SmartPE boosts prime editing efficiency in dicot crop plants

Prime editing has long promised precise genome changes in plants, but in dicot species it has been held back by low efficiency and results that vary sharply from one target site to another. A new study published in Nature Plants on 28 October 2026 reports an optimized system, called SmartPE, that substantially raises editing efficiencies in several major dicot crops.

SmartPE combines several design changes in a single framework. It uses a dual-pegRNA strategy together with deliberately designed mismatched bases in the reverse-transcription templates, and it adds cis-regulatory elements and engineered reverse transcriptases. According to the abstract, these components work together to overcome the inefficiencies that have limited broader application of prime editing in dicots.

The reported gains in protoplasts are large. Editing efficiencies with SmartPE were 6.3- to 23.0-fold higher than canonical prime editing systems in Arabidopsis thaliana (Col-0) and 8.2- to 38.2-fold higher in tomato (Solanum lycopersicum). In soybean (Glycine max) and oilseed rape (Brassica napus), more than tenfold improvements were achieved at the majority of target sites tested.

Protoplast results were followed by tests in whole plant tissues. In tomato hairy roots, SmartPE generated homozygous edit lines at a rate of 7.3 percent and heterozygous lines at 12.5 percent at the SlOR2 locus. Standard prime editing, by comparison, produced only heterozygous edits, at 1.0 percent, along with several chimeric outcomes.

The system also performed in stable transformation experiments. SmartPE enabled seamless insertion of a FLAG tag in Arabidopsis and insertion of enhancers and recombination sites in tomato, with editing efficiencies reaching up to 32.3 percent in those experiments.

The article is published as a Letter in Nature Plants.

The authors state that, taken together, these results show that SmartPE provides an efficient prime editing framework for dicot species. The reported figures come from the specific systems and target sites described in the study, and the abstract notes that the efficiency gains were measured against canonical prime editing systems under the conditions of those experiments.

Subject of Research: An optimized prime editing system, SmartPE, that improves genome editing efficiency in dicot crop plants.

Article Title: SmartPE enables efficient prime editing in dicot crops

Article References: Liu, Y., Sun, C., Xu, H., Ran, Y., Li, L., Zhang, R., & Gao, C. (2026). SmartPE enables efficient prime editing in dicot crops. Nature Plants. https://doi.org/10.1038/s41477-026-02447-w

Image Credits: AI Generated

DOI: 10.1038/s41477-026-02447-w

Keywords: prime editing, SmartPE, dicot crops, tomato, soybean, Arabidopsis, oilseed rape, genome editing, pegRNA, reverse transcriptase, plant biotechnology, Nature Plants