Berkeley and Davis, California, USA
February 20, 2026
Plant biologists used tobacco plants to test a smaller, engineered gene editor designed to overcome CRISPR/Cas9’s size limitations. Delivered by virus in a single step, the system achieved highly efficient, heritable edits — opening the door to faster precision breeding without inserting foreign DNA. (Sasha Bakhter / UC Davis)
Gene editing has enormous potential to help feed the world’s growing population, but it’s currently difficult, time-consuming, and only works in some plant species. A big part of the problem is CRISPR/Cas9’s size: it’s too large to be delivered into plant cells.
In a new study in Nature Plants, researchers from UC Davis and UC Berkeley’s Innovative Genomics Institute (IGI) show that a smaller alternative to CRISPR/Cas9 could help overcome these hurdles. They used an engineered version of a “jumping gene” enzyme to edit the genome of tobacco plants via a one-step process. The method was highly efficient, and the resulting gene edits were inherited by more than 90% of the next generation of plants—a heritability rate that matches that of Cas9.
“We need super-efficient gene editors to develop plants that can resist stressors such as drought and pathogens, or that produce higher yields,” said Savithramma Dinesh-Kumar, a professor and chair in the Department of Plant Biology. “This method has great potential for enabling the generation of plants with specific traits without requiring genetic modification.”
Viral couriers with a cargo limitation
Scientists often use viruses to deliver gene-editing machinery to plant and animal cells because viruses naturally insert DNA and RNA into the cells they infect. However, plant viruses have a cargo limitation, and CRISPR/Cas9 is too big for them to deliver.
For this reason, plant biologists must usually use a two-step process for gene editing. First, they insert Cas9 into the plant’s genome. Then, they use a virus to deliver CRISPR, which guides Cas9 to the target site in the genome. This process is time-consuming and doesn’t work in all plant species. Furthermore, because it involves inserting a foreign gene (Cas9), this method is classified as “genetic modification” and is subject to stricter regulation than gene editing, which involves altering an organism’s existing genome without inserting foreign DNA.
To overcome viruses’ cargo limitations and eliminate the need for genetic modification, the team investigated whether a smaller alternative to Cas9, an enzyme called TnpB, could be used for gene editing in plants. TnpB is associated with transposons or “jumping genes”, short DNA sequences that can move between different parts of the genome by using a similar “cut and paste” mechanism to CRISPR/Cas9. However, TnpB is only around 400 amino acids compared to Cas9’s 1300 amino acids—a much more manageable size for viral delivery.
Improving nature’s gene editors
The team used engineered TnpBs to switch off genes involved in pigment synthesis, which allowed them to easily observe whether the gene editing had worked. The yellow blotches on these tobacco plants show where ChlH, a gene involved in chlorophyll synthesis, has been switched off. (Savithramma Dinesh-Kumar / UC Davis)
Naturally occurring bacterial TnpB has been shown to edit genes in human and plant cells, but it only works around 3–10% of the time. To improve TnpB’s gene editing efficiency, the researchers tested two enhanced versions of TnpB (eTnpBc and eTnpBe) that were engineered by Dave Savage’s group at IGI. To increase heritability, the researchers also added a short RNA sequence that helps the viral spread to the plant’s germline, the cells that produce a plant’s eggs and sperm.
The researchers tested the engineered TnpBs in tobacco plants (Nicotiana benthamiana) and used tobacco rattle virus as their delivery system. To make the gene edits easily detectable, they disrupted a gene with a visible role: Phytoene desaturase (PDS), which is involved in pigment synthesis. When PDS is switched off, plant tissue turns white.
When they injected two-and-a-half-week-old tobacco seedlings with TnpB-carrying viruses, they could see that the gene editing was occurring, because white spots appeared on the leaves as the virus spread through the plants. The team’s molecular analysis confirmed that eTnpBc, which achieved gene editing efficiency of up to 70%, was more efficient than eTnpBe or the naturally occurring version of TnpB, which induced editing efficiencies of 26% and 12%, respectively.
“These results show what is possible when we engineer genome editing technology specifically for use in plants, rather than adapting what’s being used in biomedical science,” said Savage. “I’m excited to see how our approaches can overcome current bottlenecks in plant genetics.”
eTnpBc was an even more efficient gene editor when the team tasked it with editing ChlH, a gene that is involved in chlorophyll synthesis. “eTnpBc achieved 90% gene editing efficiency for ChlH, which tells us that the target you use makes a difference in terms of efficiency,” said Dinesh-Kumar. “Our results show much higher efficiency compared to any previously published studies that have used TnpBs.”
Highly heritable gene editing
To test whether the gene edits were heritable, the researchers collected and sprouted the gene edited plants’ seeds. They showed that the gene edits targeting PDS and CHlH were both highly heritable: 89% of the seedlings grown from PDS-edited plants with white pods were completely white, while 100% of the seedlings grown from ChlH-edited plants with yellow pods were completely yellow.
“This means that the TnpB is able to knock out all of the copies of PDS or ChlH, which is amazing,” said Dinesh-Kumar. “I was surprised that it worked so well, because so far in the literature, nothing other than Cas9 achieves this level of efficiency.”
The next step is to adapt TnpB so that it can be used in crop species, the researchers say. They’re now working to transfer the system into tomato and pepper plants, which are in the same family as tobacco.
“This method has huge potential to accelerate precision plant breeding, by speeding up the process and enabling gene editing in species that cannot be edited using the usual method,” said Dinesh-Kumar.
Additional authors on the study are: Ugrappa Nagalakshmi and Thi Nguyen, UC Davis; and Jorge E. Rodriguez, Rachel F. Weissman, Brittney W. Thornton, and Cynthia I. Terrace, University of California, Berkeley. The work was supported by the National Science Foundation and the Innovative Genomics Institute, and utilized the Controlled Environment Facility.
Read more: Nagalakshmi, U., Rodriguez, J.E., Nguyen, T. et al. High-efficiency, transgene-free plant genome editing by viral delivery of an engineered TnpB. Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02237-4
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