Science Friday - Scientists Identify Genes For Tomato And Eggplant Size

Episode Date: May 20, 2025

Tomatoes come in all kinds of colors, sizes, and flavors. But what’s going on at the genetic level? What makes a tomato red or yellow? Tiny or giant?Researchers are mapping the genomes of 22 varieties of nightshades—the family of plants that includes tomatoes, potatoes, and eggplants. They located the genes that control the size of tomatoes and eggplants and then used CRISPR gene editing to grow bigger fruits without sacrificing flavor.Geneticist Michael Schatz joins Host Ira Flatow to talk about his latest research into nightshade genomes and the current state of genetically modified crops.Guest: Dr. Michael Schatz, professor of computational biology and oncology at Johns Hopkins University, based in Baltimore, Maryland.Transcript will be available after the show airs on sciencefriday.com. Subscribe to this podcast. Plus, to stay updated on all things science, sign up for Science Friday's newsletters.

Calling all birders. Before we start the show, we need your help. We are looking for your high-drama bird tales, a time when birding gave you a thrill. Did you break the law to catch a glimpse of that Gunnison Sagegrouse? Did you scream when you finally saw that Kurtland's warbler? Did you fall from your two-story bird blind in pursuit of one of the birds on your life list? Surprise us. The lines are open for your bird calls, 8774-Symp. That's 877 for SciFri. Hey there, it's Ira Flato, and you're listening to Science Friday. Today on the podcast, how scientists are taking genes from eggplants to make bigger tomatoes. The modern tomatoes took hundreds of years to develop from the wild species, and now we can do it basically in one generation. It's that time of the year when I'm planting what's going into my garden, and just to be honest, I have to confess to being a tomato nerd. To me, tomatoes are the easiest to grow, the easiest to take care of, and you have such a great variety of sizes and flavors. And when I'm looking at my plants, I'm also always wondering

about what's going on at the genetic level, what's going on inside the plant? What's making tomatoes red or yellow, tiny, or giant? So, when I found out that researchers are working to map the genomes of 22 different varieties of nightshades, the family of plants, which include tomatoes, potatoes, and eggplants. Well, I just had to know more. And the exciting news, at least to we night shaders, is that they've located the genes that control the size of tomatoes and eggsplants and then use CRISPR gene editing to grow bigger fruits.

I want to know more. You're joining me to talk about his research and the current state of genetically modified crops is Dr. Michael Schatz, professor of computational biology and oncology at Johns Hopkins University in London. Baltimore, Maryland. Welcome to Science Friday. Thank you very much. It's a great pleasure to be here today. I've got to ask you first, how does a guy who's in the oncology department dealing with tomatoes? It's a great question. I would really say I would describe myself as a genome scientist. So any sort of plant, animal, human, anything that has a genome I'm interested in.

I got started in this work more than 20 years ago at a research institute called the Institute for Genomic Science, where I started in microbial genomics. And then over the years, I've just been fascinated and had the privilege to work in many different systems. Okay, so let's get right into it because can you give me an overview of the tomatoes genome? I mean, how does it compare to other fruits and vegetables? Yeah, so the actual genome has been mapped out for more than a decade now. As genomes go, it's pretty well behaved. It's about a billion bases in size, whereas the human genome is about three billion bases in size. There's two copies of every chromosomes. The plant world has great diversity there. The small genomes are much smaller, but the big genomes are much bigger. So

famously, the wheat genome is about 18 gigabases, so many times larger than humans. So it's kind of moderate size, bottom of complexity, which actually makes it a great system for doing genetics on so that we can kind of really, you know, kind of handle all that complexity. So we have fruits and vegetables that have a lot more chromosomes than we do. That's right. That's right. Even our friend, the strawberry, has 12 copies of every chromosome. Sugarcane has between nine and four. 14 copies. So there's great complexity in there. And that's actually part of the connection to oncology. That's one of the hallmarks of cancer where there's something called aneuploity, where you make it extra copies of extra chromosomes. And there's some lessons that can be shared

