TABLE 2.
Overview of recent successes in crop improvement using base editors and prime editors.
| Editor type | Target gene | Cultivar | Base editing system | Editing efficiency | Transformation method | References |
|---|---|---|---|---|---|---|
| Base editors | ||||||
| BE2 | NRT1.1B, SLR1 | Oryza sativa | APOBEC1-XTEN-Cas9(D10A) | ≤13.3% | Agrobacterium-mediated transformation | Lu and Zhu (2017) |
| BE3 | OsDEP1 | Oryza sativa | xCas9(D10A)-rAPOBEC1 | ≤30% | Agrobacterium-mediated transformation | Zhong et al. (2019) |
| BE3 | OsCERK1, OsSERK1, OsSERK2, ipa1 | Oryza sativa | APOBEC1-XTEN-Cas9n-UGI-NLS | 10%–38.9% | Agrobacterium-mediated transformation | Ren et al. (2017) |
| BE3 | OsNRT1.1B, OsSPL14, OsCDC48 | Oryza sativa | pnCas9-PBE | 43.48% | Agrobacterium-mediated transformation | Zong et al. (2017) |
| ABE | OsCDC48, OsALS, OsDEP1, OsAAT, OsNRT1.1B, OsEV, OsOD, OsACC | Oryza sativa | PABE | 3.2%–59.1% | Agrobacterium-mediated transformation | Li et al. (2018) |
| APOBEC1-CBE2/CBE3 | GhCLA, GhPEBP | Gossypium herbaceum | APOBEC1-XTEN-nCas9-UGI | 0%–57.78% | Agrobacterium-mediated transformation | Qin et al. (2020) |
| hAID-CBE3 | OsAOS1, OsFLS2, OsJAR2, OsCOI2, OsPi-D2, OsJAR1 | Oryza sativa | hAID-XTEN-nCas9 | 8.30%–73.30% | Agrobacterium-mediated transformation | Ren et al. (2018) |
| hAID-CBE3 | OsCOI2, OsBSR, OsMPK13, OsGS1, OsGSK4 | Oryza sativa | hAID-XTEN- nSpRY-UGI | 26.00%–34.15% | Agrobacterium-mediated transformation | Xu et al. (2021) |
| hAID-CBE3 | OsMPK16, OsCPK6, OsCPK5, OsMPK9, OsMPK17, OsCPK7, OsMPK15, OsCPK8 | Oryza sativa | hAID-nScCas9-UGI | 2.56%–97.92% | Agrobacterium-mediated transformation | Wang et al. (2020) |
| 0%–95.83% | ||||||
| PmCDA1-CBE2/CBE3/CBE4 | OsDEP1, OsCDC48, OsGS3 | Oryza sativa | PmCDA1-xCas9-UGI | 0%–21.10% | Agrobacterium-mediated transformation | Zhong et al. (2019) |
| PmCDA1-CBE2/CBE3/CBE4 | OsPDS | Oryza sativa | PmCDA1-nSpCas9-NG-UGI | 3.50%–56.30% | Agrobacterium-mediated transformation | Zhong et al. (2019) |
| PmCDA1-CBE2/CBE3/CBE4 | OsWaxy, OsEUI1 | Oryza sativa | PmCDA1-nScCas9+ +-UGI-UGI | 8.3%–86.1% | Agrobacterium-mediated transformation | Liu et al. (2021) |
| PmCDA1-CBE2/CBE3/CBE4 | SlALS | Solanum lycopersicum | nCas9-NG-PmCDA1-UGI | 32.00% | Agrobacterium-mediated transformation | Veillet et al. (2020) |
| Solanum tuberosum | ||||||
| ABE7.10 | OsACC, OsALS, OsOD, kjjjOsCDC48, OsAAT, OsDEP1, OsNRT1.1B, OsEV, TaEPSPS, TaGW2, TaDEP1 | Oryza sativa | TadA-TadA7.10-nCas9(D10A) | 3.20%–59.10% | Agrobacterium-mediated transformation/particle bombardment | Li et al. (2018) |
| Triticum | ||||||
| ABE7.10 | Tms9-1, OsCPK9, OsMPK15, OsMPK14, OsCPK10 | Oryza sativa | TadA-TadA7.10-nScCas9 | 50.00%–94.12% | Agrobacterium-mediated transformation | Wang et al. (2020) |
| ABE-P1S | SLR1, OsDEP1, OsACC1, OsNRT1.1B, OsSPL14, OsSERK2 | Oryza sativa | TadA7.10-nSaCas9, TadA7.10-nSpCas9 | 4.50%–96.30% | Agrobacterium-mediated transformation | Hua, Jiang, et al. (2020) |
| 0%–61.10% | ||||||
| ABE8e | OsEPSPS, OsALS, OsWaxy | Oryza sativa | TadA8e (V106W) nCas9 | 4.00%–100.00% | Agrobacterium-mediated transformation | Wei et al. (2021) |
