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 1 Summary of applications of CRISPR-Cas based gene editing systems against abiotic stresses in rice between 2020–2023

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

Stress Name	Gene/s Targeted	Gene nature/Gene function	Gene editing system/gRNA used	Results	Reference
Drought	OsPYL9	Abscisic acid receptor gene	CRISPR-Cas9/two gRNAs	Higher ABA accumulation and lower stomatal conductance	(Usman et al. 2020)
	OsmiR818b	Drought gene	CRIPSR-Cas9/ single gRNA	Lower resistance	(Chung et al. 2020)
	OsmiR535	Modulating cold stress response/negative regulator of cold stress	CRISPR-Cas9/ single gRNAs	Enhanced tolerance against cold, salinity, and drought stresses	(Yue et al. 2020)
	OsABA8ox2	an ABA catabolic gene	CRISPR-Cas9/ single gRNA	Improved drought tolerance	(Zhang et al. 2020a, b)
	OsAAA-1 and OsAAA-2	Drought sensitive genes	CRISPR-Cas9/ four gRNA	Enhanced drought tolerance along with improved grain yield	(Lu et al. 2020)
	OsSDD1 and OsRSD1	Clustering stomata	CRISPR-Cas9/two gRNAs	decreased stomatal density	(Yu et al. 2020)
	OsBC1L1 or OsBC1L8	Stomatal patterning and production	CRISPR-Cas9	stomatal clustering and stomatal production	(Li et al. 2021a, b)
	OsEPFL10 and STOMAGEN	Negative regulators	CRISPR-Cas9/ single gRNA	Increased tolerance	(Karavolias et al. 2021)
	OsMADS26	Transcription factor	CRISPR-Cas9/three gRNAs	Proof of concept	(Anjala and Augustine 2022)
	OsSAPK3	Osmotic stress protein kinases	CRISPR-Cas9/ single gRNA	Reduced sensitivity to drought	(Lou et al. 2023)
	OsIPA1	Encodes transcriptional factor	CRISPR-Cas9/ single gRNA	Improved drought tolerance by regulating SNAC1	(Chen et al. 2023a, b)
	OsLKP2	Cuticular wax biosynthesis	CRISPR-Cas9	Enhanced tolerance	(Shim et al. 2023)
	OsWRKY76	Transcription factor	CRISPR-Cas9	Weak drought tolerance	(Zhang et al. 2023a, b)
Heat	OsNTL3	Negative regulator	CRISPR-Cas9/ single gRNA	Heat sensitivity	(Liu et al. 2020a, b, c)
	OsLRK1	regulator of leaf-based dark respiration	CRISPR-Cas9/ single gRNA	Compromised growth at 35 ℃	(Qu et al. 2020)
	OsSRL10	Regulates thermotolerance and leaf morphology	CRISPR-Cas9/ single gRNA	Sensitivity to high temperature	(Zhang et al. 2023a, b)
Salinity	OsGTγ-2 (TF)	Positive regulator of salinity response in rice	CRISPR-Cas9/single gRNA	Salinity hypersensitive plants	(Liu et al. 2020a, b, c)
	Osgs3 and Osdep1 heterotrimeric G proteins	Do signal transmission	CRISPR-Cas9/single gRNA	Improved salinity tolerance	(Cui et al. 2020)
	OsMPT3;1 and OsMPT3;2	Mitochondrial phosphate transporter genes	CRISPR-Cas9/single gRNA	Increased Na+/K + ratio	(Huang et al. 2020a, b, c)
	OsPQT3	Negative regulator	CRISPR-Cas9/two gRNAs	Enhanced resistance with improved grain yield	(Alfatih et al. 2020)
	OsSERK2	co-receptor in brassinosteroids signaling	CRISPR-Cas9/two gRNAs	Salinity sensitivity	(Dong et al. 2020)
	OsqSOR1	root gravitropic responses	CRISPR-Cas9/single gRNA	Reduced the stress in saline paddy fields	(Kitomi et al. 2020)
	OsSST	regulating the release of root exudates	CRISPR-Cas9/single gRNA	Better plant adaptation under saline conditions	(Lian et al. 2020)
	OsRR22	Involved in salt tolerance in rice	CRISPR-Cas9	Higher salt tolerance	(Tripathy et al. 2021)