between the plant world and the human world and even into oncology. Yeah, that's really interesting. So I understand that you began with mapping the genome of the African eggplant. And for those of us who are unfamiliar with that, can give us an overview of what an African eggplant looks like? As you said, tomato is part of this larger family of nightshades. It includes eggplants and potatoes. But also, in addition to kind of those major crops, there's hundreds of these more indigenous crops. So African eggplant is in this nightshade family. It's grown quite extensively in Central Africa. It's grown quite extensively in South America. It's becoming more popular in the United States. In fact, at markets like Trader Joe's, you might see it. It's sometimes marketed at,

as a pumpkin on a stick because it has sort of a pumpkin-like shape, but it's actually an egg plant variety. So people are growing it. There's a lot of interest into it. The genome is pretty well-behaved. It's sort of a close relative in the same way that, I don't know, our friends, the chimps, or the gorillas are close relatives to the human genome. Right, right. So you figured out how the genes control growing these big egg plants. And how are you able to then use that to grow bigger tomatoes. Yeah. So, as I mentioned, the genome was mapped out more than 10 years ago. And there's been just a lot of research into some of the key genes and variants that modulate the size of fruits in tomato. But the opportunity is, well, there's all these other species, African eggplant,

and many others around the world that have unique flavors, unique sizes, unique colors, taste. But they're, you know, they're relatively small. They're hard to grow at sort of at large scale. Maybe they're, you know, really sensitive to the environment. For any number of reasons, there's interest to kind of develop these other plants that are sometimes called indigenous crops or sometimes just complete wild species. So we have some collaborators in Central Africa that have been growing African eggplant. And they were just really interested like we all are and, you know, what really is sort of modulating the size. Why are some bigger? Why are some smaller? And the opportunity was to take genetic information that we already knew from tomato and then try to

use that to advance our understanding and advance the development of the African egg plant. So did you actually cross a tomato with an eggplant? How do you actually use the genes from one to change the size of the tomato? Yeah, they're a little bit too far apart to do crosses like that. But thanks to all the advances in sort of the genome engineering, we can kind of do a more directed editing using that CRISPR Kast9 technology where if we thought there could be certain, you know, variants, certain sequences of DNA, we can now engineer that into this cousin. So specifically in tomato, there's a very classic gene called clavada three that has been known for many years as being important to the size of the fruits. In African eggplant, some are

large and some are small. We did a genetic analysis of what variants are really important from modulating that size in African eggplants. We expected to see clavata three would be important, and we did find that that was important. But along the way, we identified another enzyme, and it's still a little bit mysterious how it works, but we did identify another enzyme that seemed to be highly related to fruit size in African eggplant, and to validate it,

we brought that mutations of sort of the related enzyme and tomato, and it turns out that also modulates fruit size in tomatoes. So there's this great exchange of information from tomatoes into African eggplant, and then right back to tomatoes. So the whole sort of family, the whole Mike Shade system was sort of elevated through this research. Uh-huh. What part of tomato actually gets bigger when you modify it and you bring that trade in? Which part of the tomato grows and how big can you get it to grow? Yeah, you ever cut a tomato in half? It's sort of organized into these seed compartments. Those are called locusals. The loculal is a quantitative trait. In the same way, you know, healthy people kind of have 10 figures and 10 toes, you know, depending on the variety of tomato, sometimes there may just be one locule, there may be two. You know, a big beef steak will have, you know, many of these

sort of large locioles. So this clavada enzyme is really important for modulating the number of locioles. The fruits that have more locioles tend to be larger fruits. It's kind of that's cool. You know, but sometimes when you get these bigger varieties, they look pretty on the store shop when you eat them. They don't taste them. Good. I mean, could you preserve that flavor in the tomato when you modified it? That's one of the hopes we think about, you know, in the United States, the Heinz variety, the Heinz Company, you know, it was a variety that has this interesting history from Central America to Europe and then back again to North America. You know, it's grown at massive scales, but like you mentioned,

it'd be exciting and a real opportunity to bring in some of these unique flavors from all over the world of all these different varieties. I've had some nightshades that taste like a cross between a pineapple and a tomato and all these like exotic flavors that you just wouldn't encounter. And how fun and exciting it would be if those could be part of our diet as well. genetically modifying these plants versus the traditional crossbreeding. You know, you can select for size and color and flavor with the traditional modes of plant breeding, and we see all shapes and sizes of tomatoes in the grocery store.

