Bigger, tastier tomatoes and eggplants may soon become a reality thanks to groundbreaking genetic research by scientists at Johns Hopkins University and Cold Spring Harbor Laboratory. By identifying key genes responsible for fruit size, this discovery has the potential to revolutionize agriculture and expand global food production, especially in regions where local varieties have remained too small for large-scale farming.
The study, recently published in Nature, provides critical insights into the genetics of fruit development. It is part of a larger initiative to map the complete genomes of 22 nightshade crops, including tomatoes, potatoes, and eggplants. This research could lead to the creation of new heirloom varieties, improving both yield and quality for farmers and consumers alike.
According to Michael Schatz, a geneticist at Johns Hopkins University and co-lead author of the study, gene editing can have a transformative impact. “Once you’ve done the gene editing, all it takes is one seed to start a revolution,” he explained. “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.”
To better understand how fruit size is controlled at the genetic level, the researchers analyzed the genomes of different nightshade species using advanced computational tools. Their findings revealed that over millions of years, genes responsible for fruit development had undergone duplications. These duplications, known as paralogs, often resulted in significant changes to the traits of the plants.
“Over tens of millions of years, there’s this constant churn of DNA sequences being added and lost,” Schatz explained. “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 explore these genetic changes further, the team at the Boyce Thomson Institute employed CRISPR-Cas9 gene-editing technology to modify specific paralog genes. Meanwhile, collaborators at Cold Spring Harbor Laboratory cultivated the engineered plants, closely observing the effects of the genetic tweaks. Their experiments revealed that paralog genes play a crucial role in determining key plant traits, such as flowering time, fruit size, and fruit shape.
One of the most striking findings involved the CLV3 gene paralogs in Solanum linnaeanum, a wild Australian nightshade species. When both copies of this gene were turned off, the resulting plants produced deformed, “weird, bubbly, disorganized” fruits that were not viable for commercial production. However, by selectively editing just one copy of the CLV3 paralog, the researchers were able to produce larger, more desirable fruits. This discovery demonstrates the precision required in genetic modifications to ensure beneficial outcomes.
“Having full genome sequences for these species is like having a new treasure map,” said Katharine Jenike, a former Ph.D. student in Schatz’s lab who assembled the genome sequences. “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. They allowed us to find the size-genes in a really unexpected place.”
Another major breakthrough came from research on the African eggplant (Solanum aethiopicum), a species widely grown across Africa and Brazil for its edible fruits and leaves. The scientists identified a gene called SaetSCPL25-like, which controls the number of seed cavities, or locules, inside the fruit. When they edited this gene in tomato plants, they found that increasing the number of locules resulted in larger tomatoes. This discovery could be applied to breeding strategies to enhance fruit size in both eggplants and tomatoes, potentially leading to bigger, juicier crops.
Understanding the genetic basis of fruit size is more than just an academic achievement—it has direct implications for agriculture and food security. By leveraging genetic insights from multiple species, scientists can improve crops in ways that were previously unimaginable. The concept of “pan-genetics,” as Schatz calls it, highlights how studying diverse species together can accelerate progress in crop improvement.
“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.”
The potential benefits of this research extend far beyond academic curiosity. In regions where local eggplant varieties are too small to be commercially viable, these genetic advancements could help farmers cultivate larger, more marketable crops. The ability to fine-tune fruit size and shape could also improve harvesting efficiency and reduce food waste, contributing to more sustainable agricultural practices.
However, the success of gene-edited crops will depend on regulatory approvals and public acceptance. While genetic engineering has proven to be a powerful tool in agriculture, concerns over genetically modified organisms (GMOs) persist in many parts of the world. Scientists will need to work closely with policymakers, farmers, and consumers to ensure that these innovations are introduced responsibly and transparently.
If successfully implemented, this research could redefine the way we grow and consume staple crops. By harnessing the power of genetics, scientists are not only improving agricultural productivity but also opening new possibilities for global food security. With continued advancements in genome mapping and gene editing, the dream of bigger, tastier tomatoes and eggplants is becoming an achievable reality.
More information: Zachary Lippman, Solanum pan-genetics reveals paralogues as contingencies in crop engineering, Nature (2025). DOI: 10.1038/s41586-025-08619-6. www.nature.com/articles/s41586-025-08619-6