	OsMKK1, OsMKK6, and OsMKK1/6	Affect lateral root growth	CRISPR-Cas9/ two gRNAs	Increased auxin contents and enhanced lateral roots growth under salinity	(Yang et al. 2021)
	OsHKT2;1	Involved in mineral transportation	CRISPR-Cas9/ single gRNA	Enhanced salt tolerant phenotypes by reducing sodium ion and ROS accumulation.	(Wei et al. 2021a, b)
	OsbHLH024 (TF)	Involved in plant growth and stress response	CRISPR-Cas9/ single gRNA	Improved salt tolerance	(Alam et al. 2022a, b, c)
	OsRR22	Involved in salt tolerance in rice	CRISPR-Cas9/ single gRNA	Improved salt tolerance	(Han et al. 2022)
	OsVDE	Negatively regulator of salinity stress	CRISPR-Cas9/ single gRNA	Higher survival rate and stomatal conductance	(Wang et al. 2022a, b, c)
	OsbHLH024	Transcription factor	CRISPR-Cas9/ two gRNAs	Enhanced salt tolerance	(Alam et al. 2022a, b, c)
	OsBEAR1	Regulator of salt response	CRISPR-Cas9 and artificial miRNA	Mutation by both methods enhanced salt sensitivity	(Teng et al. 2022)
	OsbHLH044	Transcription factor	CRISPR-Cas9/ two gRNAs	Salinity sensitivity	(Alam et al. 2022a, b, c)
	OsXLG2 and OsXLG4	extra-large GTP-binding protein	CRISPR-Cas9/ single gRNA	Double mutant exhibited salinity tolerance	(Biswal et al. 2022)
	OsBadh2	Related to synthesis of aromatic component	CRISPR-Cas9/ single gRNA	Improved tolerance in non-aromatic variety (Huaidao#5)	(Prodhan et al. 2022)
	OsGLYI3	Sensitive gene to salinity	CRISPR-Cas9/ single gRNA	Sensitivity to salinity stress	(Liu et al. 2022)
Cold	OsGL1-11	Wax synthesis	CRISPR-Cas9	Sensitivity to salinity stress	(Zhao et al. 2022)
	OsPIN5b, OsGS3, OsMYB30	Cold sensitive	CRISPR-Cas9/ two gRNAs	Improved cold tolerance with higher yield	(Zeng et al. 2020a, b)
	OsAnn5	Positive regulator of cold stress	CRISPR-Cas9/ single gRNA	Cold sensitivity	(Que et al. 2020)
	OsTCD3	Cold induced gene	CRISPR-Cas9/ single gRNA	Cold sensitivity	(Lin et al. 2020)
	OsWRKY76	Sensitive gene	CRISPR-Cas9	Decreased cold tolerance	(Zhang et al. 2022a, b)
	OsCOLD11	Positive regulator	CRISPR-Cas9 / single gRNA	Reduce chilling tolerance	(Li et al. 2023)
Herbicide	OsHIS1	Sensitive gene	CRISPR-Cas9 cytidine deaminase fusion/ four gRNAs	Herbicide sensitive	(Komatsu et al. 2020)
	OsALS	Primary target for Bispyribac sodium herbicide	CRISPR-Cas9/ single gRNA	Herbicide tolerant	(Butt et al. 2020)
	OsALS1	Primary target for Bispyribac sodium herbicide	CRISPR-Cas base editor/ 63 gRNAs	Herbicide tolerant	(Kuang et al. 2020)
	OsALS	Primary target for Bispyribac sodium herbicide	CRISPR-Cas12a gene targeting/two crRNAs	Efficient biallelic gene targeting	(Li et al. 2020a, b)
	OsALS	Primary target for Bispyribac sodium herbicide	CRISPR-Cas9/ single gRNA	novel allele G628W after after transversion of G to T in OsALS gene regiom conferred improved herbicide tolerance	(Wang et al. 2021a, b, c, d)
	OsALS	Tolerant to bispyribac herbicide	Base editing at four different locations	Improve herbicide tolerance	(Zhang et al. 2021a, b)
	OsAFB4	Auxin receptor	CRISPR-Cas9/ two gRNAs	Improved resistance to picloram	(Guo et al. 2021)
	OsACC1	Negative regulator	prime-editing-library-mediated saturation mutagenesis	Herbicide resistant	(Xu et al. 2021a, b, c, d)
	OsPUT1/2/3	Transporter gene	CRISPR-Cas9/ single gRNA	paraquat resistance	(Lyu et al. 2022)
