Rice Science ›› 2019, Vol. 26 ›› Issue (5): 265-281.DOI: 10.1016/j.rsci.2019.08.001
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Matías Romero Fernando, Gatica-Arias Andrés()
Received:
2018-12-15
Accepted:
2019-03-07
Online:
2019-09-28
Published:
2019-05-24
Matías Romero Fernando, Gatica-Arias Andrés. CRISPR/Cas9: Development and Application in Rice Breeding[J]. Rice Science, 2019, 26(5): 265-281.
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Fig. 1. CRISPR/Cas9 system components and pathways.A, Components required for genome editing using the CRISPR/Cas9 system: a DNA endonuclease (the most commonly used is the Cas9 protein from Streptococcus pyogenes) and a customizable single guide RNA (sgRNA). B, Non-homologous end-joining (NHEJ) repair pathway. C, Homologous recombination (HR) repair pathway. PAM, Protospacer adjacent motif.
Application | Targeted gene | Strategy | Transformation method/Explant | Reference |
---|---|---|---|---|
Response to bacterial blight | SWEET14, SWEET11 | NHEJ | PEG/Protoplast | |
SWEET13 | NHEJ | Agrobacterium/embriogenic calli | ||
Rice blast resistance | EFR922 | NHEJ | Agrobacterium/embriogenic calli | |
SEC3A | NHEJ | Agrobacterium/embriogenic calli | ||
Response to saline stress | RAV2 | NHEJ | Agrobacterium/embriogenic calli | |
Response to drought stress | SAPK2 | NHEJ | Agrobacterium/embriogenic calli | |
Response to cold stress | ANN3 | NHEJ | Agrobacterium/embriogenic calli | |
Herbicide resistance | EPSPS | Exon replacement by NHEJ | Biobalistic/embriogenic calli | |
AAC | Base editing by nCas9 | Agrobacterium/embriogenic calli | ||
ALS | Base editing by nCas9 and/or dCas9 | Agrobacterium/embriogenic calli | ||
ALS | HR | Biobalistic/embriogenic calli | ||
Yield improvement | Gn1a, DEP1, GS3, IPA1 | NHEJ | Agrobacterium/embriogenic calli | |
GS3, Gn1a | NHEJ | Agrobacterium/embriogenic calli | ||
DEP1 | Gen deletion by NHEJ | Agrobacterium/embriogenic calli | ||
GW2, GW5, TGW6 | NHEJ | Agrobacterium/embriogenic calli | ||
GS3, GW2, Gn1a | NHEJ | Agrobacterium/embriogenic calli | ||
TMS5 | NHEJ | Agrobacterium/embriogenic calli | ||
Fatty acid metabolism | FAD2-1 | NHEJ | Agrobacterium/embriogenic calli | |
Flowering time | Hd2, Hd4, Hd5 | NHEJ | Agrobacterium/embriogenic calli | |
Nitrogen efficiency use | NRT1.1B | Allele replacement by HR | Biobalistic/embriogenic calli | |
Cadmium accumulation | Nramp5 | NHEJ | Agrobacterium/embriogenic calli | |
Starch metabolism | SBEI, SBEIIb | NHEJ | Agrobacterium/embriogenic calli | |
WAXY | NHEJ | Agrobacterium/embriogenic calli | ||
Transgene excision | GUS | NHEJ | Agrobacterium and biobalistic/embriogenic calli | |
Comparison between | EPFL9 | NHEJ | Agrobacterium/immature embryos | |
Cas9 and Cpf1 | ||||
Genome wide mutant Library | 12 802 genes | NHEJ | Agrobacterium/embriogenic calli | |
34 234 genes | NHEJ | Agrobacterium/embriogenic calli |
Table 1 Applications of CRISPR in rice from 2013 to mid-2018.
Application | Targeted gene | Strategy | Transformation method/Explant | Reference |
---|---|---|---|---|
Response to bacterial blight | SWEET14, SWEET11 | NHEJ | PEG/Protoplast | |
SWEET13 | NHEJ | Agrobacterium/embriogenic calli | ||
Rice blast resistance | EFR922 | NHEJ | Agrobacterium/embriogenic calli | |
SEC3A | NHEJ | Agrobacterium/embriogenic calli | ||
Response to saline stress | RAV2 | NHEJ | Agrobacterium/embriogenic calli | |
Response to drought stress | SAPK2 | NHEJ | Agrobacterium/embriogenic calli | |
Response to cold stress | ANN3 | NHEJ | Agrobacterium/embriogenic calli | |
Herbicide resistance | EPSPS | Exon replacement by NHEJ | Biobalistic/embriogenic calli | |
AAC | Base editing by nCas9 | Agrobacterium/embriogenic calli | ||
ALS | Base editing by nCas9 and/or dCas9 | Agrobacterium/embriogenic calli | ||
ALS | HR | Biobalistic/embriogenic calli | ||
Yield improvement | Gn1a, DEP1, GS3, IPA1 | NHEJ | Agrobacterium/embriogenic calli | |
GS3, Gn1a | NHEJ | Agrobacterium/embriogenic calli | ||
DEP1 | Gen deletion by NHEJ | Agrobacterium/embriogenic calli | ||
GW2, GW5, TGW6 | NHEJ | Agrobacterium/embriogenic calli | ||
GS3, GW2, Gn1a | NHEJ | Agrobacterium/embriogenic calli | ||
TMS5 | NHEJ | Agrobacterium/embriogenic calli | ||
Fatty acid metabolism | FAD2-1 | NHEJ | Agrobacterium/embriogenic calli | |
Flowering time | Hd2, Hd4, Hd5 | NHEJ | Agrobacterium/embriogenic calli | |
Nitrogen efficiency use | NRT1.1B | Allele replacement by HR | Biobalistic/embriogenic calli | |
Cadmium accumulation | Nramp5 | NHEJ | Agrobacterium/embriogenic calli | |
Starch metabolism | SBEI, SBEIIb | NHEJ | Agrobacterium/embriogenic calli | |
WAXY | NHEJ | Agrobacterium/embriogenic calli | ||
Transgene excision | GUS | NHEJ | Agrobacterium and biobalistic/embriogenic calli | |
Comparison between | EPFL9 | NHEJ | Agrobacterium/immature embryos | |
Cas9 and Cpf1 | ||||
Genome wide mutant Library | 12 802 genes | NHEJ | Agrobacterium/embriogenic calli | |
34 234 genes | NHEJ | Agrobacterium/embriogenic calli |
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