercial research under an applicable material transfer agreement subject to proof of permission from any third-party owners of all or parts of the material and to governmental regulation considerations. Completion of a stewardship plan is also required. The Corteva Agriscience inbred line PH1V5T described in this research is proprietary.

References

  1. Parisi, C., Tillie, P. & Rodríguez-Cerezo, E. The global pipeline of GM crops out to 2020. Nat. Biotechnol. 34, 31–36 (2016).

    Article  CAS  Google Scholar 

  2. Raman, R. The impact of genetically modified (GM) crops in modern agriculture: a review. GM Crops Food 8, 195–208 (2017).

    Article  Google Scholar 

  3. Voytas, D. F. Plant genome engineering with sequence-specific nucleases. Annu. Rev. Plant Biol. 64, 327–350 (2013).

    Article  CAS  Google Scholar 

  4. Gao, C. The future of CRISPR technologies in agriculture. Nat. Rev. Mol. Cell Biol. 19, 275–276 (2018).

    Article  CAS  Google Scholar 

  5. Huang, T.-K. & Puchta, H. CRISPR/Cas-mediated gene targeting in plants: finally a turn for the better for homologous recombination. Plant Cell Rep. 38, 443–453 (2019).

    Article  CAS  Google Scholar 

  6. Schmidt, C., Pacher, M. & Puchta, H. Efficient induction of heritable inversions in plant genomes using the CRISPR/Cas system. Plant J. 98, 577–589 (2019).

    Article  CAS  Google Scholar 

  7. Beying, N., Schmidt, C., Pacher, M., Houben, A. & Puchta, H. CRISPR–Cas9-mediated induction of heritable chromosomal translocations in Arabidopsis. Nat. Plants 6, 638–645 (2020).

    Article  CAS  Google Scholar 

  8. Schmidt, C., Pacher, M. & Puchta, H. From gene editing to genome engineering: restructuring plant chromosomes via CRISPR/Cas. aBIOTECH 1, 21–31 (2020).

    Article  Google Scholar 

  9. Lee, K. & Wang, K. Level up to chromosome restructuring. Nat. Plants 6, 600–601 (2020).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  11. Lowry, D. B. & Willis, J. H. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biol. 8, e1000500 (2010).

    Article  Google Scholar 

  12. Huang, K. & Rieseberg, L. H. Frequency, origins, and evolutionary role of chromosomal inversions in plants. Front. Plant Sci. https://doi.org/10.3389/fpls.2020.00296 (2020).

  13. Brunner, S., Fengler, K., Morgante, M., Tingey, S. & Rafalski, A. Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17, 343–360 (2005).

    Article  CAS  Google Scholar 

  14. Beló, A. et al. Allelic genome structural variations in maize detected by array comparative genome hybridization. Theor. Appl. Genet. 120, 355–367 (2009).

    Article  Google Scholar 

  15. Sun, S. et al. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat. Genet. 50, 1289–1295 (2018).

    Article  CAS  Google Scholar 

  16. Liu, J. et al. Gapless assembly of maize chromosomes using long read technologies. Genome Biol. 21, 121 (2020).

    Article  CAS  Google Scholar 

  17. Ou, S. et al. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nat. Commun. 11, 2288 (2020).

    Article  CAS  Google Scholar 

  18. Song, J.-M. et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat. Plants 6, 34–45 (2020).

    Article  CAS  Google Scholar 

  19. Liu, Y. et al. Pan-genome of wild and cultivated soybeans. Cell 182, 162–176 (2020).

    Article  CAS  Google Scholar 

  20. Tao, Y., Zhao, X., Mace, E., Henry, R. & Jordan, D. Exploring and exploiting pan-genomics for crop improvement. Mol. Plant 12, 156–169 (2019).

    Article  CAS  Google Scholar 

  21. Lowe, K. et al. Morphogenic regulators Baby boom and Wuschel improve monocot transformation. Plant Cell 28, 1998–2015 (2016).

    Article  CAS  Google Scholar 

  22. Lowe, K. et al. Rapid genotype “independent” Zea mays L. (maize) transformation via direct somatic embryogenesis. In Vitro Cell. Dev. Biol. Plant 54, 240–252 (2018).

    Article  CAS  Google Scholar 

  23. Mak, A. A. Y. et al. Genome-wide structural variation detection by genome mapping on nanochannel arrays. Genetics 202, 351–362 (2016).

    Article  CAS  Google Scholar 

  24. Svitashev, S. K., Pawlowski, W. P., Makarevitch, I., Plank, D. W. & Somers, D. A. Complex transgene locus structures implicate multiple mechanisms for plant transgene rearrangement. Plant J. 32, 433–445 (2002).

    Article  CAS  Google Scholar 

  25. Svitashev, S. et al. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Phys. 169, 931–945 (2015).

    Article  Google Scholar 

  26. Zhao, Y., Qian, Q., Wang, H. & Huang, D. Hereditary behavior of bar gene cassette is complex in rice mediated by particle bombardment. J. Genet. Genomics 34, 824–835 (2007).

    Article  CAS  Google Scholar 

  27. Svitashev, S., Schwartz, C., Lenderts, B., Young, J. K. & Cigan, A. M. Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nat. Commun. 7, 13274 (2016).

    Article  CAS  Google Scholar 

  28. Jones, T. et al. Maize transformation using the morphogenic genes Baby boom and Wuschel2. Methods Mol. Biol. 1864, 81–93 (2019).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank G. St Clair, S. Jones and A. Ulm for assistance with the transformation experiments, M. Yang for help with the molecular analysis of T1 progeny, T. Engelhart for cultivation of the plants in the greenhouse, and M. Fedorova, J. Gerke and W. Gordon-Kamm for critical reading of the manuscript.

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Authors and Affiliations

  1. Corteva Agriscience, Johnston, IA, USA

    Chris Schwartz, Brian Lenderts, Lanie Feigenbutz, Pierluigi Barone, Victor Llaca, Kevin Fengler & Sergei Svitashev

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  1. Chris Schwartz
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  4. Pierluigi Barone
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Contributions

S.S. conceived the project, and C.S., K.F. and S.S designed the experiments. C.S., P.B., L.F. and B.L. conducted the experiments and V.L. performed the Bionano analysis. C.S., B.L., P.B. and S.S. analysed the data. K.F., V.L., P.B. and S.S. wrote the manuscript.

Corresponding author

Correspondence to Sergei Svitashev.

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Competing interests

All authors are employed by Corteva Agriscience.

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Peer review information Nature Plants thanks Kan Wang, Lanqin Xia and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Schwartz, C., Lenderts, B., Feigenbutz, L. et al. CRISPR–Cas9-mediated 75.5-Mb inversion in maize. Nat. Plants 6, 1427–1431 (2020). https://doi.org/10.1038/s41477-020-00817-6

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