	OsCYP76C6	Cytochrome encoding gene (isoproturon herbicide)	CRISPR-Cas9/ single gRNA	Increased conjugates and isoproturon metabolites	(Zhai et al. 2022)
	OsALS	Primary target of multiple herbicides	CRISPR-Cas9/ single gRNA	Strong resistance	(Liying et al. 2022)
	OsEPSPS	Herbicide gene	Prime editing	Herbicide resistance	(Butt et al. 2020)
	OsALS	Primary target of multiple herbicides	CRISPR-Cas9	Herbicide tolerance	(Zafar et al. 2023)
	OsHPPD3	4-hydroxyphenylpyruvatedioxygenase inhibitor	CRISPR-Cas12a	Herbicide tolerance	(Wu et al. 2023)
Heavy metals	OsNRAMP5	Member of transporter gene family	CRISPR-Cas9/ single gRNA	Decreases in root uptake of Pb	(Chang et al. 2022)
	OsPMEI12	Do modification of methyl esterification	CRISPR-Cas9/ single gRNA	Better growth under phytohormone stress and increased fresh and dry weight under cd stree	(Li et al. 2022a, b, c)
	OsLCD	Involved in Cd accumulation	CRISPR-Cas9/ single gRNA	Reduce Cd translocation and enhanced Cd tolerance	(Elkonin et al. 2023)
	OsACE2	Encodes an acetyltransferase	CRISPR-Cas9	Detoxification to oxyfluorfen	(Xu et al. 2023)
	OsmiR535	Fine-tuning regulator of genes	CRISPR-Cas9	Tolerance to Cd toxification	(Yue et al. 2023)
	OsNramp5	Member of transporter gene family	CRISPR-Cas9/ single gRNA	Manganese, copper, and selenium decreased in knock out lines	(Feng et al. 2023)
	OsCERK1	Negative regulator	CRISPR-Cas9	Tolerance to cupric oxide nanoparticles	(Chen et al. 2023a, b)
Lodging	OsGW2	Primarily controls grain weight	CRISPR-Cas9/ single gRNA	Lodging resistance	(Yamaguchi et al. 2020)
	OsRhoGDI2	Plant height	CRISPR-Cas9/ single gRNA	Semi dwarf	(Wang et al. 2020a, b, c, d)
	OsSd1	Involved in plant height	CRISPR-Cas9/ two gRNAs	Lodging resistance	(Wang et al. 2022a, b, c)
	OsSd-1	Dwarfing gene	CRISPR-Cas9/ two gRNAs	Lodging resistance	(Beyene et al. 2022)
Drought and salinity	OsDST	Negative regulator	CRISPR-Cas9/ two gRNAs	Higher tolerance level against salinity and moderate against osmotic stress	(Santosh Kumar et al. 2020)
	OsbZIP72	Transcription Factor	CRISPR-Cas9/ single gRNA	Sensitivity to drought and salinity	(Baoxiang et al. 2021)
	OsNPF8.1	Positive regulator	CRISPR-Cas9	Less tolerance in knock out lines	(Diyang et al. 2023)
Drought and heat	OsNAC006	Transcription Factor	CRISPR-Cas9/ single gRNA	Drought and heat sensitivity	(Wang et al. 2020a, b, c, d)
drought and abscisic acid	OsERA1	Negative regulator	CRISPR-Cas9/ single gRNA	Hypersensitivity to ABA and enhanced drought tolerance	(Ogata et al. 2020)
drought and abscisic acid	OsAFP1	Negative regulator	CRISPR-Cas9	Decreased water loss and ABA sensitivity	(Tianshun et al. 2021)
Others	OsDOFs (TFs)	Plant specific transcription factors	CRISPR-Cas9/ gRNA	11 DOFs regulated heading date under long day conditions and 9 DOFs controlled heading date under short day conditions.	(Huang et al. 2020a, b, c)
	OsLPR3	Involved in response to phosphate	CRISPR-Cas9/ single gRNA	Improved Pi tolerance	(Lin et al. 2023)
	OsIRO3	Repressor to Fe homeostasis	CRISPR-Cas9/ single gRNA	Accumulation of Mg, Fe, and ROS increased in leaves	(Wang et al. 2020a, b, c, d)
	OsSAW1	Positive regulator	CRISPR-Cas9/ single gRNA	Male sterile plants	(Wang et al. 2020a, b, c, d)
	OsHAK8	Involved in K⁺ uptake	CRISPR-Cas9/ single gRNA	Reduced K⁺uptake	(Wang et al. 2021a, b, c, d)

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