| TadA8e (V106W)- nCas9-NG | 0%–100.00% | |||||
| pDuBE1 | OsALS, OsBADH2, OsLAZY1, OsPDS | Oryza sativa | TadA8e-nCas9-CDA1-UGI | 0.40%–87.60% | Agrobacterium-mediated transformation | Xu et al. (2021) |
| ABE8e | OsLF1, OsSPL14, OsSPL7, OsCKS2, OsIAA13, OsGBSSI, OsEUI1, OsTS | Oryza sativa | TadA8e-DBD-nSpRY, TadA8e-DBD-nSpG, and TadA8e-DBD- nCas9-NG | 0%–90.50% | Agrobacterium-mediated transformation | Tan et al. (2022) |
| 0%–92.50% | ||||||
| 0%–100.00% | ||||||
| ABE9 | OsJAR1, OsWRKY45, OsMPK6, OsGS1, OsSERK2, OsDEP2, OsETR2, OsGSK4, OsALS1, OsMPK13 | Oryza sativa | TadA9-XTEN- nScCas9, TadA9-XTEN-nSpRY, TadA9-XTEN- nSpCas9-NG, andTadA9-XTEN- nSpCas9 | 0%–97.92% | Agrobacterium-mediated transformation | Yan et al. (2021) |
| 0%–100.00% | ||||||
| 0%–37.50% | ||||||
| 0%–68.75% | ||||||
| DdCBE | 16s rRNA, rpoC1, psbA | Arabidopsis thaliana | cTP-TALE-L-nDdA- UGI-cTP-TALE-R-cDdA-UGI, PTP-TALE-L-nDdA-UGI-PTP-TALE-R-cDdA-UGI | 0%–86.40% | Agrobacterium-mediated transformation | Nakazato et al. (2021) |
| DdCBE | OspsaA | Oryza sativa | 97.50% | Agrobacterium-mediated transformation | Li et al. (2021) | |
| ABE7.10-nCas9 | 35S, AtUbi, AtRPS5A, SlRPS5A1 (Solyc11g042610), SlRPS5A2 (Solyc10g078620), SlTCTP (Solyc01g099770) and SlEF1α (Solyc06g005060) |
Solanum lycopersicum
Glycine max |
pSlEF1α-ABE-nCas9, pSlEF1α-ABE-XNG-nCas9 or pSlEF1α-ABE-nCas9-NG | 15%–40% | _ | Niu et al. (2023) |
| Prime editors | ||||||
| PE2 | ||||||
| PE2 | OsALS, OsACC | Oryza sativa | 1–3 bp substitution | Desired % | Agrobacterium-mediated transformation | Jiang et al. (2022) |
| 1.00%–7.60% | ||||||
| Undesired % | ||||||
| 0.00% | ||||||
| PE2 | OsALS, OsIPA1, OsTB1 | Oryza sativa | 2–4 nucleotide substitution, 2 bp insertion | Desired % | Agrobacterium-mediated transformation | Butt et al. (2020) |
| 0.00%–2.04% | ||||||
| pPE2 | HPTII, OsPDS, OsACC, OsWx | Oryza sativa | 1 bp substitution,1–3 bp insertion | Desired % | Agrobacterium-mediated transformation | Xu et al. (2020) |
| 0.00%–59.90% | ||||||
| pPE2 | OsCDC48, OsPDS, OsALS, OsACC | Oryza sativa | 1–2 bp substitution, 1 bp insertion | Desired % | Agrobacterium-mediated transformation | Li et al. (2022) |
| 0.00%–29.17% | ||||||
| pPE2-engineered pegRNA with mpknot) | OsPDS, OsALS, OsCDC48 | Oryza sativa | 1–2 bp substitution, 1 bp insertion | Desired % | Agrobacterium-mediated transformation | Li et al. (2022) |
| 10.42%–25.00% | ||||||
| Sp-PE2 | GFP | Oryza sativa | 2 bp substitution | Desired % | Agrobacterium-mediated transformation | Hua et al. (2020) |
| 15.60% | ||||||
| PPE | OsALS | Oryza sativa | 2 bp substitution | Desired % | Agrobacterium-mediated transformation | Zong et al. (2022) |
| 2.10% | ||||||
| pZ1WS (driven by the composite promoter CaMV35S-CmYLCV-U6) | ZmALS2, and ZmALS1 | Zea mays | 2–3 bp substitution | Desired % | Agrobacterium-mediated transformation | Jiang et al. (2020) |
| 4.80%–53.20% | ||||||
