Recently developed methods for genome editing have the potential to accelerate basic research as well as plant breeding by providing the means to modify genomes rapidly in a precise or predictable manner. Sequence-specific nucleases (SSNs) induce targeted DNA double-strand breaks (DSBs), and different genome modifications can be achieved depending on the repair pathway. Non-homologous end-joining (NHEJ) repair creates mainly insertions or deletions (in/dels) at the break sites, which can result in frameshift mutations. Such NHEJ-mediated gene modification is called targeted mutagenesis. On the other hand, when a template with homology to the sequence surrounding the DSB is available, DNA DSBs can be repaired by homologous recombination (HR) repair. Such template-mediated HR achieves gene targeting (GT); GT can be used to introduce any desired mutation because the sequence supplied on the repair template is copied and pasted into the endogenous genome. In this chapter, we provide an overview of recent advances in genome-editing technologies in rice.
KeywordsSequence-specific nuclease CRISPR/Cas9 Gene targeting DNA double-strand breaks Homologous recombination Non-homologous end-joining
This work was supported by the Cross-ministerial Strategic Innovation Promotion Program to M.E., A.N-Y., and S.T. and grants from the Japan Science and Technology Agency “Precursory Research for Embryonic Science and Technology” to A.N-Y (JPMJPR16QA).
- Kawahara A, Hisano Y, Ota S, Taimatsu K (2016) Site-specific integration of exogenous genes using genome editing technologies in zebrafish. Int J Mol Sci 17(5) pii: E727Google Scholar
- Laufs J, Wirtz U, Kammann M, Matzeit V, Schaefer S, Schell J, Czernilofsky AP, Baker B, Gronenborn B (1990) Wheat dwarf virus Ac/Ds vectors: expression and excision of transposable elements introduced into various cereals by a viral replicon. Proc Natl Acad Sci U S A 87(19):7752–7756CrossRefPubMedPubMedCentralGoogle Scholar
- Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z, Kondo A (2016) Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353(6305)Google Scholar
- Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, Teramura H, Yamamoto T, Komatsu H, Miura K, Ezura H, Nishida K, Ariizumi T, Kondo A (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nat Biotechnol 35(5):441–443CrossRefPubMedGoogle Scholar
- Suzuki K, Tsunekawa Y, Hernandez-Benitez R, Wu J, Zhu J, Kim EJ, Hatanaka F, Yamamoto M, Araoka T, Li Z, Kurita M, Hishida T, Li M, Aizawa E, Guo S, Chen S, Goebl A, Soligalla RD, Qu J, Jiang T, Fu X, Jafari M, Esteban CR, Berggren WT, Lajara J, Nuñez-Delicado E, Guillen P, Campistol JM, Matsuzaki F, Liu GH, Magistretti P, Zhang K, Callaway EM, Zhang K, Belmonte JC (2016) In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540(7631):144–149CrossRefPubMedPubMedCentralGoogle Scholar
- Wang M, Lu Y, Botella JR, Mao Y, Hua K, Zhu ZK (2017b) Gene targeting by homology-directed repair in rice using a geminivirus-based CRISPR/Cas9 system. Mol Plant S1674-2052(17):30072–30072Google Scholar
- Yamauchi T, Johzuka-Hisatomi Y, Fukada-Tanaka S, Terada R, Nakamura I, Iida S (2009) Homologous recombination-mediated knock-in targeting of the MET1a gene for a maintenance DNA methyltransferase reproducibly reveals dosage-dependent spatiotemporal gene expression in rice. Plant J 60(2):386–396CrossRefPubMedGoogle Scholar
- Zong Y, Wang Y, Li C, Zhang R, Chen K, Ran Y, Qiu JL, Wang D, Gao C (2017) Precise base editing in rice, wheat and maize with a Cas9- cytidine deaminase fusion. Nat Biotechnol. https://doi.org/10.1038/nbt.3811