CRISPR-Cas System, a Possible “Savior” of Rice Threatened by Climate Change: An Updated Review

Shaheen, Nabeel; Ahmad, Shakeel; Alghamdi, Salem S; Rehman, Hafiz Mamoon; Javed, Muhammad Arshad; Tabassum, Javaria; Shao, Gaoneng

doi:10.1186/s12284-023-00652-1

Rice

Table 2 Summary of last 3-year applications of CRISPR-Cas mediated gene editing systems against biotic stresses in rice

From: CRISPR-Cas System, a Possible “Savior” of Rice Threatened by Climate Change: An Updated Review

Disease/Biotic Stress	Targeted gene/s	Gene nature	Gene editing system/gRNA used	Results	Reference
Rice blast	OsBsr-d1	Regulation of redox stage of plant cells	CRISPR-Cas9/single gRNA	Enhanced resistance against rice blast	(Zhu et al. 2020)
	OsFLR1 and OsFLR13	Involved in rice-Magnaporthe oryzae intercation	CRISPR-Cas9/16 gRNAs	Increased susceptibility	(Huang et al. 2020a, b, c)
	OsFLR2 and OsFLR11			Enhanced resistance
	OsFLR1			Enhanced pathogen attack
	OsFLR2			Delayed pathogen attack
	OsDjA2 and OsERF104	Susceptibility genes	CRISPR-Cas9/two gRNAs	Improved resistance	(Távora 2021)
	OsUGT74J1	SA-glucosyltransferases	CRISPR-Cas9/two gRNAs	Enhanced Salicylic Acid accumulation and resistance against RB	(Tezuka et al. 2021)
	OsWRKY93	Transcription factor	CRISPR-Cas9/ single gRNA	Sensitivity to pathogen	(Li et al. 2021a, b)
	OsGRF18	Positive regulator	CRISPR-Cas9/ single gRNA	Improved resistance	(Yudong et al. 2021)
	OsUBC26	a rice ubiquitin-conjugating enzyme	CRISPR-Cas9	Compromised resistance	(Liu et al. 2021a, b, c)
	OsXa7	Broad spectrum resistance gene	CRISPR-Cas9/two gRNAs	Sensitivity to pathogen	(Chen et al. 2021)
	OsECBS	Produce casbane-type diterpenoids	CRISPR-Cas9/ RNAs	Impaired resistance	(Liang et al. 2021)
	OsPita-Fuhui2663	Negative regulator	CRISPR-Cas9/ single RNA	Resistance	(He et al. 2022)
	OsPib	R gene	CRISPR-Cas9/ single RNA	Displayed more symptoms after pathogen inoculation	(Xie et al. 2022)
	OsWRKY7	Transcription factor	CRISPR-Cas9/ single RNA	Sensitivity to blast fungus	(Tun et al. 2023)
Rice blast	Ospi-ta	Susceptibility gene	Intron-targeted insertion strategy of CRISPR-Cas9/single gRNA	Disease resistance with improved agronomic characteristics	(Xu et al. 2020)
	OsPi21	Broad spectrum resistance gene	CRISPR-Cas9/two gRNAs	Resistance without affecting agronomic traits	(Nawaz et al. 2020)
	OsPiPR1	Partial R gene	CRISPR-Cas9/single gRNA	Partially reduced blast resistance	(Liu et al. 2020a, b, c)
	OsDjA2 and OsERF104	Susceptibility genes	CRISPR-Cas9/single gRNA	Improved resistance	(MILAzzo et al. 2022)
	OsDjA2 and OsERF104	Susceptibility genes	CRISPR-Cas9/single gRNA	Resistance	(Távora et al. 2022)
	OsHRC	Negative regulator	CRISPR-Cas9	Resistance	(Ding et al. 2023)
Bacterial blight	OsXa13 promoter	Sensitive gene	CRISPR-Cas9/two gRNAs	Disease resistance	(Li et al. 2020a, b)
	OsSWEET14	Susceptibility gene	CRISPR-Cas9/three gRNAs	Resistance against bacterial blight	(Zafar et al. 2020)
	OsSWEET14	Susceptibility gene	CRISPR-Cas9/two gRNAs	Strong resistance with improve plant height	(Zeng et al. 2020a, b)
	OsEBEAvrXa23	Susceptible gene	CRISPR-Cas9 knock-in	Resistant	(Wei et al. 2021a, b)
	OsTFIIAγ1 or OsTFIIAγ5 (TF)	Involved in pathogen interaction	CRISPR-Cas9/ two gRNAs	Resistance	(Xu et al. 2021a, b, c, d)
	OsSWEET14	Susceptibility gene	CRISPR-Cas9/single gRNA	Moderate to high resistance	(Arulganesh et al. 2021)
	OsSWEET14	Susceptibility gene	CRISPR-Cas9/single gRNA	Improved resistance	(Duy et al. 2021)
