Tomatoes on the vine

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Tomato study reveals juicy genes

In genomic study of 100 tomato varieties, scientists uncover more than 230,000 DNA variations that can be manipulated to affect the size, flavor, and harvestability of tomatoes

When Grammy-winning rapper Kendrick Lamar said "I got riches buildin' in my DNA," he almost certainly wasn't talking about the humble tomato. But a new study unveiling more than 230,000 DNA differences across 100 tomato varieties, which will allow breeders and scientists to engineer larger, juicier, more profitable plants, proves that this food staple has riches buildin' in its DNA, too.

"The vast majority of the DNA differences we discovered are completely new," says Michael Schatz, Bloomberg Distinguished Associate Professor of computer science and biology at Johns Hopkins University and the co-corresponding author of the study, which was published online today in Cell.

One of the largest commercial fruit crops in the world, tomatoes make up a $190 billion global industry that relies on pinpointing which large-scale difference between genomes, or structural variants, are responsible for the variety of tomato shapes, colors, and tastes we see at the store.

"We've taken processes that used to take hundreds, or in some cases even thousands, of years, and performed them very rapidly."
Michael Schatz
Bloomberg Distinguished Associate Professor of computer science and biology

Previous technologies, however, didn't allow scientists to read large portions of a genome, only allowing for small bits to be read at a time.

"Like a big jigsaw puzzle with hundreds of millions of small pieces, maybe you manage to put together the corners, but not the big blue sky," Schatz says. "The new technology used in this study allowed us to zoom in and get larger, clearer puzzle pieces."

Using new DNA sequencing technology and software, Schatz and more than 30 collaborators from around the world in a self-proclaimed "tomato consortium" were able to sequence and compare the genomes of 100 different tomato types. In doing so, they found more than 230,000 structural variants.

From there, the team dove deeper with detailed genetic experiments to understand how some of those variants affect tomato traits. In one experiment, they found that duplication of a particular gene causes a plant's tomatoes to be about 20% larger. Next, they discovered a gene that contributes to a smoky flavor in some tomatoes. And in a third set of experiments, the researchers uncovered a complex interaction involving four structural variants that can mitigate a potential trade-off between a feature that simplifies tomato harvesting and another that reduces productivity.

The scale of their investigation has never been accomplished for any other crop, says Cold Spring Harbor Laboratory professor and Howard Hughes Medical Institute investigator Zachary Lippman, who co-led the project.

"I think it sets the foundation for what other crops and people working on those crops should be thinking about," Lippman says. "All crops are based on mutations. Everything that we eat is based on mutations and up until now it's been a pretty slow process to identify and evaluate the importance of those mutations."

Adds Schatz: "We've taken processes that used to take hundreds, or in some cases, even thousands of years, and performed them very rapidly. From here, we can apply our understanding of genetics to very rapidly domesticate some of the species related to tomatoes and create new crops to feed the world with."