The typical supermarket tomato: ripe red, firm to the touch, free of blemishes—and of flavor. Since at least the 1970s, U.S. consumers have lamented the beautiful but bland fruits that farmers breed not for taste, but rather for high yield and durability during shipping. Recently, organic farmers and foodies have championed the superior flavors of heirloom tomatoes—older varieties that come in an assortment of shapes, sizes and colors. In a new study, researchers took a close look at the chemical composition of both standard tomatoes and hundreds of different heirloom varieties, which they also fed to 170 volunteers in a taste test. Their new findings confirm what scientists have learned in recent years: a tomato's flavor depends not only on the balance of sugars and acids within the fruit, but also on subtle aromatic compounds—many of which are lacking in the modern supermarket tomato. In the future the researchers hope to work with seed companies and farmers to breed tomatoes that produce large quantities of flavorful fruits packed with aromatic compounds—a healthier solution than engineering super-sugary tomatoes.

Although many people regard the tomato as a vegetable, the crimson orbs are the berries of the tomato plant; like most fruit, they develop from flowers and contain seeds. The tomato plant originated in South America—likely in Peru—and first spread across Mexico and Central America, where one of the earliest varieties grown for food probably looked like a yellow cherry tomato. Once European explorers introduced the plant to the Old World, the people of Spain, Italy and France soon began to eat the tomato regularly—although they also used the bright fruit as table decor. In the late 16th century barber–surgeon and herbalist John Gerard convinced most of England that the tomato was poisonous, but his fellow countrymen—along with the rest of the world—learned to enjoy the fruit less warily by the late 18th century.

Today, farmers grow more than 7,000 types—or cultivars—of tomatoes worldwide. Tomatoes range in size from tiny tomberries to chunky beefsteaks and boast more colors than iPods: they might be red, yellow, orange, pink, purple, black or green. Some tomatoes are perfect globes, others oval and still others are ribbed like pumpkins. The most commercially successful tomatoes, however, are not the funky, colorful varieties, but the classic round, red, spotless fruits that farmers harvest while the crop is still green and ripen with ethylene, a plant hormone. Over the generations, farmers have bred the plants that produce these familiar tomatoes to yield as much fruit as possible.

The more fruit an individual tomato plant produces, the less sugar it can invest in each tomato, which partially explains why standard supermarket tomatoes taste so bland, says Harry Klee of the University of Florida (U.F.), who has been studying tomato flavor for the past 10 years. Knowing that tomato flavor depends on so much more than sugar, however, Klee and his colleagues began a research project three years ago to analyze the chemical potpourri that determines a tomato's taste. Klee thinks what he has found suggests a new way to enhance the flavor of tomatoes without sacrificing the economy of high-yielding plants.

Klee and his colleagues grew 152 varieties of heirloom tomatoes in fields and greenhouses at the University of Florida and bought standard tomatoes from a local supermarket. The scientists sliced up the fruit and offered the wedges to 170 volunteers who carefully chewed, tasted and swallowed each piece of tomato, rating the texture, the intensity of sweetness, sourness and bitterness as well as the overall tomato flavor and how much they enjoyed eating that particular sample. Between taste tests, the volunteers took a bite of an unsalted cracked and a sip of water to clear their palates.

In research stretching back to at least the 1960s, scientists have established that the balance of sugars and acids within a tomato largely determines its flavor. People generally like a tomatoes with a lot of fructose and glucose, although some also enjoy tangier, more acidic heirloom varieties. As expected, the volunteers in Klee's new study preferred the flavor of tomatoes with a lot of sugar to less sweet fruits—but sugar content did not entirely explain their preferences. Chemicals known as volatile compounds also contributed to flavor. The results were published May 24 in Current Biology.

Most plants release a bouquet of chemicals into the surrounding air, especially when they are injured, need to attract a pollinator or deter herbivores—think of the smell of cut grass, the pungent scent of a pine tree or the delicate perfume of orange blossoms. When we squeeze and sniff a tomato, evaluating its ripeness, volatile compounds drift away from the fruit and into our nostrils. When we bite into one—or chomp down on a tortilla chip laden with salsa—chewing forces the same volatile compounds up behind the palate and into the nasal cavity.

In Klee's analysis, the most abundant volatile compounds in a tomato—the C6 volatiles—barely influenced what people thought of the fruit's flavor. When volunteers compared the taste of ordinary tomatoes and mutant tomatoes that were genetically modified to lack C6 volatiles, they could tell the two apart, but they did not have much of a preference for one over the other. In contrast, a less prevalent volatile compound named geranial made a huge difference to tomato flavor. Klee noticed that many of the tomatoes the taste testers preferred contained moderate to high levels of geranial. When volunteers tried mutant tomatoes with normal levels of sugar, but low levels of geranial, they did not rate the fruits highly. Geranial, Klee concluded, somehow improves a tomato's overall flavor, perhaps by enhancing the fruit's innate sweetness. Supporting this reasoning, a majority of taste testers in an earlier study enjoyed the flavor of tomatoes engineered to contain lemon basil geraniol, which is related to geranial. Compared with heirloom varieties, standard supermarket tomatoes generally have less geranial and other volatime compounds. "They're kind of like lite beer," Klee says. "Even if all the chemicals are there, they are at lower levels."

No one chemical compound determines tomato flavor. And even if scientists identified every single flavorful compound in a tomato, the way the fruit is handled will still change its taste. Putting tomatoes in a refrigerator, for example, diminishes their flavor. Even off the vine, the tomato remains alive; if it gets too cold, the enzymes that assemble volatile compounds presumably stop working and the flavor evaporates. Similarly, picking tomatoes before they ripen—which is standard practice for many farmers—cuts the fruit off from the plant's supply of sugar and other nutrients. By breeding or genetically modifying tomatoes to contain lots of the volatile compounds that taste testers prefer, scientists could produce new supersweet and flavorful varieties without increasing the fruits' sugar content.