For decades, farmers have faced a trade-off between size and flavor when growing tomatoes and eggplants. The hefty tomatoes stacked in supermarkets today may be impressive in size, but many consumers lament their lack of flavor. Meanwhile, smaller, wild varieties burst with sweetness but remain impractical for large-scale farming. Now, scientists say they have cracked the genetic code to finally get the best of both worlds.

A pair of recent studies, one led by researchers at Johns Hopkins University and Cold Spring Harbor Laboratory and another by scientists at the Agricultural Genomics Institute in China, reveal key genes that govern both the size and sugar content of tomatoes. By tweaking these genes, the first group grew larger tomatoes while the second made sweeter variants. This exciting series of developments could reshape global agriculture by making tomatoes and eggplants more appealing to both farmers and consumers.

The Key to Bigger Fruits

For the Johns Hopkins study, researchers mapped the genomes of 22 crops in the nightshade family, including tomatoes, potatoes, and eggplants. “Over tens of millions of years, there’s this constant churn of DNA sequences being added and lost,” said Michael Schatz, a geneticist at Johns Hopkins. “The same process can occur for gene sequences, where entire genes duplicate or disappear.”

In simple terms, gene duplications allow plants to evolve in unpredictable ways. Some duplicated genes become inactive relics, while others take on entirely new functions. This means that a genetic tweak that works in one species might fail—or cause unintended changes—in another.

One of the gene duplicates, called CLV3, was found to influence fruit size. By using CRISPR-Cas9 gene-editing technology, scientists tweaked copies of the gene in forest nightshade native to Australia. When both copies were turned off, the results were bizarre— “weird, bubbly, disorganized” fruit that were unfit for commercial use. But when only one copy was edited, the result was larger, more uniform fruit.

The researchers also examined an African eggplant species and identified a gene called SaetSCPL25-like, which controls the number of seed cavities, or locules, inside the fruit. More locules meant bigger eggplants. When the team introduced the gene into tomatoes, they grew out of proportion.

Solving the Sweetness Problem

While the Johns Hopkins study focused on size, a separate team in China tackled another major issue—flavor.

Scientists at the Agricultural Genomics Institute in Shenzhen discovered two genes that act as “sugar brakes” in tomatoes, limiting their sweetness during ripening. While wild tomatoes naturally produce small, intensely sweet fruit, the cultivated varieties grown for commercial use prioritize size and yield instead.

Using CRISPR once more, the researchers disabled these sugar-limiting genes, allowing tomatoes to retain up to 30% more sugar without sacrificing size or yield. “As farmers want larger tomatoes and higher yield, the consumers want sweeter tomatoes,” said Sanwen Huang, who led the study. “Our discovery of the sugar brake genes leads to [breeding of a] sweeter tomato without sacrificing fruit size and yield, breaking the negative relationship between yield and quality.”

The implications could be enormous. If gene-edited tomatoes become widely accepted, supermarkets may soon offer tomatoes that are not only large but also taste as good as their wild ancestors. According to Huang, sweeter varieties could appear on shelves within three to five years. Even though regulatory hurdles remain, countries like Japan are already enjoying gene-edited tomatoes.

A New Era of Crops

These genetic breakthroughs are part of a growing movement to rethink crop breeding. Traditional selective breeding has long forced trade-offs between size and flavor. But the future is here, and there’s a way around these constraints as scientists fine-tune crops to meet both agricultural and consumer demands.

And tomatoes are just the beginning. By studying many species together, scientists are uncovering new genetic pathways that could be applied to a range of crops. “We call this ‘pan-genetics,’” Schatz explained. “It opens endless opportunities to bring many new fruits, foods, and flavors to dinner plates around the world.”

Both studies appeared in the journal Nature (first and second).