| Modification type | Crop | System | Target | Purpose | Reference |
| Removal of transgenic elements | Apple | Flp/Frt | NPTII, RVI6 | Marker gene excision, scab resistance | [30] |
| Barley | phiC31 | GFP | Excision assessment | [31] | |
| Barley | Cre/LoxP | BAR | Marker gene excision | [32] | |
| Grapevine | Flp/Frt | NPTII | Marker gene excision | [33] | |
| Maize | Cre/LoxP | GAT, CFP | Excision assessment | [34] | |
| Maize | Cre/LoxP | GFP | Marker gene excision | [35] | |
| Mustard | Cre/LoxP | HPT | Marker gene excision | [22] | |
| Oilseed rape | Cre/LoxP | NPTII | Marker gene excision | [36] | |
| Orange | Cre/LoxP | AATCB, IPT | Canker resistance, marker gene excision | [37] | |
| Potato | Cre/LoxP | BAR | Marker gene excision | [38] | |
| Rice | Cre/LoxP | NOS terminator | Transgenic element excision | [39] | |
| Rice | Flp/Frt | HPT, TC | Enhancement of tocopherol content, marker gene excision | [40] | |
| Soybean | Cre/LoxP | NPTII | Marker gene excision | [41] | |
| Tobacco | Cre/LoxP | NPTII | Marker gene excision | [42] | |
| Tobacco | CinH-RS2 | GFP | Excision assessment | [43] | |
| Tobacco | ParA-MRS, CinH-RS2 | RFP | Marker gene excision | [44] | |
| Wheat | Cre/LoxP | BAR | Marker gene excision | [45] | |
| Gene integration | Maize | Cre/LoxP | RFP | Insertion assessment | [26] |
| Maize | Flp/Frt | PMI, RFP | Insertion assessment | [46] | |
| Oilseed rape | Cre/LoxP, Flp/Frt | RFP, GFP | Insertion assessment | [47] | |
| Rice | Cre/LoxP | GUS | Insertion assessment | [48] | |
| Rice | Cre/LoxP, ZFN | UBI promoter, clone sites for genes of interest | Insertion assessment | [49] | |
| Soybean | Flp/Frt | ALS, CFP | Insertion assessment | [50] | |
| Tobacco | R/Rs | LUC | Insertion assessment | [51] |