Cardboard. Memory foam. Wet cotton balls. There are many ways to describe the flavor of the modern-day supermarket tomato. It may be the only fruit in America to qualify as a biological tragedy.

Back in 1989, a molecular biologist named Harry Klee was hired by Monsanto to create a genetically modified tomato with better flavor. After years of research and $10 million, Klee managed to develop one — but it tasted only marginally superior to what was available in supermarkets. Determined to keep at it, in 1995 he joined the Horticultural Sciences Department at the University of Florida, where he has spent the past 22 years studying what makes tomatoes taste good.

Last month, Klee and a team of collaborators, including scientists from China, Spain, and Israel, published a paper in Science analyzing flavor-associated chemicals in 398 modern, heirloom, and wild tomatoes. The results are pretty intriguing. I spoke to Klee to find out exactly what went wrong with tomatoes and why, and whether the damage can be undone.

Mark Schatzker

The first line of your Science paper says, “Modern commercial tomato varieties are substantially less flavorful than heirloom varieties.” Is there now scientific proof that supermarket tomatoes really do taste terrible?

Harry Klee

Since 2010, we’ve run about 40 taste panels, consisting of around 100 people each, to rate 160 different varieties of tomatoes. Supermarket tomatoes, for the most part, struggle to get out of the bottom third of the ratings.

Mark Schatzker

What’s wrong with them?

Harry Klee

Roughly half of the flavor compounds are significantly worse in modern varieties. They’re also much lower in sugar. We found this by running a complete chemical profile of every tomato variety and asking, what’s in the tomatoes people like and what’s in the ones people don’t like? Then we took it a step further and used software that goes through the entire tomato genome and checks every nucleotide to see if it’s correlated with a particular flavor compound. When we took all the modern varieties and grouped them together and compared their flavor compounds with the old varieties, what we found the modern varieties are way lower.

Mark Schatzker

How did this happen?

Harry Klee

For decades, tomato breeders have selected traits related to performance — yield, disease resistance, how well tomatoes ship, how well they last on a shelf. Those are the things they can measure and do measure, and they’ve done very well at it. But they never select for flavor. And if you don’t select for flavor, you are selecting against it.

In the case of sugar, it’s a little bit different. We found there is a definite trade-off between sugar content and fruit size. And the tomatoes you find in the store these days are gigantic. But this actually goes way back. The pre-Columbian natives who domesticated tomatoes were themselves selecting for bigger fruit that has less sugar.

Mark Schatzker

Wouldn’t the tomato breeders have noticed their new tomato varieties tasted bland?

Harry Klee

Probably not. In a single generation, they would have only lost one flavor compound, so the difference would have been extremely subtle. Over several generations, however, the effect is huge. The best analogy I can come up with is an orchestra. If you pull out one instrument, you don’t miss it unless you’re really discerning. But if you slowly remove 12 members of the orchestra, at that point it sounds different.

Mark Schatzker

Could you use the gene-editing technology CRISPR to plug the good flavor genes back into modern tomatoes?

Harry Klee

CRISPR is very powerful technology, but at this point you can only knock things down or out. We don’t know how to make more of things with CRISPR. You can’t use it to put in a genetic trait that’s not there.

Mark Schatzker

So what is the blueprint to fix tomatoes?

Harry Klee

What we need to do is get the flavor from heirlooms into modern tomatoes but leave behind everything else we don’t want — the thin skin, the mushy texture, the low yield, and the poor disease resistance. If you do that through classical breeding, it will take many generations. Instead, we’re using something called molecular breeding.

Basically, you cross an heirloom and a modern tomato, grow it to the seedling stage, and then screen it for the genetic markers you want. It might take a million seedlings, but eventually you will find the rare cross that inherited the one chromosome with the gene you want from the heirloom but not the other 11. With molecular breeding you can do in three generations what it would take a traditional breeder to do in seven. That’s a year and a half versus three years.

Mark Schatzker

So in a year and a half, will all tomatoes be delicious?

Harry Klee

No, because it’s not one gene we’re after. It’s a minimum of five. And many of them are found in different heirloom parents. So five genes will require about three years of molecular breeding.

But we will still run into a problem with sugar. Tomato growers know consumers prefer sweeter tomatoes. They also know that sweeter means smaller fruit size. And they don’t want to grow smaller tomatoes, because that pushes their labor costs up.

So until we can convince consumers to pay more money for smaller tomatoes, they’re just not going to taste like that Brandywine you picked in your backyard. That said, I think we can have a major impact by focusing on flavor compounds. I think you would eat that tomato and say, “This is noticeably better.”

Mark Schatzker

If scientists studied other fruits and vegetables for flavor loss the way you have with tomatoes, do you think we would see similar blandness in modern varieties?

Harry Klee

I think most people recognize that the gigantic strawberries you get in the store are not nearly as good as the tiny ones you pick in the wild. Any crop that has been heavily bred and not screened for flavor or nutrition is going to suffer. The blueberries grown in Florida are gigantic, and they’re also tasteless.

Mark Schatzker

So is there, similarly, the potential to make other members of the produce aisle taste better?

Harry Klee

Absolutely. We call it “consumer-assisted selection.” It means you start with the consumer rather than end with the consumer, and I think that’s the real breakthrough here. It’s common sense, but hardly anyone does it. And it drives me crazy.

Mark Schatzker

Do you think we will see that happen?

Harry Klee

I do. But it might not happen here. Right now, China is probably spending 10 times what we are on basic plant research. We had to go to China to find a collaborator to sequence all these tomato genomes. You know who the No. 1 producer of tomatoes in the world is? China. They’re going to be ahead of us. It’s inevitable.

Mark Schatzker is the author of The Dorito Effect: The Surprising New Truth About Food and Flavor.

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