Increasing fidelity and efficiency by modifying cytidine base-editing systems in rice

The efficiency of plant cytidine base-editing systems is limited, and unwanted mutations frequently occur in transgenic plants. We increased the cytidine editing frequency and fidelity of the plant base editor 3 (BE3) and targeted activation-induced cytidine deaminase (CDA) (target-AID) systems by coexpressing three copies of free uracil–DNA glycosylase (UDG) inhibitor (UGI). The editing efficiency of the improved BE3 and CDA systems reached as high as 88.9% and 85.7%, respectively, in regenerated rice plants, with a very low frequency of unwanted mutations. The low editing frequency of the BE3 system in the GC context could be overcome by the modified CDA system. These results provide a high-fidelity and high-efficiency solution for rice genomic base editing.