Editor's Note: This is the first in a series of six features on the science of food, running daily from March 30 through April 6, 2009.

Famous for their taste, color and, well, homeliness, heirloom tomatoes tug at the heartstrings of gardeners and advocates of locally grown foods. The tomato aficionado might conclude that, given the immense varieties—which go by such fanciful names as Aunt Gertie's Gold and the Green Zebra—heirlooms must have a more diverse and superior set of genes than their grocery store cousins, those run-of-the-mill hybrid varieties such as beefsteak, cherry and plum.

No matter how you slice it, however, their seeming diversity is only skin-deep: heirlooms are actually feeble and inbred—the defective product of breeding experiments that began during the Enlightenment and exploded thanks to enthusiastic backyard gardeners from Victorian England to Depression-era West Virginia. Heirlooms are the tomato equivalent of the pug—that "purebred" dog with the convoluted nose that snorts and hacks when it tries to catch a breath.

"The irony of all this," says Steven Tanksley, a geneticist at Cornell University, "is all that diversity of heirlooms can be accounted for by a handful of genes. There's probably no more than 10 mutant genes that create the diversity of heirlooms you see." But rather than simply debunking a myth about the heirloom’s diversity, Tanksley's deconstruction of the tomato genome, along with work by others, is showing how an unassuming berry from the Andes became one of the world's top crops. Genetics work will also point the way to sturdier, more flavorful tomatoes—albeit hybrid varieties whose seeds cannot be passed down from generation to generation but must be purchased anew by growers each season.*

New World Discovery
The cultivated tomato is a member of the nightshade family that includes New World crops such as potato and chili pepper, which spread around the world after Christopher Columbus brought them back to Spain in the 15th century.* But whereas scientists have uncovered a wealth of archaeological evidence—including microscopic starches on pottery shards that point to the taming of many crops from the Americas as far back as 10,000 years ago—the record is blank when it comes to the tomato.

Known scientifically as Solanum lycopersicum, the modern tomato seems to have its wild origins in the Peruvian Andes and may have been domesticated in Vera Cruz, Mexico—an agricultural hot spot. Primitive varieties still grow throughout the Americas. All told, botanists call some 13 species "tomatoes" and consider an additional four to be close allies. One might assume that one of these known wild species became today's cultivated crop, but that's not the case: the Mother Tomato has never been found. The closest relative is the currant tomato—Solanum pimpinellifolium—which, based on genetic comparisons, split from today's tomato some 1.4 million years ago.

So researchers like Tanksley have to work backward, crossing tomato varieties and species in order to understand how various genes influence shape and size. Once isolated, Tanksley later inserts those genes into other tomato varieties to make his case with a dramatic transformation.

Size and shape drive the selection
Tanksley concludes from his analyses that, in their effort to make bigger, tastier and faster-growing fruit, our ancestors ultimately exploited just 30 mutations out of the tomato’s 35,000 genes. Most of these genes have only small effects on tomato size and shape, but last May in Nature Genetics Tanksley and his colleagues reported that they found a gene they dubbed fasciated that bumps up fruit size by 50 percent.

It was probably the single most important event in domestication. The first written record of tomatoes—from Spain in the 1500s—confirms that this mutation, which enlarges tomatoes by producing compartments known as locules, existed back in the same yellow tomatoes that gave Italians the word pomodoro, or golden apple. A cherry tomato typically has two compartments filled with seeds and jelly, whereas a Jumbo Red can have up to eight locules. This gene, along with another size-governing gene called fw2.2, which Tanksley identified 10 years earlier, was the key step in making tomatoes a dietary staple.

Besides size, tomato farmers also selected for shape. To discover those genes, Esther van der Knaap, a Tanksley alumnus now at The Ohio State University, says she went straight for the heirlooms, which exhibit a range from the Jersey Devil's small, chili-pepper shape to plump, cracked beefsteaks known as Radiator Charlie's Mortgage Lifter. "I just went to catalogues and ordered everything that had a cute shape," she says.

She plucked a gene called SUN from one heirloom tomato and inserted it into a wild relative. As a result, the tiny fruits bulged like pears, a remarkable makeover that made the cover of the journal Science last March. SUN's effect dwarfs that of another shape gene called OVATE—yet another Tanksley discovery—and both seem to have been nurtured in Europe in the last several hundred years to ease mechanical harvesting and processing.

Weak and Wimpy
The selection of these traits has taken a toll on the heirloom's hardiness: They are often plagued by fungal infections that cause the fruit to crack, split and otherwise rot quickly. Wild plants must continuously evolve to fend off natural pathogens, points out Roger Chetelat of the Tomato Genetics Resource Center at the University of California, Davis. But in their quest for size, shape and flavor, humans have inadvertently eliminated defensive genes. As a result, most possess only a single disease-resistance gene.

Perhaps that's the price to pay for a good, flavorful fruit? Hardly, Chetelat says, because the heirlooms' taste may have less to do with its genes than with the productivity of the plant and the growing environment. Any plant that sets only two fruits, as heirlooms sometimes do, is bound to produce juicier, sweeter and more flavorful fruit than varieties that set 100, as commercial types do.* Plus, heirlooms are sold ripened on the vine, a surefire way to get tastier results than allowing them to mature on the shelf.

So breeders feel confident that getting germ-beating genes back into heirlooms won't harm the desirable aspects of the fruit. Modern breeding has resuscitated grocery store tomatoes with an influx of wild genes; in the past 50 years, researchers have bred back some 40 disease-resistance genes into commercial crops.

Restoring Heirloom's Health
Now, Monsanto wants to do the same for the heirloom. In 1996 a tomato breeder and former Tanksley student named Doug Heath began a pet project at Seminis VegetableSeeds, a Monsanto subsidiary. After 12 years of traditional breeding with the help of molecular markers, he has created a new rainbow-streaked tomato less prone to cracking and also endowed with 12 disease-resistant genes. The original plant, Heath explains, had defective flowers, which is one reason why it set only two fruits compared with the 30 he gets from his new variety. He claims he is also able to maintain a comparable flavor and sugar profile even on productive plants. It turns out that the heirloom's defects are neither quirky nor cute, just an accident of a single-pronged breeding strategy left over from the dawn of genetics.

Heath's new plants may be available to home gardeners next year and on commercial markets in the next three to five. "I see them as coming to a pinnacle," he says of the Rainbow and two other varieties he has improved with modern stocks.

But will heirloom adherents appreciate the look-alikes with hybrid seeds? "There will be a contingent of people," he says, "who will believe these are poor imitations of the originals."

*Note: These sentences have been altered since publication.