So sell it to me, what's the benefit of? It's a great question. And, you know, and of course that opportunity still exists, and of course we still pursue it. But I would argue it's slow, it's limited. It sometimes will accidentally, while we're maybe targeting, you know, say fruit size or the shape or whatnot, along the way we may lose other important genes for disease resistance. Some of the flavor profiles may sort of accidentally get lost. But now thanks to all these advances in the biotechnology, we have, you know, we have

exquisite technology to sequence genomes. We have exquisite technology to modify them rather than kind of, you know, waiting for some random event to occur. Now, you know, with laser-like precision, we can get in there and apply the edits very, very specifically. And we also have a lot of understanding of what they're doing. so it's not that we're just poking around on the dark, we can do this in a very focused way

to very rapidly advance on this. The moderate tomatoes took hundreds of years to develop from the wild species, and now we can do it basically in one generation. So in one season, we can very rapidly advance on it. When are we going to see these guys in the grocery store? And that must be the goal, right? I mean, we're already seeing this, you know,

some of the more progressive grocery stores are starting to accomplish. consumer tastes. And I already mentioned that, you know, these so-called pumpkins on a stick are sometimes available, mostly as an ornamental. I think there's interest from consumers, there's interest from the producers. They just, the yield is low. This is kind of that simple. So if we can sort of accelerate the yield, you know, through larger fruits, I think that will be a huge advance to make them more productive here in the United States. And I will say, you know, in other parts of the world, this is a major food crop. And if, you know, if there's any sort of food sensitivities, there's

just immediate benefit to be able to sort of just develop larger fruits and just have more calories and just sort of make sure there's food security around the world. But speaking of other parts of the world, there's also a great pushback to genetically modified organisms, right? Genetically modified food, which this is. I mean, has that pushback gotten less over the years? Is it going away or is it still there? I think it's still there. I think some people are very and are very interested in sort of the opportunity to, you know, bring in new flavors, bring in advances on size or disease resistance. But I do think that, you know, there are others that are still have some concerns. And, you know, as a person, also as a father, you know,

I'm worried about the security of my foods for my children, you know, that would be the last thing I'd want to do is give them something that was dangerous. But I think that's, you know, another thing to realize about these technologies is, again, because we have so much control and laser-like precision to introduce these edits, we can do it incredibly safely. I should comment, you know, the varieties that we've done today are not commercially available as a food product. This is a research product. But our goal here is to work with some of the breeders, you know, and help them advance on this so that it could be available as a food crop. We have to take a quick break, but don't go away. More on this when we come back.

Now, if you can find the genes that control the size of the nightchades, the eggplants, the tomato, can you find the genes that control the flavors of them also? In addition to fruit size, we're interested in a variety of other traits. One is that's really important is called flowering time. And that really is sort of as important as you kind of take crops to different parts of the world where sometimes the days could be longer or shorter, just depending on where the sun is. That's a really important crop for making it productive. And then like you suggested, we're also very interested in some of the flavors.

A few years ago, we did a study in tomatoes, and we could find it. find out some of the genes and some of the variants that were associated with the flavor profiles. So absolutely. We're very interested in the genetic basis of that as well. You know, I have a catalog of nothing but tomato seed. Yes. Tomato plants, right? You may be familiar with it yourself. And there are so many different colors and varieties. I mean, and last year, home gardeners are really excited about a genetically modified purple

tomatoes. I mean, photos of it look almost unbelievable by how purple it is. It was crossed with a purple snap dragon plant. Could we see the demand for these kinds of specialty fun plants increasing? Absolutely. Yeah, there's been some great work on these purple tomatoes that were kind of developed through crosses and they have some interesting kind of antioxidant capabilities there. My understanding is when that became sort of commercially available, you know, basically sold out in one day.

