GAINESVILLE, Fla.  — Tasty tomatoes can be hard to come by, but scientists are starting to unravel clues about how to put the flavor back into one of the nation’s most beloved vegetables.

Professor Harry Klee of the University of Florida’s horticultural sciences department discovered the gene that helps filter the enzymes, or proteins, that make a tomato taste sweet and juicy instead of watery.

“Most people feel that the quality of the supermarket tomato leaves much to be desired. What we want to do is in a nutshell help the breeders make a better-tasting tomato,” Klee said. “In order to do that, we have to identify the genes that control the components of flavor.”

The gene that Klee recently discovered, called CXE1, controls a protein by the same name that triggers chemical reactions in a tomato that remove its bad-tasting compounds.

“There’s a huge range of flavor components out there in the tomato world. Our goal is to identify the best versions of these genes,” Klee said. “Our ultimate goal is to assemble a tool kit for the breeder.”

Klee compares the process of selecting for good tomatoes to the Human Genome Project, which identifies genes that make people susceptible to certain diseases.

Another potential outcome of the Human Genome Project, albeit a controversial one, is the ability to select good genes for positive traits — in other words, to potentially design people.

“We’re doing the same with plants,” Klee said. “We’re giving the breeder the genetic tools to pick out the best versions that he or she needs.”

Breeders have traditionally focused on external factors that influence taste such as soil quality or disease-resistant vines, Klee added. “What we’re trying to do is give (breeders) the ability to go back 100 years. The flavor was always there,” Klee said. “We just lost it because we haven’t been able to select for it.”

One of the challenges to making a good-tasting tomato is meeting year-round market demand. “It’s hard to get a good tomato into the marketplace 12 months a year,” said Jay Scott, a professor in horticulture department at UF/IFAS Gulf Coast Research and Education in Wimauma.

Not all tomato growers are trying to get a better breed, however. Rusty Ludlam, a farmer from Suwannee County who sells tomatoes and other vegetables at Alachua County farmers markets, said the tomatoes he grows taste just as good as the tomatoes he grew up eating from his parents’ two-acre garden decades ago.

Ludlam said store-bought tomatoes have lost their flavor because people pick them prematurely and refrigerate them during shipping.

“They ripen and get soft. That’s why they don’t ship very well,” said Ludlam, adding that Heirlooms were later bred for firmness to be shipped.

And now that scientists are trying to turn back the clock and breed Heirlooms and other tomatoes back to their original form, Ludlam pointed out, “You’ve still got to ship them.”

And that may be a later challenge. But for now, “The challenge is to put the flavor back into something the commercial grower will actually want to grow,” Klee said. “Prices will fall, so everyone can buy tomatoes year-round.”