The mass-produced tomatoes we buy at the grocery store tend to taste more like cardboard than fruit. Now researchers have discovered one reason why: a genetic mutation, common in store-bought tomatoes, that reduces the amount of sugar and other tasty compounds in the fruit.

For the last 70-odd years, tomato breeders have been selecting for fruits that are uniform in color. Consumers prefer those tomatoes over ones with splotches, and the uniformity makes it easier for producers to know when it’s time to harvest.

But the new study, published this week in Science, found that the mutation that leads to the uniform appearance of most store-bought tomatoes has an unintended consequence: It disrupts the production of a protein responsible for the fruit’s production of sugar.

Mass-produced tomato varieties carrying this genetic change are light green all over before they ripen. Tomatoes without the mutation — including heirloom and most small-farm tomatoes — have dark-green tops before they ripen. There is also a significant difference in flavor between the two types of tomatoes, but researchers had not previously known the two traits had the same root cause.

The study authors set out to pin down the genetic change that makes tomatoes lose their dark-green top. They focused their attention on two genes — GLK1 and GLK2 — both known to be crucial for harvesting energy from sunlight in plant leaves.

They found that GLK2 is active in fruit as well as leaves — but that in uniformly colored tomatoes, it is inactivated.

Adding back an active GLK2 gene to bland, commercial-style tomatoes through genetic engineering created tomatoes that had the heirloom-style dark-green hue. The darker green comes from greater numbers of structures called chloroplasts that harvest energy from sunlight.

The harvested energy is stored as starches, which are converted to sugars when the tomatoes ripen.

The vast majority — 70% to 80% — of the sugar in tomatoes travels to the fruit from the leaves of the plant. But the remaining amount of sugar is produced in the fruit. This contribution is largely wiped out in uniform, commercial-style tomatoes — and thus they won’t be as sweet.

Study coauthor Ann Powell, a biochemist at UC Davis, noted that this isn’t the only cause of the uninspiring flavor of modern mass-produced tomato varieties, but said it definitely contributes.

Though the scientists were not even able to taste their own creation because ofU.S. Department of Agricultureregulations, they could show through chemical tests that the sugar levels were 40% higher in their engineered fruit. Chemicals called carotenoids, which also significantly contribute to flavor, were more than 20% higher.

But don’t expect to find a tastier, transgenic tomato based on this finding on store shelves anytime soon. Plant biologist Jim Giovannoni of Cornell University, a study coauthor, said that such a product is unlikely to be developed.

“There are very few examples of genetically modified fresh-market fruit crops,” he said. Most such crops are corn and soy varieties that have been bred to resist viruses and pests, not fruits and vegetables sold on store shelves.

Still, the results could lead breeders to slightly change the way they select tomatoes for production, Giovannoni added.

“There will probably continue to be selection for uniform tomatoes,” he said. But “now that it’s known that this mutation has negative consequences, you may find that growers begin selecting for fruit that is uniformly darker green, rather than uniformly lighter green.”

Harry Klee, a specialist in the chemistry of fruit flavor at the University of Florida who was not involved in the study, said the work was a good step toward a better understanding of tomato flavor.

“This is not the entire reason the modern tomato stinks — but it’s a real significant part of it,” he said. “I promise you, if I gave you two tomatoes that were 10% different in their sugar contents, you’d be able to tell the difference.... This is a very nice piece of science that really illustrates the pitfalls of breeding without knowing precisely what you’re doing.”

The lesson for consumers is that tomatoes with less-uniform hues are a better flavor bet.

“If this information gets out there, you could see people saying, ‘If I see this tomato is not uniformly ripe, that means that it’s not the cardboard junk that they’ve been producing for the past 30 years,’” Klee said.

“It’s almost like a badge of honor.”

jon.bardin@latimes.com