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Wild Tomatoes Still Hold the Flavor We Bred Away: New Map Shows Breeders Where to Look

posted by mrcoolbp on Tuesday October 13, @05:29PM

hubie writes:

https://btiscience.org/wild-tomatoes-still-hold-the-flavor-we-bred-away-new-map-shows-breeders-where-to-look/

Modern tomatoes are a breeding success story. Generations of selection have made them bigger, firmer, more productive, and easier to ship. But that progress came at a cost. Domestication and breeding reduced much of the crop's genetic diversity, and flavor has proven stubbornly hard to breed back in.
Tomato's wild relatives still carry much of what was lost. Some pack their fruit with high levels of the red pigment lycopene, and some store sugar differently. Others, like Solanum pennellii and Solanum neorickii, never turn red at all. Breeders have long wanted to know which genetic controls produce these traits, and which ones are worth bringing back.
A new study by researchers at the Boyce Thompson Institute (BTI) offers a detailed map of those controls. The team compared how genes behave in cultivated tomato and three wild relatives, across different fruit tissues and stages of development and ripening. That let them pinpoint the genetic "dimmer switches" behind color, sweetness, bitterness, and aroma, giving breeders a list of targets for developing tastier, more nutritious tomatoes.
[...] "Wild tomatoes are an enormous reservoir of diversity for flavor, nutrition, and resilience, 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. This can be countered with precise information on how the genes responsible for such traits are controlled," said Catala.
Think of each gene as a lamp. Some shine brightly, some glow faintly, and how bright they are shapes how a fruit grows, ripens, and tastes. Something can change a lamp's brightness in two ways.
One is through a dimmer built into the lamp itself. Scientists call this a cis effect: a change in the section of DNA sitting right next to the gene, which controls how strongly that one gene turns on. The other is through the building's wiring. That's a trans effect: a change somewhere else in the genome that alters the power supply, often affecting many genes at once.

[Continues...]

From the outside, the two look the same, because either one makes a lamp dimmer or brighter. To tell them apart, the team crossed cultivated tomato with each wild species to produce hybrid plants. A hybrid carries one copy of every gene from each parent, and both copies operate within the same cells. In effect, it plugs the cultivated lamp and the wild lamp into the same outlet, on the same wiring.
"The hybrid gives us a natural controlled experiment," said Fei. "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."
[...] The regulatory map helps explain several well-known fruit traits. In the green-fruited species, cis changes boost genes that steer the pigment pathway away from lycopene, the red pigment that gives tomatoes their color and much of their nutritional value. That explains why these fruits stay green.
A matched pair of sugar-related genes explains the difference in sweetness. A gene that breaks down sucrose and another gene that blocks this process are regulated in a coordinated way in the green-fruited species, allowing those fruits to retain more sucrose.
The data also show a developmental switch for bitterness. Early in fruit development, trans regulation helps maintain high levels of bitter, defensive compounds called glycoalkaloids in young fruit. Later, cis changes in cultivated tomato turn those compounds into non-bitter forms as the fruit ripens—a pattern described in the study as "defense early, edibility at maturity."
"Breeders have always known wild tomatoes hold valuable traits, but their use in breeding introduces undesirable traits as well, necessitating time- and labor-intensive cleanup," said Giovannoni. "What they've lacked 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, at specific moments in fruit development and ripening."
The team has made its data, including two newly assembled wild tomato genomes, freely available, giving breeders and researchers worldwide a head start on bringing the best traits of wild tomatoes back to the table.

Journal Reference: Zhao, J., Nicolas, P., Xu, Y. et al. Allele-specific expression reveals complex regulatory divergence underlying fruit phenotypic differences between cultivated and wild tomato species. Genome Biol (2026). https://doi.org/10.1186/s13059-026-04279-5

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