Something is amiss with the flavor of tomatoes these days. If you're accustomed to today's supermarket tomato, perhaps you haven't noticed. But your taste buds are unwittingly being deprived of flavors that your great grandparents once relished.

We may have an opportunity to return the tomato to its former flavor glory, however. Harry Klee, a professor of horticultural sciences at the University of Florida, is working to identify the key chemical elements that give tomatoes their flavorful pop, with the ultimate aim of engineering the ubiquitous fruit to once again taste like it did 100 years ago, reports Phys.org.

"We're just fixing what has been damaged over the last half century to push them back to where they were a century ago, taste-wise," said Klee. "We can make the supermarket tomato taste noticeably better."

Klee wants to make clear that he's not interested in genetic modification. He wants to employ the methodology of classical genetics, to restore tomato flavors by breeding them the old-fashioned way. First though, he had to identify exactly what it is that has changed about their flavor.

The answer lies in alleles

Klee's team looked at the chemical underpinnings of how our olfactory sense works when we taste a tomato. What should we expect from the sugar content of these fruits? Which volatile chemicals are critical to better flavor? The team then analyzed the genetics behind the production of these chemicals, and were able to identify several alleles — or genetic variations — that have been unintentionally bred out of many modern tomato varieties that control for flavor.

"We wanted to identify why modern tomato varieties are deficient in those flavor chemicals," Klee said. "It's because they have lost the more desirable alleles of a number of genes."

The 2017 research, which appeared the journal Science, made use of a genome-wide assessment study to map out the key genes at play, which should make it possible to focus in on these traits and efficiently pinpoint them in breeding programs. Because Klee doesn't want to go the route of genetic modification, it's estimated that it will take breeders about three to four years to get tomatoes back to where they once were in regards to flavor.

Fast-forward a couple of years

To accomplish this goal, Klee joined forces with an international team of researchers led by Zhangjun Fei, a plant geneticist at Cornell University in Ithaca, New York, and James Giovannoni, a molecular biologist at Cornell and a USDA scientist. In 2019, that team dug deeper into the modern tomato's missing genetics, creating a pan-genome for 725 tomato varieties. The group published their work in Nature Genetics in May 2019.

A pan-genome is exactly what it sounds like: The entire gene set of all strains, which makes it easier to separate the core genome from the variable genome. They compared this data to a reference genome. What they found amplified Klee's theory, revealing almost 5,000 missing genes that explain why that store-bought tomato almost always lacks a certain zing.

They narrowed their focus to a specific gene called TomLoxC, which through regular domestication has been pushed aside. TomLoxC was known to control color, but now we know it's also a key contributor to flavor. And as Discovery reported in its coverage of the study, that flavor gene is making a slow-but-sure comeback.

The rare version of TomLoxCused used to only be present in about 2 percent of tomato varieties. But in recent years, as breeders have begun to focus more on flavor, more and more modern tomato varieties have the gene. Nowadays, about 7 percent of tomatoes have it, meaning breeders have started selecting for it.

So if you're a tomato-lover, your continued patience will pay off. In a few more years, even those who don't have a farmers market nearby may get the chance to fall in love with the tomato all over again.

Editor's note: This story has been updated since it was first written in January 2017.

Bryan Nelson ( @@brynelson ) writes about everything from environmental problems here on Earth to big questions in space.

Tomatoes tasted much better 100 years ago. Can their flavor be restored?
Researchers are digging deeper into how tomato flavors have changed over time, and now they've found a specific gene that's missing in many modern varieties.