Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9

Nature Plants

Volumn 2, Issue 10, 2016, Pages

  Li, Jun ^a,b   Meng, Xiangbing ^a   Zong, Yuan ^a,b   Chen, Kunling ^a   Zhang, Huawei ^a   Liu, Jinxing ^a   Li, Jiayang ^a   Gao, Caixia ^a  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; DNA END JOINING REPAIR; GENE EXPRESSION REGULATION; GENE KNOCKOUT; GENETICS; INTRON; ORYZA;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; DNA END-JOINING REPAIR; GENE KNOCKOUT TECHNIQUES; INTRONS; MUTAGENESIS, INSERTIONAL; ORYZA;

EID: 84990199472     PISSN: None     EISSN: 20550278     Source Type: Journal    
DOI: 10.1038/nplants.2016.139     Document Type: Article

References (31)

1. Voytas, D. F. and Gao, C. Precision genome engineering and agriculture: opportunities and regulatory challenges. PLoS Biol. 12, e1001877 (2014).
2. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
3. Mali, P. et al. RNA-Guided human genome engineering via Cas9. Science 339, 823-826 (2013).
4. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
5. Symington, L. S. and Gautier, J. Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 45, 247-271 (2011).
6. Gorbunova, V. and Levy, A. A. Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions. Nucleic Acids Res. 25, 4650-4657 (1997).
7. Kim, H. and Kim, J. S. A guide to genome engineering with programmable nucleases. Nat. Rev. Genet. 15, 321-334 (2014).
8. Weeks, D. P., Spalding, M. H. and Yang, B. Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnol. J. 14, 483-495 (2016).
9. Puchta, H., Dujon, B. and Hohn, B. Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc. Natl Acad. Sci. USA 93, 5055-5060 (1996).
10. Bibikova, M., Beumer, K., Trautman, J. K. and Carroll, D. Enhancing gene targeting with designed zinc finger nucleases. Science 300, 764 (2003).
11. Cermak, T., Baltes, N. J., Cegan, R., Zhang, Y. and Voytas, D. F. High-frequency, precise modification of the tomato genome. Genome Biol. 16, 232 (2015).
12. Townsend, J. A. et al. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459, 442-445 (2009).
13. Sun, Y. et al. Engineering herbicide-resistant rice plants through CRISPR/Cas9- mediated homologous recombination of acetolactate synthase. Mol. Plant 9, 628-631 (2016).
14. Shukla, V. K. et al. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459, 437-441 (2009).
15. Svitashev, S. et al. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 169, 931-945 (2015).
16. Zhang, Y. et al. Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol. 161, 20-27 (2013).
17. Terada, R., Urawa, H., Inagaki, Y., Tsugane, K. and Iida, S. Efficient gene targeting by homologous recombination in rice. Nat. Biotechnol. 20, 1030-1034 (2002).
18. Shimatani, Z., Nishizawa-Yokoi, A., Endo, M., Toki, S. and Terada, R. Positivenegative- selection-mediated gene targeting in rice. Front. Plant Sci. 5, 748-754 (2014).
19. Baltes, N. J., Gil-Humanes, J., Cermak, T., Atkins, P. A. and Voytas, D. F. DNA replicons for plant genome engineering. Plant Cell 26, 151-163 (2014).
20. Baerson, S. R. et al. Glyphosate-resistant goosegrass. Identification of a mutation in the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase. Plant Physiol. 129, 1265-1275 (2002).
21. Yu, Q. et al. Evolution of a double amino acid substitution in the 5-enolpyruvylshikimate-3-phosphate synthase in Eleusine indica conferring high-level glyphosate resistance. Plant Physiol. 167, 1440-1447 (2015).
22. Bae, S., Park, J. and Kim, J. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475 (2014).
23. Xing, H. L. et al. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol. 14, 327-338 (2014).
24. Hiei, Y. and Komari, T. Agrobacterium-mediated transformation of rice using immature embryos or calli induced from mature seed. Nat. Protoc. 3, 824-834 (2008).
25. Wang, Y. et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat. Biotechnol. 32, 947-951 (2014).
26. Reddy, A. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu. Rev. Plant Biol. 58, 267-294 (2007).
27. Matlin, A. J., Clark, F. and Smith, C. W. Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol. 6, 386-398 (2005).
28. Zhang, H. et al. The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol. J. 12, 797-807 (2014).
29. Shan, Q. et al. Rapid and efficient gene modification in rice and Brachypodium using TALENs. Mol. Plant 6, 1365-1368 (2013).
30. Shan, Q., Wang, Y., Li, J. and Gao, C. Genome editing in rice and wheat using the CRISPR/Cas system. Nat. Protoc. 9, 2395-2410 (2014).
31. Li, L., Qu, R., Kochko, A., Fauquet, C. and Beachy, R. An improved rice transformation system using the biolistic method. Plant Cell Rep. 12, 250-255 (1993).