CRISPR Breakthrough Unlocks the Genetic Blueprint for Super-Sized Produce

A genetic breakthrough may soon bring bigger and better tomatoes and eggplants to the world.

Scientists have mapped the genomes of nightshade crops, discovering key genes that determine fruit size. With CRISPR, they’ve unlocked ways to control these genes, paving the way for larger, tastier produce.

Bigger, Tastier Tomatoes on the Horizon

Bigger and more flavorful tomatoes and eggplants may soon become a reality, thanks to a team of scientists at Johns Hopkins University and Cold Spring Harbor Laboratory. Their research has identified key genes that influence fruit size, paving the way for new crop varieties that could enhance both taste and agricultural efficiency.

This breakthrough could lead to the development of improved heirloom tomato and eggplant varieties, particularly in regions where existing local crops are too small for large-scale farming. By enabling the cultivation of larger, more commercially viable produce, these discoveries have the potential to support global agriculture.

Findings were published today (March 5) in the journal Nature.

A Genetic Revolution in Agriculture

“Once you’ve done the gene editing, all it takes is one seed to start a revolution,” said co-lead author Michael Schatz, a geneticist at Johns Hopkins University who worked on the Telomere-to-Telomere human genome project. “With the right approvals, we could mail an engineered seed to Africa or anywhere it’s needed and open up entirely new agricultural markets. There’s huge potential to translate these advances into real-world impact.”

This research is part of a broader initiative to map the complete genomes of 22 nightshade crops, including tomatoes, potatoes, and eggplants, in an effort to better understand and enhance their genetic traits.

Using computational analysis, the researchers compared the genome maps and traced how the genes evolved over time: more than half, the researchers found, had been duplicated at some point in the past.

Unlocking the Secrets of Gene Duplication

“Over tens of millions of years, there’s this constant churn of DNA sequences being added and lost,” Schatz said. “The same process can occur for gene sequences, where entire genes duplicate or disappear. When we started looking, we noticed these changes were very widespread, but we didn’t yet know what those changes meant for the plants.”

To find out, collaborators at the Boyce Thomson Institute used CRISPR-Cas9 gene-editing technology to tweak one or both duplicates of a gene, and collaborators at Cold Spring Harbor grew the engineered plants to see how the tweaks changed the mature plants.

The genetic duplicates, or paralogs, ended up being important for determining traits like flowering time, fruit size, and fruit shapes. Turning off both copies of the CLV3 gene paralogs in the forest nightshade native to Australia, for example, resulted in plants that the researchers described as “weird, bubbly, disorganized” shapes—not viable to sell as produce in grocery stores. But careful editing of just one copy of CLV3 led to larger fruits.

A Treasure Map of Genetic Secrets

“Having full genome sequences for these species is like having a new treasure map. We can see where and when one genetic path diverges from another and then explore that place in the genetic information where we wouldn’t have thought to look,” said Katharine Jenike, who assembled the genome sequences and was a PhD student in Schatz’s lab at the time of the research. “They allowed us to find the size-genes in a really unexpected place.”

In the African eggplant, a species grown across the African continent and in Brazil for its edible fruits and leaves, the researchers identified a gene, SaetSCPL25-like, that controls the number of seed cavities, or locules, inside the fruit. When they edited the SaetSCPL25-like genes in the tomato plant, the researchers found they could grow tomatoes with more locules: the more numerous the locules, the bigger the tomato.

The discovery could usher in a new era of tasty tomatoes, if done properly, the researchers said.

A Future of Flavorful, Plentiful Produce

“This work shows the importance of studying many species together,” Schatz said. “We leveraged decades of work in tomato genetics to rapidly advance African eggplants, and along the way we found entirely new genes in African eggplants that reciprocally advance tomatoes. We call this ‘pan-genetics,’ and it opens endless opportunities to bring many new fruits, foods, and flavors to dinner plates around the world.”

Reference: “Solanum pan-genetics reveals paralogues as contingencies in crop engineering” by Matthias Benoit, Katharine M. Jenike, James W. Satterlee, Srividya Ramakrishnan, Iacopo Gentile, Anat Hendelman, Michael J. Passalacqua, Hamsini Suresh, Hagai Shohat, Gina M. Robitaille, Blaine Fitzgerald, Michael Alonge, Xingang Wang, Ryan Santos, Jia He, Shujun Ou, Hezi Golan, Yumi Green, Kerry Swartwood, Nicholas G. Karavolias, Gina P. Sierra, Andres Orejuela, Federico Roda, Sara Goodwin, W. Richard McCombie, Elizabeth B. Kizito, Edeline Gagnon, Sandra Knapp, Tiina E. Särkinen, Amy Frary, Jesse Gillis, Joyce Van Eck, Michael C. Schatz and Zachary B. Lippman, 5 March 2025, Nature.
DOI: 10.1038/s41586-025-08619-6

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