For years, Zachary Lippman and his team of gene trackers at Cold Spring Harbor Laboratory have been on the trail of secrets tucked in the genome of tomatoes.

In 2010, he and his collaborators zeroed in on the single gene that boosts not only the bounty of tomatoes in general but the sweetness of their fruit. In 2012, they figured out how the Heinz variety -- used in its ketchup -- became large, fat and juicy.

Now, Lippman, an associate professor, has uncovered the origins of the big daddy among all tomatoes -- the beefsteak -- often prized for its role in transforming a slab of grilled ground beef into the all-American burger.

"We found the genes that are responsible for why we have beefsteak tomatoes," said Lippman, who defines the newly discovered DNA as a sequence of genes that govern stem cell production. Mutations in these genes, he said, explain how the beefsteak came to be.

The tomato is an ancient fruit native throughout many parts of South America, according to Lippman's research appearing in Monday's online version of Nature Genetics.

Original tomatoes were puny, some even berry-sized. But an unexpected genetic quirk, possibly in Mexico, led to a colossal-sized mutant that became a prized fruit.

Beefsteaks are big, often bright red tomatoes and noteworthy for what Lippman calls their locules -- seed compartments. They can weigh in at more than a pound and are most commonly propagated by home gardeners.

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But the beefsteak's emergence, Lippman said, occurred hundreds of years ago and was based on a random change in the plant's genes. The affected DNA is involved in the number of stem cells in the beefsteak's growing tip, a structure technically known as the meristem. The mutation emerged long before Europeans embarked for the New World and were amazed by the supersized fruit.

Lippman said the mutation is in a gene called CLAVATA3, which results in a flurry of stem cell production in the meristem. Think of stem cells as biological blank slates capable of morphing into any kind of tissue and also bearing an influence on that tissue's shape and size.

In the case of the beefsteak, Lippman said, the random change produced a fruit so large and succulent that indigenous farmers kept planting the seeds of the giant mutants to maintain an ongoing bounty.

"It was very exciting to find out how this worked molecularly," Lippman said.

Esther van der Knaap, an associate professor in the College of Food, Agricultural and Environmental Sciences at Ohio State University, helped Lippman trace the beefsteak's genetic origins.

Seven years ago, van der Knaap, who also specializes in tomato genetics, discovered the DNA that controls the shape of tomatoes of all kinds, helping to unravel the mystery behind why various tomatoes look the way they do. She is also investigating how domestication has colored the destiny of the tomato.

The plants belong to the diverse Solanaceae, or nightshade family of trees, vegetables and flowers, such as the petunia, Lippman and van der Knaap said.

But to understand the beefsteak, added Lippman, is to grasp the human history behind the worldwide propagation of the gargantuan fruit. The beefsteak's story, he said, is steeped in a cast of characters who include the Spanish conquistador Hernan Cortez, who in the 16th century helped destroy Aztec society in Mexico.

"In addition to the gold and silver and everything else he carried back to Spain, he was excited about the beefsteak tomato," Lippman said, noting that before Cortez there were no tomatoes in Europe.

"What Cortez brought to Europe was already a beefsteak tomato," he added, and when European colonizers came to the Americas, they brought beefsteak seeds with them, reintroducing the tomato to the New World.