Scientists Identify Genes For Tomato And Eggplant Size

IRA FLATOW: This is Science Friday. I’m Ira Flatow. It’s that time of the year when I’m planning 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 nightshaders, is that they’ve located the genes that control the size of tomatoes and eggplants, and then use CRISPR gene editing to grow bigger fruits. I want to know more. 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 Baltimore, Maryland. Welcome to Science Friday.

MICHAEL SCHATZ: Thank you very much. It’s a great pleasure to be here today.

IRA FLATOW: I’ve got to ask you first, how does a guy who’s in the oncology department dealing with tomatoes?

MICHAEL SCHATZ: [LAUGHS] 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.

IRA FLATOW: OK, so let’s get right into it because– can you give me an overview of the tomato’s genome. I mean, how does it compare to other fruits and vegetables?

MICHAEL SCHATZ: 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 chromosome.

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 moderate size model of complexity, which actually makes it a great system for doing genetics on–

IRA FLATOW: Wow.

MICHAEL SCHATZ: –so that we can really handle all that complexity.

IRA FLATOW: So we have fruits and vegetables that have a lot more chromosomes than we do.

MICHAEL SCHATZ: That’s right, that’s right. [CHUCKLES] Even our friend the strawberry has 12 copies of every chromosome. Sugar cane has between 9 and 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 aneuploidy 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.

IRA FLATOW: 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 you give us an overview of what an African eggplant looks like?

MICHAEL SCHATZ: As you said, tomato is part of this larger family of nightshades that includes eggplants and potatoes, but also, in addition to 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 as a pumpkin on a stick because it has sort of a pumpkin-like shape, but it’s actually an eggplant variety.

So people are growing it. There’s a lot of interest into it. The genome is pretty well behaved. It’s sort of similar to tomato. 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.

IRA FLATOW: Right, so you figured out how the genes control growing these big eggplants. And how were you able to then use that to grow bigger tomatoes?

MICHAEL SCHATZ: 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, tastes. But they’re relatively small. They’re hard to grow at large scale. Maybe they’re really sensitive to the environment. For any number of reasons, there’s interest to 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, in 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 eggplant.

IRA FLATOW: mm-hmm, 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?

MICHAEL SCHATZ: Yeah, they’re a little bit too far apart to do crosses like that. But thanks to all the advances in the genome engineering, we can do a more directed editing using that CRISPR Cas9 technology, where if we thought there could be certain variants, certain sequences of DNA, we can now engineer that into this cousin.

So specifically in tomato, there’s a very classic gene called clavata 3 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 for modulating that size in African eggplants.

We expected to see clavata 3 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 the related enzyme in tomato. And it turns out that also modulates fruit size in tomatoes.

IRA FLATOW: Wow.

MICHAEL SCHATZ: So there’s this great exchange of information from tomatoes into African eggplant, and then right back to tomato. So the whole sort of family, the whole nightshade system was sort of elevated through this research.

IRA FLATOW: What part of tomato actually gets bigger? When you modify it and you bring that trait in, which part of the tomato grows, and how big can you get it to grow?

MICHAEL SCHATZ: [LAUGHS] Yeah, if you ever cut a tomato in half, it’s sort of organized into these seed compartments.

IRA FLATOW: Right.

MICHAEL SCHATZ: Those are called locules. The locule is a quantitative trait. In the same way, healthy people have 10 fingers and 10 toes, depending on the variety of tomato, sometimes there may just be one locule, there may be two. A big beefsteak will have many of these large locules.

So this clavata enzyme is really important for modulating the number of locules. The fruits that have more locules, tend to be larger fruits. It’s kind of that simple.

IRA FLATOW: Ah, but sometimes when you get these bigger varieties, they look pretty on the store shelf, but when you eat them, they don’t taste that good.

MICHAEL SCHATZ: Yeah.

IRA FLATOW: I mean, could you preserve that flavor in the tomato when you modified it?

MICHAEL SCHATZ: That’s one of the hopes. We think about, in the United States, the Heinz variety, the Heinz Company. It was a variety that had this interesting history from Central America to Europe and then back again to North America. 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 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.

IRA FLATOW: Well, what’s the benefit of genetically modifying these plants versus the traditional crossbreeding? 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?

MICHAEL SCHATZ: It’s a great question. 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, 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 accidentally get lost.

But now, thanks to all these advances in the biotechnology, we have exquisite technology to sequence genomes. We have exquisite technology to modify them. Rather than waiting for some random event to occur, now 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 in the dark. We can do this in a very focused way to very rapidly advance on this. The minor 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.

