For most city dwellers, the luscious taste of a vine-ripened garden tomato bursting in the mouth is little more than a distant memory. Sadly for supermarket shoppers, the standard grocery varieties have grown bigger, blander and hardier for cross-country shipping and storage. Now scientists have charted the genetic path that made today’s tomatoes nearly unrecognizable from their more flavorful predecessors.

By uncovering the tomato's genetic journey, researchers have identified key flavor-enhancing genes that have dwindled or disappeared as the tomato changed over the years. Armed with this new knowledge, they believe they can return that taste to today’s supermarket tomatoes—with a little genetic fiddling.

Tomatoes are the world's highest-value fruit or vegetable crop, with farmers producing more than 170 million tons of them worldwide in 2014, according to the Food and Agriculture Organization of the U.N. But our insatiable appetite for this bright fruit has had consequences. The mass-produced varieties regularly available in world markets travel well, store for weeks, and cost relatively little—but they’ve also lost what made them so desirable in the first place.

Today's fruit simply doesn't pack the flavor of the old-fashioned tomato, finds a new genome study published today in the journal Science. “Genomic technologies, like the ones the authors used in this research, really enable us to study what happened to the tomato in a very effective way,” says Esther van der Knaap, a plant geneticist at the University of Georgia who was not involved in the new study. “What did we leave behind, and what are we carrying through?”

To trace the fruit's genetic history from its ancient Andean ancestors to today, crop genetics researcher Harry Klee and colleagues sequenced the genomes of 398 tomato varieties and relatives—a mix of modern commercial, heirloom and wild plants. Then, they asked panels of taste testers to rate the characteristics of 101 tomato varieties.

Comparing the genetic fingerprints of each fruit with taster reviews and preferences revealed dozens of chemical compounds, and the corresponding genes behind them, that tasters heavily associated with flavor—many of which have been lost over centuries of breeding.

The results also revealed something unusual about the essence of true tomato taste: It’s incredibly complex. Flavor is already an intricate combination of what the tongue tastes and the nose smells. But the tomato's flavor is especially layered, involving chemicals like acids and sugars (which switch on taste receptors) as well as compounds known as volatiles (which get our smell receptors in gear).

It's this beguiling combination of taste and smell that delivers the distinctive tomato flavor—and is largely responsible for the taste problem tomatoes face today. “The tomato is not like many of the common fruits you might think of, like bananas or strawberries, where if I just gave you one volatile you’d say ‘Oh, that's a banana,’” explains Klee, of the University of Florida. “There are at least 25 different volatile chemicals, the aroma compounds, that all contribute to the flavor of a tomato.”

In all that complexity, two factors may have outsize importance for tomato flavor: size and sugar. As you might expect, sugar makes tomatoes taste better. And the bigger a tomato, the less sugar you tend to find in it.

The new study revealed in minute genetic detail how tomatoes simultaneously grew larger and less sweet over time. Thanks to modern breeding techniques, tomatoes have expanded in size as much as 1000-fold since they were domesticated. Scientists previously pinpointed the genes responsible for the explosion in tomato sizes after domestication, including one named fw2.2 and another, called fasciated, that can boost tomato sizes by up to 50 percent.

But modern farmers aren't entirely to blame, the genetic study found. “The selection for big fruit and against sugar is dramatic in the modern varieties,” says Klee. “But it goes way back to pre-Columbian days when the Native Americans were already selecting for bigger fruit with lower sugar content.”

Putting more tasty sugar back into mainstream tomatoes may simply not be feasible with today’s production realities, says Klee. That's because most growers aren't paid for flavor; they're paid by the pound. It costs just as much to have a worker pick a small tomato as to pick a huge one, which is a big reason why today's commercially-produced tomatoes (Solanum lycopersicum) can be so much more massive than their tiny wild ancestors.

“The breeders have selected plants to produce massive amounts of fruit, all at the same time, and they want bigger fruit on to the plant. The plant just can't keep up with that, so what happens is you dilute out all of the flavor chemicals,” says Klee.

The study also revealed another surprise in the tomato’s path to blandness. Much of the dilution of tomato flavor over time wasn’t just the necessary result of breeding for larger fruit—it was an accidental side effect. Since breeders aren’t regularly genetically testing their tomatoes, it’s easy for any of the 25 different chemicals involved in tomato aroma to simply drop out one by one over the generations, when the allele for poorer flavor choice is randomly selected.

It seems that, in the case of tomatoes, no one noticed this slow dilution until the cumulative impact of all those lost genes became obvious. “Out of the 25 volatiles 13 of them are significantly reduced in the modern varieties, “ Klee says. “Its almost exactly what you'd predict would occur randomly, but the net effect is that you've diluted out flavor.”

Klee likens this tomato tragedy to the piecemeal dismantling of a symphony orchestra: “If you pull out a single instrument and then listen you don't notice the difference. Then you pull out a second instrument, and you don't notice, until if you keep going all of a sudden you reach a point where you say wait a minute, this just doesn't sound right.”

How can we restore those lost instruments? Fortunately, bringing back tomato aroma doesn't seem to involve the same trade-offs that plague the sugar-size relationship, says Klee.

“There's no obvious tie with things that needed to be selected to improve the crop, like shelf life or firmness, so I think we can do it without undoing that good work that the breeders have done,” he says. “Humans are exquisitely sensitive to smells and the levels of these compounds in the fruit are actually quite low, even though we can detect them quite readily. So doubling the levels of a lot of these compounds, even just pushing them back to the level where there were in an heirloom tomato 50 years ago, is probably not all that challenging.”

Klee believes that restoring heirloom quality flavor to standard tomatoes would require a drop in the yield, meaning farmers would only be able to produce perhaps 90 percent of their current crop size. Prices on those tomatoes would also have to rise accordingly. The question is: Will these high-taste, high-quality, and inevitably higher-cost tomatoes sell? Klee, for one, believes they will. “Look at craft beers, or what's happened with coffee, over the past couple of decades,” he says.

But beyond specialty tomatoes, there are limits to what can be done to the average commercial tomato, which is bred to endure travel and long periods of storage. “A really good tasting tomato is one that ripens on the vine, so they are always going to be soft,” says van der Knaap. “They cannot be produced over long distances, and can't be stored in a grocery store for four weeks without rotting.”

How tomatoes are handled also influences their ultimate flavor—both along the way from farm to store and also in the buyer's home. “If you want to destroy the flavor of a tomato it's simple: Just put them in the refrigerator,” she says.

Still, both researchers believe it’s feasible to make significant improvements to your average run-of-the-mill grocery tomato. “If those tomatoes can be even slightly improved it will be a big gain for consumers, and this study certainly shows a road map of how that can be done,” says van der Knaap.

Klee's University of Florida lab is now going further than just making a road map. They’re testing varieties, with a little help from home gardeners. For a donation to the tomato research project, citizen tomato scientists can receive a package of the group's Garden Gem and Garden Treasure tomato seeds to plant them and document for the project. Of course, volunteers also get to enjoy eating the fruits of their labor, even if grocery shoppers won't enjoy quite the same taste.

“I think that we're not going to produce heirloom flavor in a commercial tomato. Because the growers aren't going to be able to budge on yield and reducing yield is the only way to get more sugars,” Klee says. “It's not going to be like a fresh Brandywine picked in your backyard, but it is going to be a lot better.”