CRISPR/Cas9: Development and Application in Rice Breeding

doi:10.1016/j.rsci.2019.08.001

Abstract

Abstract:

Rice (Oryza sativa L.) is an important staple food crop worldwide due to its adaptability to different environmental conditions. Because of its great economic and social importance, there is a constant requirement for new varieties with improved agronomic characteristics, such as tolerance to different biotic (such as bacterium, fungus, insect and virus) and abiotic stresses (such as salinity, drought and temperature), higher yield and better organoleptic and nutritional value. Among the new genome editing technologies, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) (CRISPR/Cas) system allows precise and specific edition in a targeted genome region. It is one of the most frequently used techniques for the study of the function of new genes and for the development of mutant lines with enhanced tolerance to biotic and abiotic stresses, herbicide resistance or improved yield. The wide varieties of applications for this technology include simple non-homologous end joining, homologous recombination, gene replacement, and base editing. In this review, we analyzed how some of these applications have been used in rice cultivars to obtain rice varieties better adapted to current environmental conditions and market requirements.

Key words: rice, CRISPR, Cas, genome editing, biotic stress, abiotic stress, yield, off-target, mutation

Matías Romero Fernando, Gatica-Arias Andrés. CRISPR/Cas9: Development and Application in Rice Breeding[J]. Rice Science, 2019, 26(5): 265-281.

Figures/Tables 2

References 92

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Application	Targeted gene	Strategy	Transformation method/Explant	Reference
Response to bacterial blight	SWEET14, SWEET11	NHEJ	PEG/Protoplast	Jiang et al, 2013
Response to bacterial blight	SWEET13	NHEJ	Agrobacterium/embriogenic calli	Zhou et al, 2015
Rice blast resistance	EFR922	NHEJ	Agrobacterium/embriogenic calli	Wang et al, 2016
Rice blast resistance	SEC3A	NHEJ	Agrobacterium/embriogenic calli	Ma et al, 2018
Response to saline stress	RAV2	NHEJ	Agrobacterium/embriogenic calli	Duan et al, 2016
Response to drought stress	SAPK2	NHEJ	Agrobacterium/embriogenic calli	Lou et al, 2017
Response to cold stress	ANN3	NHEJ	Agrobacterium/embriogenic calli	Shen et al, 2017
Herbicide resistance	EPSPS	Exon replacement by NHEJ	Biobalistic/embriogenic calli	Li et al, 2016a
	AAC	Base editing by nCas9	Agrobacterium/embriogenic calli	Li et al, 2018
	ALS	Base editing by nCas9 and/or dCas9	Agrobacterium/embriogenic calli	Shimatani et al, 2017
	ALS	HR	Biobalistic/embriogenic calli	Sun et al, 2016
Yield improvement	Gn1a, DEP1, GS3, IPA1	NHEJ	Agrobacterium/embriogenic calli	Li et al, 2016b
	GS3, Gn1a	NHEJ	Agrobacterium/embriogenic calli	Shen et al, 2016
	DEP1	Gen deletion by NHEJ	Agrobacterium/embriogenic calli	Wang et al, 2017
	GW2, GW5, TGW6	NHEJ	Agrobacterium/embriogenic calli	Xu et al, 2016
	GS3, GW2, Gn1a	NHEJ	Agrobacterium/embriogenic calli	Zhou et al, 2018
	TMS5	NHEJ	Agrobacterium/embriogenic calli	Zhou et al, 2016
Fatty acid metabolism	FAD2-1	NHEJ	Agrobacterium/embriogenic calli	Abe et al, 2018
Flowering time	Hd2, Hd4, Hd5	NHEJ	Agrobacterium/embriogenic calli	Li et al, 2017
Nitrogen efficiency use	NRT1.1B	Allele replacement by HR	Biobalistic/embriogenic calli	Li et al, 2018
Cadmium accumulation	Nramp5	NHEJ	Agrobacterium/embriogenic calli	Tang et al, 2017
Starch metabolism	SBEI, SBEIIb	NHEJ	Agrobacterium/embriogenic calli	Sun et al, 2017
Starch metabolism	WAXY	NHEJ	Agrobacterium/embriogenic calli	Zhang et al, 2018
Transgene excision	GUS	NHEJ	Agrobacterium and biobalistic/embriogenic calli	Srivastava et al, 2017
Comparison between	EPFL9	NHEJ	Agrobacterium/immature embryos	Yin et al, 2017
Cas9 and Cpf1	EPFL9	NHEJ	Agrobacterium/immature embryos	Yin et al, 2017
Genome wide mutant Library	12 802 genes	NHEJ	Agrobacterium/embriogenic calli	Meng et al, 2017
Genome wide mutant Library	34 234 genes	NHEJ	Agrobacterium/embriogenic calli	Lu et al, 2017