IRA FLATOW: When are we going to see these guys in the grocery stores?

MICHAEL SCHATZ: [LAUGHS].

IRA FLATOW: I mean, that must be the goal, right?

MICHAEL SCHATZ: I mean, we’re already seeing this– some of the more progressive grocery stores are starting to accommodate consumer tastes. And, I already mentioned that 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. The yield is low. It’s just kind of that simple. So if we can accelerate the yield, 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, in other parts of the world, this is a major food crop. And if there’s any sort of food sensitivities, there’s this immediate benefit to be able to just develop larger fruits and just have more calories and just make sure there’s food security around the world.

IRA FLATOW: But speaking of other parts of the world, there’s also a great pushback to genetically modified organisms, 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?

MICHAEL SCHATZ: I think it’s still there. I think some people are very progressive and are very interested in the opportunity to bring in new flavors, bring in advances on size or disease resistance. But I do think that there are others that still have some concerns.

And as a person, also as a father, I’m worried about the security of my foods for my children. That would be the last thing I would want to do is give them something that was dangerous. But I think that’s 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, 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 and help them advance on this so that it could be available as a food crop.

IRA FLATOW: Now, if you can find the genes that control the size of the nightshades, the eggplants, the tomatoes, can you find the genes that control the flavors of them, also?

MICHAEL SCHATZ: In addition to fruit size, we’re interested in a variety of other traits. One that’s really important is called flowering time. And that really is important. as you 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 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.

IRA FLATOW: I have a catalog of nothing but tomato seeds–

MICHAEL SCHATZ: Yes. [CHUCKLES]

IRA FLATOW: –tomato plants, right? You may be familiar with it yourself. And there are so many different colors and varieties.

MICHAEL SCHATZ: Yeah.

IRA FLATOW: And last year, home gardeners were really excited about genetically modified purple tomatoes. Photos of it look almost unbelievable by how purple it is. It was crossed with a purple snapdragon plant. Could we see the demand for these kinds of specialty fun plants increasing?

MICHAEL SCHATZ: Absolutely, yeah, there’s been some great work on these purple tomatoes that were developed through crosses. And they have some interesting antioxidant capabilities there.

My understanding is, when that became commercially available, basically, sold out in one day. There was 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.

IRA FLATOW: Wow.

MICHAEL SCHATZ: 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 even better at doing the editing, better at predicting and understanding which variants are associated with which traits.

IRA FLATOW: Could you get a tomato to glow in the dark?

MICHAEL SCHATZ: [LAUGHS] I bet we could. I bet we could. We haven’t tried it yet, but I bet we could.

IRA FLATOW: 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 WNYC studios.

Now, you’ve been doing this a long time, as you’ve said. You must have watched the technology improve to genetically-modified crops. Tell us what you’ve seen here.

MICHAEL SCHATZ: Yeah, absolutely, so as I said, I’ve been in genomics now about 25 years. And we’ve basically emerged from, 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 ringspot. 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– this predates the identification, the discovery of CRISPR, so there was a very classic way of doing this, using something called a gene gun, where small particles of gold would basically pierce through the cell membrane. That would allow for bacteria to sneak inside of the cells, and then, in a very random way, that would induce small fragments of DNA to be incorporated into 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, that basically saved the industry in Hawaii. That was the early days, it was a very random, very sort of stone-tool approach.

But like I said, now it’s Space Age where 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 whatever we need it to be to manifest the trait that we’re interested in.

IRA FLATOW: Right, the final question to you, I actually am coming full circle because I began the interview talking about your work as in oncology and cancers.

MICHAEL SCHATZ: Yeah.

IRA FLATOW: You also work with the human genome there. What is the most exciting application of genomic sequencing you’re working on right now?

MICHAEL SCHATZ: It’s many. So as I mentioned, our ability to sequence genomes has advanced enormously over the last 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 a reference sample. But what’s really exciting to me, is now we can apply this to patient samples.

So at Johns Hopkins, I have a collaboration with Winston Tymp and Alison Klein. Alison 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. It just runs through the family such that it looks like there’s a genetic component to this.

So Alison 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.

IRA FLATOW: Wow, that’s quite the range that you’re studying there, from tomatoes to cancer.

MICHAEL SCHATZ: [LAUGHS]

IRA FLATOW: I’d like to thank you for your work, Dr. Schatz and for taking time to be with us today.

MICHAEL SCHATZ: Thank you so much. It’s been a pleasure.

IRA FLATOW: Dr. Michael Schatz, Professor of Computational Biology and Oncology at Johns Hopkins University, based in Baltimore.

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