Today, scientists revealed a small but intriguing chapter in that story: A genetic mutation that seemed like a real improvement in the tomato's quality, but which actually undermined its taste.
Before we get to the mutation, though, let's start with the old tomatoes - the varieties that people grew a century or more ago.
Thanks to enthusiastic seed savers and heirloom tomato enthusiasts, you can still find many of them. Eric Rice, owner of Country Pleasures Farm near Middletown, Maryland, first encountered heirloom tomatoes when he was a graduate student in North Carolina.
"I decided I really liked them," he says. He liked the vivid taste and the unusual colors, from orange to purple. These tomatoes also have great names: Cherokee Purple; Dr. Wyche; Mortgage Lifter.
Rice now grows these tomatoes to sell at a farmer's market in Washington, D.C. But he admits that all that tomato personality can make heirlooms harder to grow and sell. "Heirloom tomatoes don't ship very well, because they're softer. And frankly, they're all different shapes and sizes." This makes them more difficult to pack.
There's something else you'll notice as these tomatoes start to get ripe something central to this story. The part of the tomato near the stem - what's called the shoulder of the fruit - stays green longer.
"I think it is an issue for the consumer," says Rice. "Because people do buy with their eyes. And green shoulders also mean it's not entirely ripe, or not as soft and tasty there."
Those green shoulders turn out to be more significant than you might think. In this week's issue of the journal Science, scientists are reporting that when they disappeared from modern tomatoes, some of the tomato's taste went with them.
Here's how. Sometime before 1930, somewhere in America, a tomato grower noticed a plant that was producing distinctive fruit. These fruit turned red from stem to tip in a uniform way. They didn't have any of those bothersome green shoulders.
It was a new mutation, and plant breeders saw it as the next big thing.
They called it the "uniform ripening" trait. In 1930, the agricultural experiment station in Fargo, N.D., released a new tomato variety containing this mutation. The variety was called All Red.
Ann Powell, a researcher at the University of California, Davis, says it spread through the entire tomato industry. "It's a little hard to find a variety in modern production that doesn't have it," she says.
Powell is one of the scientists who now has discovered the genetic change responsible for "uniform ripening."
She was studying some genetically engineered tomato plants for another reason when she noticed that one of the added genes resulted in green tomatoes that were really dark green. It struck her as odd. "The leaves were not dark green. It was only the fruit that were dark green," she recalls.
Since this foreign gene had interesting effects on the ripening of fruit, Powell and her colleagues started looking for a similar gene that occurs naturally in tomatoes. They found it and by coincidence, so did another research team on the other side of the country, at Cornell University.
The researchers discovered that this natural tomato gene, when it works properly, produces those green shoulders on tomatoes. The darker green color comes from the chlorophyll in plant structures called chloroplasts, which is what converts sunlight into sugars for the plant. In fact, those dark green shoulders were making those old tomatoes sweeter, and creating more flavor.
The uniform ripening mutation disabled this gene.
"We find out that, oh my goodness, this is one of the factors that led to the deterioration of flavor in the commercial tomato!" says Harry Klee, a professor of horticulture at the University of Florida.
Klee has been exploring the chemistry and genetics of tomato taste. He says tomato breeders made a lot of compromises like this over the years as they created tomato plants that produce more fruit that was also rugged enough to hold up under rough handling.
Now, Klee says, with some of this new science, we have a chance to undo some of those decisions. "What I tell people is, we can have 100 percent of the flavor [of heirloom varieties] with 80 percent of the agricultural performance of the modern varieties, with very little work."
Breeders can start with some of the best heirlooms, then bring in some of the disease resistance genes that modern varieties have. They should also be able to increase yields somewhat, he says.
But consumers may have to change their expectations, Klee says. "They're going to have to go in and say, 'That one's got that little discoloration at the top; that means it must be good!"
And, the only way they're likely to show up in your local grocery store is if consumers can recognize them and are willing to pay a bit more for them.
Still, for the best flavor, you might want to grow your own.