| pPE2 (an engineered pegRNA with evopreQ1) | OsALS, OsACC, OsCDC48, OsPDS | Oryza sativa | 1–2 bp substitution, 1 bp insertion | Desired % | Agrobacterium-mediated transformation | Li et al. (2022) |
| 2.08%–50.00% | ||||||
| ePPE (replaced M-MLV-RT to M-MLV-RT-ΔRNaseH) | OsALS | Oryza sativa | 2 bp substitution | Desired % | Agrobacterium-mediated transformation | Zong et al. (2022) |
| 11.30% | ||||||
| PE3 | ||||||
| PE3 | HPTII, OsEPSPS | Oryza sativa | 3–7 bp substitution | Desired % | Particle bombardment | Li et al. (2020) |
| 2.22%–9.38% | ||||||
| Sp-PE3 | APO1, GFP, OsALS | Oryza sativa | 1–2 bp substitution | Desired % | Agrobacterium-mediated transformation | Hua et al. (2020) |
| 0.00%–17.10% | ||||||
| PE-P2 (nCas9-M-MLV-T2A-hpt) | OsACC, OsDEP1, OsALS | Oryza sativa | 1–4 bp substitution | Desired % | Agrobacterium-mediated transformation | Xu et al. (2020) |
| 1.70%–26.00% | ||||||
| Undesired % | ||||||
| 0.00%–8.00% | ||||||
| PE-P2-RT-S (N- terminal M-MLV + one target mutation in RTT) | OsPSR1OsDEP1, OsSD1, OsALS, OsACC, OsGRF4, OsChalk5, OsWaxy, OsEPSPS, OsCold1, OsGS3, OsChalk5 | Oryza sativa | 1 bp substitution | Desired % | Agrobacterium-mediated transformation | Xu et al. (2022) |
| 0.00%–61.40% | ||||||
| Undesired % | ||||||
| 0.00%–15.00% | ||||||
| pCXPE03 (the RPS5A promoter derives that) | SlGAI, SlALS, SlPDS | Solanum lycopersicum | 2 bp substitution, 2 bp insertion | Desired % | Agrobacterium-mediated transformation | Lu et al. (2021) |
| 0.00%–6.70% | ||||||
| PE3 | OsSPL14, OsDHDPS, OsNR2 | Oryza sativa | 2–3 nucleotide substitution | Desired % | Particle bombardment | Li et al. (2022) |
| 0.00%–1.00% | ||||||
| PE3 | OsALS, OsACC, OsEPSPS | Oryza sativa | 1–3 bp substitution | Desired % | Agrobacterium-mediated transformation | Jiang et al. (2022) |
| 1.30%–70.30% | ||||||
| Undesired % | ||||||
| 9.00%–37.90% | ||||||
| PPE3 | OsCDC48, OsALS | Oryza sativa and Triticum | 1–3 bp substitution, 6 bp deletion | Desired % | Agrobacterium-mediated transformation | Lin et al. (2020) |
| 2.60%–21.8% | ||||||
| pPE3 | OsWx, OsACC | Oryza sativa | 1 bp substitution | Desired % | Agrobacterium-mediated transformation | Xu et al. (2020) |
| 0.00%–16.70% | ||||||
| PE-P1 | OsALS, OsDEP1, OsACC | Oryza sativa | 1–4 bp substitution | Desired % | Agrobacterium-mediated transformation | Xu et al. (2020) |
| 0.00%–1.40% | ||||||
| Undesired % | ||||||
| 0.00% | ||||||
| pPE3b | OsACC | Oryza sativa | 1 bp substitution | Desired % | Agrobacterium-mediated transformation | Xu et al. (2020) |
| 6.25% | ||||||
| PE4 | ||||||
| PE4 | OsACC, OsALS | Oryza sativa | 1–3 bp substitution | Desired % | Agrobacterium-mediated transformation | Jiang et al. (2022) |
| 5.20%–27.10% | ||||||
| Undesired % | ||||||
| 0.00%–2.10% | ||||||
| PE5 | ||||||
| PE5 | OsACC, OsALS, OsEPSPS | Oryza sativa | 1–3 bp substitution | Desired % | Agrobacterium-mediated transformation | Jiang et al. (2022) |
| 1.60%–64.10% | ||||||
| Undesired % | ||||||
| 6.40%–18.30% | ||||||
| PPE2 | OsDLT | Oryza sativa | 1–2 bp substitution | Desired % | Agrobacterium-mediated transformation | Xue et al. (2023) |
| 2.5%–84.9% | ||||||