Table 1.

Applications of base editing in plants.

Editor	Structural features	Plant	Target genes	Gene function	Phenotype/Trait improvement	Editing efficiency (%)	Reference
BE3	pnCas9-PBE	Rice	OsCDC48, OsNRT1.1B, OsSPL14	OsCDC48 regulates senescence and cell death. NRT1.1B encodes a nitrogen transporter. OsSPL14 controls grain yield and grain number	Reduced senescence and death.	43.48	Zong et al., 2017
BE2	APOBEC1-XTEN-Cas9(D10A)	Rice	NRT1.1B, SLR1	NRT1.1B encodes a nitrogen transporter. SLR1 encodes a DELLA protein	Editing in NRT1.1B increased nitrogen use efficiency Substitution in SLR1 led to plants with semi-dwarf phenotype	≤13.3	Lu and Zhu, 2017
BE3	APOBEC1-XTEN-Cas9n-UGI-NLS	Rice	OsCERK1, OsSERK1, OsSERK2, ipa1	Encodes receptor-like kinase. Ipa1 encodes OsSPL14 involved in regulating rice plant architecture	Detect the efficiency of rBE3	10–38.9	Ren et al., 2017
BE4	APOBEC1-XTEN-Cas9n (VQR)-UGI-NLS	Rice	pi-ta	Blast susceptible protein	-	18.2
Target-AID	nCas9Os-PmCDA1At	Rice	ALS	Encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid	Herbicide resistance	6–89	Shimatani et al., 2017
ABE	PABE	Rice	OsALS, OsCDC48, OsAAT, OsDEP1, OsACC, OsNRT1.1B, OsEV, OsOD	OsALS encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid OsCDC48 regulates senescence and cell death.	Development of efficient ABE PABE-7	3.2–59.1	Li et al., 2018
ABE	pRABEsp-OsU6	Rice	OsSPL14, OsSPL16, OsSPL18	They control grain yield and grain number	High yield	>4.8	Hua et al., 2018
ABE	pRABESA-OsU6sa	Rice	OsSPL14, OsSPL17, OsSPL16, OsSPL18	They control grain yield and grain number	High yield	>17
ABE	VQR-Cas9 (D10A)/VRER-Cas9 (D10A)	Rice	OsSPL14, OsSPL17, OsSPL16, OsSPL18	Controls grain yield and grain number	High yield	≤74.3	Hua et al., 2019a
BE3	xCas9(D10A)-rAPOBEC1	Rice	OsDEP1	Controls yield associated traits	-	≤30	Zhong et al., 2019
Target-AID	xCas9(D10A)-PmCDA1	Rice	OsDEP1	Controls yield associated traits	-	<20
Target-AID	Cas9-NG (D10A)-PmCDA-UGI	Rice	OsDEP1, OsCDC48	OsDEP1 controls yield associated traits OsCDC48 regulates senescence and cell death	-	0–56.3
Target-AID	NGv1 (D10A)	Rice	EPSPS, ALS, DL	Herbicide tolerance	Herbicide tolerance	5–95.5 4.2–86.3	Endo et al., 2019
BE	NGv1 (D10A)	Rice	EPSPS, ALS, DL	Herbicide tolerance	Herbicide tolerance	4.3–21.8
BE3 Target-AID ABE	eBE3, eCDA, eABE	Rice	OsACC	Herbicide tolerance	Herbicide tolerance	–	Liu et al., 2020
BE3 ABE	Base-Editing-mediated Gene Evolution (BEMGE)	Rice	OsALS1, OsALS2, OsALS3	Encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid	Herbicide tolerance	–	Kuang et al., 2020
BE3 Target-AID	xCas9-epBE	Rice	OsMPK2, OsMPK5, OsALS, OsNRT1.1B	OsALS encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid. NRT1.1B encodes a nitrogen transporter. OsMPK2 and OsMPK5 encode a stress-responsive rice mitogen-activated protein kinase	-	5–64.3	Zhang et al., 2020b