Application	Targeted gene	Strategy	Transformation method/Explant	Reference
Response to bacterial blight	SWEET14, SWEET11	NHEJ	PEG/Protoplast	Jiang et al, 2013
Response to bacterial blight	SWEET13	NHEJ	Agrobacterium/embriogenic calli	Zhou et al, 2015
Rice blast resistance	EFR922	NHEJ	Agrobacterium/embriogenic calli	Wang et al, 2016
Rice blast resistance	SEC3A	NHEJ	Agrobacterium/embriogenic calli	Ma et al, 2018
Response to saline stress	RAV2	NHEJ	Agrobacterium/embriogenic calli	Duan et al, 2016
Response to drought stress	SAPK2	NHEJ	Agrobacterium/embriogenic calli	Lou et al, 2017
Response to cold stress	ANN3	NHEJ	Agrobacterium/embriogenic calli	Shen et al, 2017
Herbicide resistance	EPSPS	Exon replacement by NHEJ	Biobalistic/embriogenic calli	Li et al, 2016a
	AAC	Base editing by nCas9	Agrobacterium/embriogenic calli	Li et al, 2018
	ALS	Base editing by nCas9 and/or dCas9	Agrobacterium/embriogenic calli	Shimatani et al, 2017
	ALS	HR	Biobalistic/embriogenic calli	Sun et al, 2016
Yield improvement	Gn1a, DEP1, GS3, IPA1	NHEJ	Agrobacterium/embriogenic calli	Li et al, 2016b
	GS3, Gn1a	NHEJ	Agrobacterium/embriogenic calli	Shen et al, 2016
	DEP1	Gen deletion by NHEJ	Agrobacterium/embriogenic calli	Wang et al, 2017
	GW2, GW5, TGW6	NHEJ	Agrobacterium/embriogenic calli	Xu et al, 2016
	GS3, GW2, Gn1a	NHEJ	Agrobacterium/embriogenic calli	Zhou et al, 2018
	TMS5	NHEJ	Agrobacterium/embriogenic calli	Zhou et al, 2016
Fatty acid metabolism	FAD2-1	NHEJ	Agrobacterium/embriogenic calli	Abe et al, 2018
Flowering time	Hd2, Hd4, Hd5	NHEJ	Agrobacterium/embriogenic calli	Li et al, 2017
Nitrogen efficiency use	NRT1.1B	Allele replacement by HR	Biobalistic/embriogenic calli	Li et al, 2018
Cadmium accumulation	Nramp5	NHEJ	Agrobacterium/embriogenic calli	Tang et al, 2017
Starch metabolism	SBEI, SBEIIb	NHEJ	Agrobacterium/embriogenic calli	Sun et al, 2017
Starch metabolism	WAXY	NHEJ	Agrobacterium/embriogenic calli	Zhang et al, 2018
Transgene excision	GUS	NHEJ	Agrobacterium and biobalistic/embriogenic calli	Srivastava et al, 2017
Comparison between	EPFL9	NHEJ	Agrobacterium/immature embryos	Yin et al, 2017
Cas9 and Cpf1	EPFL9	NHEJ	Agrobacterium/immature embryos	Yin et al, 2017
Genome wide mutant Library	12 802 genes	NHEJ	Agrobacterium/embriogenic calli	Meng et al, 2017
Genome wide mutant Library	34 234 genes	NHEJ	Agrobacterium/embriogenic calli	Lu et al, 2017