Tiny CRISPR tool opens door to faster, simpler plant genome editing

Plant breeding plays a vital role in ensuring global food security by increasing crop yields, improving nutritional quality and creating crops that are adaptable to climate change. However, current plant transformation methods present significant hurdles — they’re labor-intensive, costly and don’t work for many important plant species.

A breakthrough UCLA-led study, published in Nature Plants, overcomes these limitations by developing a streamlined method for heritable, transgene-free genome editing in plants using a miniature CRISPR system delivered by a common plant virus.

Collaborating with CRISPR-Cas9 co-inventor Dr. Jennifer Doudna and Dr. Jill Banfield at UC Berkeley, Dr. Steven Jacobsen, a distinguished professor of molecular, cell and developmental biology at UCLA, engineered the tobacco rattle virus to carry a compact CRISPR-like enzyme called ISYmu1 to target specific DNA sequences in the model mustard plant Arabidopsis thaliana. Importantly, the genome changes can be passed on to future generations and the novel system doesn’t leave behind the virus or any foreign DNA in the edited plant.

“CRISPR has the potential to make a huge impact in agriculture — one that can be customized to local needs around the world,” said Doudna, a Nobel laureate and founder of the Innovative Genomics Institute. “This study combined the strengths of my lab with our friends in the Jacobsen lab at UCLA to develop a new approach to precision CRISPR engineering in crops to help make that promise a reality.”

Jacobsen, the study’s senior author and a member of the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, breaks down why this technology represents a major advancement in plant breeding.

What are the key developments of this paper?

Our research team developed a miniature CRISPR system that uses the tobacco rattle virus to deliver gene-editing tools directly to the germ cells, or the reproductive cells, of the Arabidopsis thaliana plant, creating genetic changes that are passed on to future generations.

Plant breeding has long faced a critical bottleneck: efficiently delivering gene-editing tools to the right cells. Traditional methods require complex lab techniques where plant tissue is cultivated in petri dishes under specific conditions, modified one cell at a time and then regrown into complete plants — a process that takes years to develop for each plant species and simply doesn’t work for many valuable crops like the common bean. 

While plant viruses are a great delivery mechanism, conventional CRISPR systems are too large to be packaged into these viruses. We’ve overcome this size limitation by utilizing a CRISPR-like DNA-cutting enzyme that’s small enough to fit inside the tobacco rattle virus.

How did you reach these findings?

First, our team screened various miniature CRISPR systems in plant cells, identifying the compact enzyme ISYmu1 as our most effective gene-editing tool.

We then engineered the tobacco rattle virus to carry this tiny editor and used a natural soil bacterium to introduce the virus into Arabidopsis thaliana plants. Once inside, the virus spread throughout the plants, delivering the CRISPR system wherever it traveled.

Successful editing produced a clear visual marker — affected areas turned white, including seedlings, confirming the edits reached reproductive cells. Since plants naturally block viruses from entering seeds, only the DNA modification gets transmitted to the seeds and inherited by the next generation.

So, in one step and in just one generation, this system allows for the creation of perfectly normal plants except for the single intended DNA change.

What excites you about these developments?

This system marks the beginning of a new generation of genome-editing tools that can revolutionize crop improvement. If editing can be made more efficient in plants where current modifications are feasible and possible in previously unmodifiable plants, we can accelerate the development of crops with higher yields, enhanced nutritional profiles and better adaptation to climate change.

What makes this approach especially promising is that the tobacco rattle virus can infect over 400 plant species. So, we might be able to use this exact system for tomatoes and potentially many other important crops.

With my background in agriculture — growing up on an almond ranch in California and studying the field throughout my career — I recognize delivery as a major bottleneck in plant biotechnology. I’m particularly passionate about applying this technology to underinvested crops grown in developing countries, where traditional genome-editing techniques are just not available.

Can you talk about the collaboration with Dr. Jennifer Doudna and Dr. Jill Banfield, and how your labs’ areas of expertise are complementary?

This collaboration is a neat example of what’s possible when science is a team sport. Dr. Jennifer Doudna is an expert in CRISPR, Dr. Jill Banfield is an expert in screening through giant numbers of sequences for new CRISPR systems and I’m an expert in plants. The UC Berkeley labs specialized in the discovery and characterization of these tiny CRISPR systems, while our team screened those systems in plant cells and identified the optimal virus for the application. We’re excited to continue working together to refine this tool that could greatly improve plant breeding.

What are the next steps in the study?

We’re starting to test this technology in other plants, including important crops.

Currently, this system can only make one change to the plant DNA at a time. Our next step is to engineer the tool to develop multiplexing capability — allowing multiple genome edits at once.

We’re also focusing on improving efficiency. We plan to enhance both the CRISPR system itself and the frequency of infection to dramatically increase success rates.