BE4 ABE	xCas9n-CBE, Cas9n-NG-CBE, eCas9n-NG-CBE xCas9n-ABE, Cas9n-NG-ABE, eCas9n-NG-ABE	Rice	OsWaxy, OsEUI1, OsCKX2, OsWaxy, OsEUI1, OsCKX2	OsWaxy encodes starch synthase enzyme I. OsEUI1 (Elongated Uppermost Internode 1). OsCKX2 encodes a cytokinin oxidase/dehydrogenase	-	9.1–45.5 2–6.5	Zeng et al., 2020
ecTadA∗7.10-nSaCas9	ABE-P2S	Rice	SPX-MSF2, OsSPL14, OsSPL17, OsSPL16, OsSPL18	Control grain yield and grain number		15.9–61.1	Hua et al., 2020a
ecTadA∗7.10-nSaKKH-Cas9	ABE-P5S	Rice	OsSPL13, SNB	OsSPL13 controls grain yield and grain number SNB regulates the transition of spikelet meristems into floral meristems in rice	-	6.1–33.9
ABE	ABE7.10-nSpCas9-NGv1	Rice	sgOs-siteG1, sgOs-site2, sgOs-site3, sgOs-site4	-	-	29.2–45.8	Negishi et al., 2019
PE	Sp-PE2, Sp-PE3, Sa-PE3	Rice	ALS, APO1, SLR1, OsSPL14, APO2	ALS encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid. SLR1 encodes a DELLA protein. OsSPL14 controls grain yield and grain number. APO1 and APO2 are positive regulators of panicle size and grain number.	-	0–17.1	Hua et al., 2020b
PE	pPE2, pPE3, pPE3b	Rice	OsPDS, OsACC1, OsWx	OsACC1 plays a role in herbicide tolerance OsPDS is involved in nutritional improvement.	-	0–31.3	Xu et al., 2020b
PE	PE-P1, PE-P2	Rice	OsALS, OsACC, OsDEP1	Herbicide tolerance	Herbicide tolerance	≤26	Xu et al., 2020c
STEME	APOBEC3A–ecTadA–ecTadA* nCas9 (D10A)	Rice	OsACC	Herbicide tolerance	Herbicide tolerance	15.10	Li et al., 2020a
PE	pCXUN-Ubi-NLS-nCas9(H840A)-Linker1 (33aa)-M-MLV-RT-Linker2 (14aa)-NLS-PolyA-E9-Actin-Nos	Rice	hptll, OsEPSPS	HptII confers hygromycin resistance. OsEPSPS gene encodes a key enzyme in the synthesis of aromatic amino acids	-	2.22–9.38	Li et al., 2020c
APOBEC3A	A3A-PBE	Wheat	TaALS, TaMTL, TaLOX2	TaALS encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid. TaLOX2 encodes a lipoxygenase enzyme involved in the hydrolysis of polyunsaturated fatty acids	-	16.7–22.5	Zong et al., 2018
BE3	PBE	Wheat	TaALS-P174	Encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid	Herbicide resistance	33–75	Zhang et al., 2019
Target-AID	pDeSpnCas9-NG_PmCDA1_UGI	Tomato	ALS	Encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid	Herbicide resistance	32	Veillet et al., 2020b
BE3	CBE3	Watermelon	ALS	Encodes acetolactate synthase, which functions in the biosynthesis of the branched amino acid	Herbicide resistance	23	Tian et al., 2018
BE3	GhBE3	Cotton	GhCLA, GhPEBP	GhCLA functions in chloroplast development. GhPEBP participates in the multiplex‐branch developmental process	-	26–58	Qin et al., 2020
BE3	pTF101.1-sgRNA-BE	Soybean	GmFT2a, GmFT4	Function in flowering induction in soya bean.	-	≤18.2	Cai et al., 2020
BE3	CBE	Oilseed rape	BnALS1	Herbicide tolerance	Herbicide tolerance	1.8	Wu et al., 2020

-, not reported.