	OsUPT box	Promoter region	CRISPR-Cas12a/ single crRNA	Improved resistance	(Yu et al. 2021)
	OsSWEET14	Susceptibility gene	CRISPR-Cas9/single gRNA	Less susceptibility	(Kim et al. 2021)
	OsPrx30	Bacterial blight responsive gene	CRISPR-Cas9/single gRNA	Increased resistance	(Liu et al. 2021a, b, c)
	OsSWEET13	Susceptibility gene	CRISPR-Cas9/single gRNA	Could interfere with binding site of pathogen effector binding element	(Diana et al. 2022)
	OsXa13	Recessive pleiotropic gene	CRISPR-Cas9/ two gRNA	Disease resistance	(Li et al. 2022a, b, c)
	OsCPK24	Positive regulator	CRISPR-Cas9/single gRNA	More susceptibility to BLB	(Lu et al. 2023)
Sheath blight	OsPP2A-1	Positive regulator	CRISPR-Cas9/single gRNA	Susceptible	Lin et al. (2021)
Rice blast and bacterial blight	OsPi21, OsBsr-d1, and OsXa5	Susceptibility genes	CRISPR-Cas9/single gRNA	Resistance	(Tao et al. 2021)
Bacterial blight and leaf streak	OsSWEET11, OsSWEET14 and OsSULTR3;6	Susceptibility genes	CRISPR-Cas9/single gRNA	Resistance	(Ni et al. 2021)
Bacterial blight and leaf streak	OsBsr-d1, OsPi21 and OsERF922	Resistant genes	CRISPR-Cas9/single gRNA	Improved resistance in both single and triplet mutants	(Zhou et al. 2022)
Rice tungro disease	OseIF4G	Required to translate viral RNA viruses	CRISPR-Cas9/single gRNA	Enhanced tolerance	(Nithya et al. 2020)
Rice black-streaked dwarf virus	OseIF4G	Required to translate viral RNA viruses	CRISPR-Cas9/single gRNA	Enhanced tolerance	(Wang et al. 2021a, b, c, d)
Rice black-streaked dwarf virus	OsAGO2	Negative regulator	transposon-insertion or CRISPR/Cas9	Over-expression enhanced susceptibility and mutant showed resistance	(Wang et al. 2021a, b, c, d)
Southern rice black-streaked dwarf virus	OsARF17 (TF)	Resistance gene	CRISPR-Cas9/single gRNA	Increased susceptibility	(Zhang et al. 2020a, b)
Southern rice black-streaked dwarf virus	Osv-ATPase d	Mediating virus resistance	CRISPR-Cas9/single gRNA	Resistance	(Lu et al. 2021)
Bacterial leaf streak	OsSULRT3; 6	Susceptibility gene	CRISPR-Cas9/single gRNA	Resistance	(Xu et al. 2021a, b, c, d)
Brown plant hopper	OsAOC and OsMYC2	Involved in signaling	CRISPR-Cas9/single gRNA	Pathogen performed better on knock out lines	(Xu et al. 2021a, b, c, d)
Brown plant hopper	OsCKXs	Negative regulator	CRISPR-Cas9	Enhanced resistance	(Zhang et al. 2022a, b)
Meloidogyne graminicola	OsBet v1	Involved in defense against microbial pathogens	CRISPR-Cas9/ two gRNAs	Increased susceptibility	(Li et al. 2022a, b, c)
Rice blast and bacterial blight	OsMORE1a	Immunity related gene	CRISPR-Cas9/single gRNA	Resistance to M. oryzae and Xanthomonas oryzae pv. oryzae but increased susceptibility to Cochliobolus miyabeanus,	(Kim et al. 2022)
Rice blast, bacterial blight and sheath blight	OsUMP1	natural allele of proteasome maturation factor	CRISPR-Cas9	Broad spectrum resistance to Magnaporthe oryzae, Rhizoctonia solani, Ustilaginoidea virens and Xanthomonas oryzae pv. oryzae	(Hu et al. 2023)
Rice black-streaked dwarf virus disease and southern rice black-streaked dwarf virus disease	OsAP47	Negatively regulates the resistance	CRISPR-Cas9/ two gRNAs	Enhances resistance against both stresses	(Wang et al. 2022a, b, c)
Yellow mottle virus	OsCPR5.1	Nucleoporin paralogs	CRISPR-Cas9/ two gRNAs	Disruption resulted in RYMV resistance	(Arra et al. 2023)
Yellow mottle virus	OsCPR5.2	Nucleoporin paralogs	CRISPR-Cas9/ two gRNAs	Susceptibility after disruption	(Arra et al. 2023)

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