There's just such huge demand to grow these unique varieties. And people are just really excited about it. Another great example is there's another sort of ornamental plant, the petunia. And then there is a commercially available called the Firefly Petunia that glows in the dark. And it's just really fun to have. It's just amazing to think about what's possible today. And then even more so in the future as we get sort of even better at doing the editing, better at predicting and understanding which variants are associated with which trades.

Could you get a tomato to glow in the dark? I bet we could. I bet we could. We haven't tried it yet, but I bet we could. In case you're just joining us, I'm talking with Dr. Michael Schatz, professor of computational biology and oncology at Johns Hopkins University, about his work using gene editing to grow bigger tomatoes and eggplants. This is Science Friday from WNIC Studios.

Now, you've been doing this a long time, as you've said. You must have watched the technology improve to genetically modify crops. Tell us what you've seen here. Yeah, absolutely. So, you know, as I said, I've been in genomics now about 25 years. And we've basically emerged from the, I don't know, the Stone Age into the space age. One of the first projects I worked on about 20 years ago was we were looking at, in Hawaii, there's a variety of papaya that was really susceptible to a virus that was being passed around. It's something called the papaya ring spot. And it was basically killing off the industry in Hawaii. So there was an early effort there, to do genetic engineering to make it resistant to this virus. But the technology available, you know, this predates the, you know, kind of the identification, the discovery of CRISPR.

So there was a very sort of classic way of doing this using something called a gene gun or small particles of gold would basically pierce through the cell membrane that would allow for bacteria to kind of sneak inside of the cells. And then in a very random way that would sort of induce small fragments of DNA to be incorporated in the genome. It takes a lot of, I don't know, artisanal work to make that gene technology effective, but to their credit, the researchers were able to develop that transgenic variety, the sunup variety of papaya.

They basically saved the industry in Hawaii. That was the early days. You know, it was a very random, very sort of stone tool approach. But like I said, now it's space age where, you know, with laser-like precision, we can specifically identify out of the billions of bases that are there, we can say, yes, this A has to be changed to a C or a T or a REC or, whatever we needed to be, to manifest the trait that we're interested in. Right.

All right. Final question to you. Actually, I'm coming full circle because I began the interview talking about your work as an oncology in cancers. You also work with the human genome there. What is the most exciting application of genomic sequencing you're working on right now? It's many. So as I mentioned, our ability to sequence genomes has advanced enormously over the last

a few decades. I was part of something called the telomere to telomere consortium, where a couple of years ago we put forth the first complete picture of a complete human genome. And that was out of sort of a reference sample, but what's to me, exciting to me, is now we can apply this to patient samples. So at Johns Hopkins, I have a collaboration with Winston Timp and Alison Klein. Ellison is a world's expert in pancreatic cancer and especially familial cancers where it runs in the family, where a patient will have pancreatic cancers, but then their brothers and sisters or their parents, aunts and uncles, grandparents, you know, just runs through the family, so just that it looks like there's a genetic component to this. So Allison has been for many years trying to identify the specific genes and

variants that are associated with that familial cancers. But collectively, that only explains a few percent of all the cases. So we're really excited to take these technologies to read off complete genomes, and if we can read off the complete genome, there's just no place left for these mutations to hide. And then the hope is potentially using CRISPR or other technologies, we can introduce some sort of therapeutic that will prevent the cancer from forming in the first place. So I'm really excited about the possibilities to advance on human health in addition to our food security. Wow, that's quite the range that you're studying there. From tomatoes to cancer. I'd like to thank you Well, for your work, Dr. Shats, and for taking time to be with us today.

Thank you so much. It's been a pleasure. Dr. Michael Shatz, Professor of Computational Biology and Oncology at Johns Hopkins University, based in Baltimore. That's about all the time we have for now. A lot of people help make this show happen. John Denkoski. Annie Niro. Jason Rosenberg.

Rasha Reedy. I'm Ira Flato. Thanks for listening.