A team of scientists in China has developed a genome engineering platform that can stack multiple favorable traits into a single crop variety at a speed and scale that existing tools cannot match.
The platform, called TRIM, was developed by a team led by Gao Caixia at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences. The study was published in Nature Biotechnology on June 5, according to a report by Phys.org. It targets rice, wheat, and maize, three of the world's most important food crops.
Trait stacking, the process of combining multiple desirable genetic characteristics into one plant variety, is a central goal of modern crop breeding. A disease-resistant crop that also tolerates drought and produces higher yields is worth far more than a plant engineered for just one of those traits. But current methods for achieving that kind of stacking are slow and often inefficient, requiring multiple rounds of editing and crossing.
The foundation of the TRIM platform is a new gene knockout tool called twin prime editing-mediated gene knockout, or TKO. Standard gene editing using Cas9 systems can produce unpredictable results when multiple genes are targeted at once, because mutations can accumulate in ways that cancel each other out or reduce effectiveness. TKO avoids that problem by inserting a small fragment containing a stop codon cluster at a precise target site, which disrupts the gene in a controlled and predictable way.
In tests on regenerated rice plants, TKO achieved an average single gene knockout efficiency of 96.8 percent. The researchers also developed 10 separate orthogonal TKO systems, which allowed them to knock out up to 10 genes simultaneously without the editing of one gene interfering with another.
From there, the team built two integrated platforms on top of TKO. TRIM1 combines the knockout tool with prime editing, allowing a researcher to simultaneously knock out one gene while also making precise substitutions, insertions, deletions, duplications, or inversions at three additional targets. In regenerated rice plants, TRIM1 achieved that four-way simultaneous editing with an efficiency of 22.8 percent.
TRIM2 adds a prime editor fused to a Cre recombinase protein, which opens the door to much larger-scale changes. That includes kilobase-scale DNA insertions, replacements, deletions, inversions, and even chromosomal translocations, where segments of DNA are moved between chromosomes. That kind of large-scale chromosome engineering has historically been difficult to achieve in crop plants.
Together, the two platforms form the unified TRIM system. Unlike existing genome editing tools that are generally limited to one category of modification at a time, TRIM integrates small-scale precise edits and large-scale chromosome engineering within a single framework. The researchers describe it as an all-in-one approach to rapidly stacking multiple favorable traits into a crop variety.
The work was carried out in protoplasts as well as in regenerated plant lines, and the results held across rice, wheat, and maize, suggesting the platform could be broadly applicable to major grain crops rather than limited to a single species.
