By comparing gene activity in hybrids, researchers pinpoint the regulatory switches behind color, sweetness and bitterness in wild tomato relatives.

The modern supermarket tomato is a triumph of breeding: large, firm, uniform and tough enough to survive a long trip in a truck. What it often lacks is taste. Generations of selection for yield and shelf life narrowed the crop’s genetic diversity, and flavor has proven hard to win back.

Wild relatives of the tomato never went through that bottleneck. “Wild tomatoes are an enormous reservoir of diversity for flavor, nutrition, and resilience,” said Carmen Catala, a senior research associate at the Boyce Thompson Institute (BTI), an independent research institute affiliated with Cornell University. “But bringing those traits into modern varieties can come at the expense of other traits that breeders have spent decades improving, like yield, fruit size, or shelf life.”

The solution, she said, is better information: “This can be countered with precise information on how the genes responsible for such traits are controlled.” A new study in Genome Biology from Catala and colleagues provides exactly that kind of map.

A natural experiment in every cell

The team crossed cultivated tomato with three wild species: Solanum pimpinellifolium, the wild species closest to the domesticated crop, and the more distant S. neorickii and S. pennellii. In the resulting hybrids, each gene exists in two versions, one inherited from each parent.

“The hybrid gives us a natural controlled experiment,” said Zhangjun Fei, a professor at BTI. “Both versions of each gene sit in the same cells and receive the same regulatory signals. If one version is more active than the other, we know the difference is written into the DNA right next to that gene.”

Those nearby changes are known as cis effects. Changes elsewhere in the genome that influence a gene’s activity, such as differences in the proteins that switch genes on and off, are called trans effects. The researchers measured gene activity in three fruit tissues, the fleshy outer wall, the placenta and the gel around the seeds, at up to four stages from early development through ripening.

Mostly local switches

Cis changes dominated. They affected up to 23.5 percent of active genes, while trans changes affected no more than 4.6 percent. The number of genes with regulatory differences roughly doubled in the more distant wild species compared with S. pimpinellifolium, and many of the switches were active only in one tissue at one moment in development.

The map explains several familiar traits. In the green-fruited wild species, cis changes boost genes that divert the pigment pathway away from lycopene, the red pigment of ripe tomatoes, which is why those fruits stay green. In the same species, a gene that breaks down sugar and another that blocks that process are regulated in tandem, helping the fruit hold on to more sucrose.

Bitterness follows a neat developmental logic. Trans regulation keeps bitter compounds called glycoalkaloids high in young fruit, deterring pests, while in cultivated tomato cis changes convert those compounds into non-bitter forms as the fruit ripens. The release sums it up as defense early, edibility at maturity.

Targeted breeding

“Breeders have always known wild tomatoes hold valuable traits,” said James Giovannoni, an adjunct professor at BTI and a USDA scientist, “but their use in breeding introduces undesirable traits as well, necessitating time- and labor-intensive cleanup.” What breeders have lacked, he said, “is a way to tell which of thousands of genetic differences is behind each trait to make selection more targeted.”

“Now we can point to specific genes for selection, with effects in specific tissues,” Giovannoni said, “at specific moments in fruit development and ripening.”

The team also assembled two new wild tomato genomes, and all of the data are freely available to breeders and researchers.

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Notes

1. “Allele-specific expression reveals complex regulatory divergence underlying fruit phenotypic differences between cultivated and wild tomato species.” Genome Biology, 12 September 2026. DOI: 10.1186/s13059-026-04279-5.
2. Boyce Thompson Institute. “Wild tomatoes still hold the flavor we bred away: new map shows breeders where to look.” EurekAlert!, 29 September 2026. https://www.eurekalert.org/news-releases/1145917.

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