Development and Application of CRISPR/Cas System in Rice

doi:10.1016/j.rsci.2019.01.001

Abstract

Abstract:

In the past several years, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) system has been harnessed as an efficient and powerful tool for targeted genome editing in different prokaryotic and eukaryotic species. Here, we review the development and application of CRISPR/Cas system in rice, emphasizing different varieties of CRISPR/Cas systems have been applied, strategies for multiplex editing, methods for precise gene insertion and replacement, and efficient systems for base editing and site-specific transcriptional regulation. In addition, the biosecurity of CRISPR/Cas system is also discussed, including transgene-free methods and off-target effects of CRISPR/Cas system. Thus, the development and application of CRISPR/Cas system will have significant impact on functional genomic research and variety improvement in rice.

Key words: rice, CRISPR, Cas, genome editing, protospacer adjacent motif

Ren Jun, Hu Xixun, Wang Kejian, Wang Chun. Development and Application of CRISPR/Cas System in Rice[J]. Rice Science, 2019, 26(2): 69-76.

Figures/Tables 1

References 63

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Property/Tool	PAM	Target gene	Reference
CRISPR/SpCas9	NGG	OsPDS, OsBADH2, Os02g23823, OsMPK2	Shan et al, 2013
		OsMPK5	Xie et al, 2013
		OsPDS, OsPMS3, OsEPSPS, OsDERF1, OsMSH1, OsMYB5, OsMYB1, OsROC5, OsSPP, OsYSA	Zhang et al, 2014
		OsFTL11, Os07g0261200, Os02g0700600, OsGSTU, OsMRP15, OsWaxy	Ma et al, 2015
		OsPDS, Os02g23823, OsMPK2	Wang et al, 2015
		OsPDS, OsYSA, OsDEP1	Tang et al, 2016
		OsBADH2, OsDEP1, OsGn1a, OsGS3, OsGW2, OsHd1, OsEP3, OsLPA1	Shen et al, 2017a
		OsMPK5, OsPDS, OsMPK2, OsMPK1	Ding et al, 2018
	NAG	OsRAD51A, OsDMC1, OsNAL1, OsLPA1, OsLG1, OsGL1-1	Meng et al, 2018
CRISPR/SpCas9-VQR	NGA	OsNAL1, OsLPA1, OsLG1, OsGL1-1	Hu et al, 2016
CRISPR/SpCas9-VRER	NGCG	OsNAL1, OsLG1, OsGL1-1	Hu et al, 2016
CRISPR/SaCas9	NNGRRT	OsDL, OsCYP72A33, OsCYP72A32, OsVIP1, OsVIP1-like gene	Kaya et al, 2016
CRISPR/FnCpf1	TTN	OsDL, OsALS	Endo et al, 2016
		OsRLK-798, OsRLK-799, OsRLK-802, OsRLK-803	Wang et al, 2017b
		OsPDS, OsMPK2, OsMPK5	Ding et al, 2018
CRISPR/LbCpf1	TTTN	OsBEL-230, OsBEL-240, OsBEL-250, OsBEL-260	Wang et al, 2017b
		OsPDS, OsDEP1, OsROC5	Tang et al, 2017
		OsPDS, OsBEL	Xu et al, 2017
		OsNAL1, OsLG1	Hu et al, 2017
		OsPDS, OsMPK2, OsMPK5	Ding et al, 2018
CRISPR/AsCpf1	TTTN	OsPDS, OsDEP1, OsROC5	Tang et al, 2017
CRISPR/AsCpf1	TTTN	OsNAL1, OsLG1	Hu et al, 2017
CRISPR/LbCpf1-RR	TYCV	OsPDS, OsSBEIIb	Li et al, 2018b
	TYCV	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
	CCCC	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
CRISPR/LbCpf1-RVR	TATG	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
CRISPR/FnCpf1-RR	CCCC	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
CRISPR/FnCpf1-RR	TYCY	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
CRISPR/FnCpf1-RVR	TATG	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
PAM, Protospacer adjacent motif. N represents A/T/G/C base. R represents A/G base. Y represents T/C base. V represents A/C/G base.

Property/Tool	PAM	Target gene	Reference
CRISPR/SpCas9	NGG	OsPDS, OsBADH2, Os02g23823, OsMPK2	Shan et al, 2013
		OsMPK5	Xie et al, 2013
		OsPDS, OsPMS3, OsEPSPS, OsDERF1, OsMSH1, OsMYB5, OsMYB1, OsROC5, OsSPP, OsYSA	Zhang et al, 2014
		OsFTL11, Os07g0261200, Os02g0700600, OsGSTU, OsMRP15, OsWaxy	Ma et al, 2015
		OsPDS, Os02g23823, OsMPK2	Wang et al, 2015
		OsPDS, OsYSA, OsDEP1	Tang et al, 2016
		OsBADH2, OsDEP1, OsGn1a, OsGS3, OsGW2, OsHd1, OsEP3, OsLPA1	Shen et al, 2017a
		OsMPK5, OsPDS, OsMPK2, OsMPK1	Ding et al, 2018
	NAG	OsRAD51A, OsDMC1, OsNAL1, OsLPA1, OsLG1, OsGL1-1	Meng et al, 2018
CRISPR/SpCas9-VQR	NGA	OsNAL1, OsLPA1, OsLG1, OsGL1-1	Hu et al, 2016
CRISPR/SpCas9-VRER	NGCG	OsNAL1, OsLG1, OsGL1-1	Hu et al, 2016
CRISPR/SaCas9	NNGRRT	OsDL, OsCYP72A33, OsCYP72A32, OsVIP1, OsVIP1-like gene	Kaya et al, 2016
CRISPR/FnCpf1	TTN	OsDL, OsALS	Endo et al, 2016
		OsRLK-798, OsRLK-799, OsRLK-802, OsRLK-803	Wang et al, 2017b
		OsPDS, OsMPK2, OsMPK5	Ding et al, 2018
CRISPR/LbCpf1	TTTN	OsBEL-230, OsBEL-240, OsBEL-250, OsBEL-260	Wang et al, 2017b
		OsPDS, OsDEP1, OsROC5	Tang et al, 2017
		OsPDS, OsBEL	Xu et al, 2017
		OsNAL1, OsLG1	Hu et al, 2017
		OsPDS, OsMPK2, OsMPK5	Ding et al, 2018
CRISPR/AsCpf1	TTTN	OsPDS, OsDEP1, OsROC5	Tang et al, 2017
CRISPR/AsCpf1	TTTN	OsNAL1, OsLG1	Hu et al, 2017
CRISPR/LbCpf1-RR	TYCV	OsPDS, OsSBEIIb	Li et al, 2018b
	TYCV	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
	CCCC	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
CRISPR/LbCpf1-RVR	TATG	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
CRISPR/FnCpf1-RR	CCCC	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
CRISPR/FnCpf1-RR	TYCY	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
CRISPR/FnCpf1-RVR	TATG	OsROC5, OsPDS, OsDEP1	Zhong et al, 2018
PAM, Protospacer adjacent motif. N represents A/T/G/C base. R represents A/G base. Y represents T/C base. V represents A/C/G base.