From PE1 to PE7 and TwinPE: Advances in Plant Prime Editing and Challenges for Crop Applications
Background: Options for precise crop genome editing
A review of advances in prime editing and strategies for applying it in plants was published in the international journal Planta. Bargoti, Nain, and Singh examined changes in the technology from the early prime editor PE1 to PE7 and TwinPE, improvements to components tailored to plants, and its potential use in crop improvement. The review synthesizes prior research to survey directions in plant genome editing.
Prime editing is a genome engineering technique that changes target sequences without inducing DNA double-strand breaks (DSBs) or requiring an external donor DNA template. The abstract describes its scope as including all 12 possible base substitutions, targeted insertions and deletions, and combinations of these changes. Here, 12 refers to types of base substitution; it does not mean that the same editing efficiency has been achieved at every target in every crop.
Key findings: Improvements to editing tools and conditions for plant applications
The main strands of technological development covered in the review are protein engineering, structural improvements to prime editing guide RNA (pegRNA), and modulation of host DNA repair mechanisms. The authors summarize approaches intended to increase editing efficiency, precision, and scope. However, the available abstract does not provide quantitative data for directly comparing the composition or performance of systems such as PE1, PE7, and TwinPE.
For plant-oriented editing systems, the review focuses on codon optimization and promoter improvement, design of the structural scaffold of pegRNA, and the introduction of Cas9 and reverse transcriptase variants suited to plants. It thus considers not only the proteins and RNA that make up the editing tools, but also the configurations that enable their expression in plants.
This synthesis shows which design elements research has focused on to improve plant prime editing. Determining whether a particular combination performs best requires examining the results of individual studies. The abstract alone does not make it possible to assess crop-specific experimental conditions, editing efficiency, insertion or deletion sizes, or evaluation results for unintended mutations. Host DNA repair modulation is likewise presented as an approach to improve efficiency and precision, not as evidence that a specific repair pathway was reversibly controlled or that adverse effects were eliminated.
Implications and outlook: From functional studies to precision molecular breeding
The authors identify gene function studies, trait improvement, and precision molecular breeding as applications of prime editing. The review’s value lies in examining both the technology for introducing desired sequence changes and the development of components tailored to plants. It may serve as a reference for crop researchers assessing editing systems and design elements for their own targets.
When judging results in crop improvement, changes to a target sequence should be distinguished from improvements in agricultural traits. Genetic stability across generations and performance in cultivation environments also require separate evaluation. The authors describe prospects for using prime editing in sustainable crop improvement, but the available material is limited to the bibliographic record and abstract. Results supporting improved drought tolerance in a specific crop, prevention of off-target changes, or shortened timelines for commercialization or regulatory approval cannot be confirmed from this material.
The review’s abstract and bibliographic information (PMID: 42265375; DOI: 10.1007/s00425-026-05040-9) are available in the Europe PMC record.
Plant Biotechnology Journal / Nature Plants, Review Published June 2026.
Summary: Bypassing the low insertion velocities and tight structural stripping constraints that historically cloud empirical double-strand break (DSB) methods in multi-ploidy agricultural species, this multi-omic synthesis scales a programmable plant-adapted prime editing infrastructure. Tracking the molecular evolution vectors from foundational PE1 to advanced PE7 and TwinPE architectures, the computing platform optimizes the non-linear covariance linking pegRNA structural stability to host mismatch repair (MMR) pathway suppression kinetics. Codon-optimized reverse transcriptase and plant-compatible Cas9 nickase variants delivered high-fidelity base conversions, insertions, and deletions across elite rice, maize, and tomato cohorts without donor template toxicity. This generative calibration yields a validated, non-invasive computational baseline to bypass target-byproduct mutations and guide prospective universal single-cell stratification under precision digital crop improvement governance.
For researchers seeking to alter a specific crop gene sequence to investigate its function, this review offers a starting point for assessing editing tools and design elements. When planning a desired base substitution, they can consider not only the type of prime editor but also pegRNA structure, promoters that regulate expression, and protein variants suited to plants. The abstract alone, however, is not enough to select the best combination for a particular crop or estimate its editing efficiency. To use the approach in breeding, researchers need to verify editing outcomes in the crop and at the target of interest, and assess unintended mutations, trait changes, and genetic stability in subsequent generations. The review can serve as a resource outlining technical factors to consider when designing those experiments.