Genome Editing Strategies Towards Enhancement of Rice Disease Resistance

doi:10.1016/j.rsci.2021.01.003

Abstract

Abstract:

The emerging pests and phytopathogens have reduced the crop yield and quality, which has threatened the global food security. Traditional breeding methods, molecular marker-based breeding approaches and use of genetically modified crops have played a crucial role in strengthening the food security worldwide. However, their usages in crop improvement have been highly limited due to multiple caveats. Genome editing tools like transcriptional activator-like effector nucleases and clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease Cas9 (CRISPR/Cas9) have effectively overcome limitations of the conventional breeding methods and are being widely accepted for improvement of crops. Among the genome editing tools, the CRISPR/Cas9 system has emerged as the most powerful tool of genome editing because of its efficiency, amicability, flexibility, low cost and adaptability. Accumulated evidences indicate that genome editing has great potential in improving the disease resistance in crop plants. In this review, we offered a brief introduction to the mechanisms of different genome editing systems and then discussed recent developments in CRISPR/Cas9 system-based genome editing towards enhancement of rice disease resistance by different strategies. This review also discussed the possible applications of recently developed genome editing approaches like CRISPR/Cas12a (formerly known as Cpf1) and base editors for enhancement of rice disease resistance.

Key words: genome editing technology, rice improvement, CRISPR/Cas9, CRISPR/Cas12a, base editor, disease resistance

Mishra Rukmini, Zheng Wei, Kumar Joshi Raj, Kaijun Zhao. Genome Editing Strategies Towards Enhancement of Rice Disease Resistance[J]. Rice Science, 2021, 28(2): 133-145.

Figures/Tables 3

Fig. 1. Sequence specific nucleases used for genome editing. A, Sequence specific nucleases including zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 or CRISPR/Cas12a create double-stranded breaks (DSBs) at the target site which is subsequently repaired either by non-homologous end joining (NHEJ) or homologous recombination (HR) by cellular system leading to gene disruption by insertion/deletion, gene addition or replacement, respectively. The cleavage of the targeted DNA is facilitated by FokI endonuclease in ZFNs and TALENs and Cas endonucleases in CRISPR/Cas9 and CRISPR/Cas12a. CRISPR/Cas9 makes use of a 100 nt single guide (sgRNA) comprising of crisprRNA (crRNA) and trans-acting crispr RNA (tracrRNA) while CRISPR/Cas12a requires only a 40-45 nt long crRNA to facilitate gene editing. B, Base editing platforms used for target specific single base modification. Cytidine base editor (CBE) uses Cas9 nickase together with a cytidine deaminase rAPOBEC3 and an uracil DNA glycosylase inhibitor (UGI) to facilitate cytosine to thymine conversions. Adenine base editor (ABE) consists of Cas9 nickase fused with E. coli derived ecTadA(WT)-ecTadA* heterodimer to facilitate adenosine to guanine conversions.

Fig. 2. Genome editing strategies towards disease resistance in plants. Multiple genome editing platforms can facilitate disease resistance through knock-out of susceptibility (S) genes (A), homology directed replacement of novel alleles (B), knock-in of resistance (R) genes (C), regulatory modification of R/S gene expression (D) and multiplex editing of resistance and susceptibility factors (E). HR, Homologous recombination; ZFN, Zinc finger nuclease; NHEJ, Non-homologous end joining; ABE, Adenine base editor; CBE, Cytidine base editor; UGI, Uracil DNA glycosylase.

Table 1. List of genes targeted by genome editing tools for rice disease resistance.

Pathogenic perspective	Target gene	Editing tool	Function	Reference
Resistance to bacterial infection	OsSWEET13	TALENs	Enhanced resistance to BLB	Li et al, 2012
	OsSWEET13	TALENs	Enhanced resistance to BLB	Zhou et al, 2015
	OsSWEET13	TALENs	Enhanced resistance to BLB	Blanvillain-Baufume et al, 2017
	Os09g29100	TALENs	Enhanced resistance to BLB	Cai et al, 2017
	Os8N3 (OsSWEET11)	CRISPR/Cas9	Enhanced resistance to BLB	Kim et al, 2019
	OsSWEET11 and OsSWEET14	CRISPR/Cas9	Broad spectrum resistance to BLB	Xu et al, 2019
	OsSWEET11, OsSWEET13 and OsSWEET14	CRISPR/Cas9	Broad spectrum resistance to BLB	Olivia et al, 2019
Resistance to fungal infection	OsERF922	CRISPR/Cas9	Enhanced resistance to blast disease	Wang et al, 2016
	OsSEC3A	CRISPR/Cas9	Enhanced resistance to blast disease	Ma et al, 2018
	OsPFT1	CRISPR/Cas9	Resistance to rice sheath blight	Shah et al, 2019
Resistance to viral infection	eIF4G	CRISPR/Cas9	Enhanced resistance to tungro disease	Macovei et al, 2018

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