Successful development and application of a comprehensive gene editing system (Prime editing) for restoring mutated gene function in rice

08/04/2025

The emergence and advancement of gene editing technology through the CRISPR/Cas system have led to groundbreaking achievements across various research fields, from fundamental studies to applied sciences worldwide. Scientists continue to refine and develop new gene-editing systems with higher efficiency and comprehensiveness. Prime editing, a novel genome editing tool developed in 2019, has been recognized for its superior precision and flexibility compared to traditional gene-editing systems such as CRISPR/Cas9, CRISPR/Cas12, or base editing. This Prime editing technology enables a wide range of DNA modifications, including multiple nucleotide substitutions, precise DNA insertions, and targeted DNA deletions. However, in plants, the application of Prime editing remains in its early stages, with successful implementation being limited to a few laboratories due to the system’s relatively low gene-editing efficiency.

Recently, Dr. Nguyen Xuan Cuong and colleagues at the Plant Cell Technology Laboratory, Institute of Biotechnology – Vietnam Academy of Science and Technology, have successfully improved and developed the Prime editing system to enhance rice quality traits. This achievement stems from the research project titled "Attracting Young Scientists to Work at the Vietnam Academy of Science and Technology" (Project Code: THTNTE.01/24-25), led by Dr. Nguyen Xuan Cuong. During the project, the research team developed the dual Prime editing system TwinPE, combined with optimized pegRNA expression sequences, boosting gene-editing efficiency to 44.2%—four times higher than conventional Prime editing systems. Notably, in this study, the team employed Prime editing to precisely insert a 14bp DNA sequence to restore the function of the Rc gene, which regulates grain color and flavonoid compounds in the model rice variety Kitaake. The accuracy and efficiency of the Prime editing system were validated through genetic sequencing analysis, grain color transformation, and the expression of related genes.

Prime Editing System and modified model for restoring the mutated Rc gene in rice varieties

This research breakthrough presents significant opportunities for fundamental gene function studies and crop improvement in Vietnam. It also serves as a scientific foundation for advancing Prime editing technology in other essential crop species both in Vietnam and globally. The research findings have been published by the authors in a prestigious Q1-ranked journal on plant cell and genetic technology, Plant Cell Reports (2025) 44:57 https://doi.org/10.1007/s00299-025-03450-9.

Gene sequence analysis of edits made using the Prime editing system (A).
Rice grain color transformation following the restoration of Rc gene function (B).
Growth and development of gene-edited rice plants in a greenhouse environment.

Translated by Phuong Huyen
Link to Vietnamese version