Short Wave - An Apple Is An Ovary: The Science of Apple Breeding

Episode Date: November 18, 2025

What's your favorite apple? Maybe it's the crowd-pleasing Honeycrisp, the tart Granny Smith or the infamous Red Delicious. Either way, before that apple made it to your local grocery store or orchard it had to be invented — by a scientist. So today, we're going straight to the source: Talking to an apple breeder. Producer Hannah Chinn reports how apples are selected, bred, grown ... and the discoveries that could change that process. Plus, what's a "spitter"?Read more of Hannah's apple reporting.Want to know how science impacts other food you eat? Email us at [e-mail] and we might cover your food of choice on a future episode!Listen to every episode of Short Wave sponsor-free and support our work at NPR by signing up for Short Wave+ at plus.npr.org/shortwave.See pcm.adswizz.com for information about our collection and use of personal data for sponsorship and to manage your podcast sponsorship preferences.NPR Privacy Policy

You're listening to Shortwave from NPR. Hey, shortwavers, Emily Kwong here with producer Hannah Chin. Hey, Emily. And a fridge full to the brim of apples that I picked with my family at Rock Hill Orchard in Maryland. I forgot, Hannah, there's so many varieties out there. There's sun crisp, but also Rome and this new apple I hadn't heard of called a rosalie. I think that's my new favorite. Ooh.

You know, Emily, what's really cool is that those rosalie apples that you saw, they're the same rosell Rosalie's that I might see apple picking in New York. They're clones. They're clones? Yeah, basically if I buy a Rosalie in a grocery store in New York, and you buy a rosalie in an orchard in Maryland, our rosalie apples are going to be genetically the exact same, because they're all from the same original plant. So you're telling me all apples are copies of each other. Exactly. Well, in botanist terms, they're propagated.

Every leaf has the genetic potential to make a tree. So this is Susan Brown, and she's supervised a lot of propagation in her time because she's the head of the apple breeding program at Cornell Agritech in Geneva, New York, which is where I met her for this reporting trip. So we take a leaf from the tree that we want to propagate, so in this case, let's say Connie Crisp, and we put it on a rootstock. by matching the bud to the growing material. And then when that heals in, it's cut off and it makes a new tree.

Oh, this is what people do with house plant cuttings when they propagate them. They like snip off a bit, put it in water. You're telling me that the new plant is genetically the exact same as the old plant? Yeah, when people do that, they're basically cloning their houseplants. So when Susan propagates apple trees, she's basically just copy and paper. tasting them. And that means all of the apples on that Honeycrisp tree are going to be genetically identical. So then if that's the case, Hannah, how do you create a new kind of apple? Like that Rosalie apple, I know that's a cross between a Honeycrisp and a Fuji, but I got to admit I have

no idea how that happens. It's science. And the science of Apple rating is fascinating. Like, Emily, there's 7,500 varieties of apples grown around the world. That is so many. I thought I knew a whole bunch of types of apples, but I didn't realize there were thousands. Yeah. Most of them, like Ruby Frost or Snapdragon, are invented by breeders like Susan. She's basically the Willy Wonka of apples. Wait, I think I've eaten Snapdragons in New York. They're really crunchy. That's Susan's apple. And as the Willy Wonka of apples, she's always on the hunt for a better one. Because even my favorite apple, Honeycrisp, turns out it's not perfect. Honeycrisp is a wonderful apple. Great name, great marketing, really popular with people.

But only about 40% of the honey crisp makes it from the orchard to the grocery store. So when breeders are experimenting with apples, oftentimes they're trying to increase storability or disease resistance, basically to minimize the loss and maximize the benefits of any given apple variety. So today on the show, the science of apples. how apples are selected, bred, and grown, and the discoveries that are changing that process. Plus, how scientists are preserving the apples of the past and hopes they'll lead us to the free to the future. You're listening to Shorewave, the science podcast from NPR. Okay, Anna, so we're going to talk about apple breeding, how to make new kinds of apples.

I actually have no idea how this happens at all, like zero understanding. Can you help me out? Totally. Let's start with like the basics. like how apples breed in nature. All right. So when an apple tree is still in flower, bees visit, right? They drop their pollen. That flower combines its genetic material with the pollen,

sheds its petals, and that apple flower becomes an apple, which you can kind of think of like a fertilized ovary. Oh, an apple is an ovary? Yeah. And then the seed inside that ovary, inside that apple, is totally unique. Just like you're a genetic. combination of your two parents. An apple seed is a genetic combination of its two parents. And its two parents are like the apple tree and then the pollen from some other tree.

Exactly. But the bees are really busy, right? So they bring a lot of different pollen from a lot of different trees. Okay. So it's like a Mori-povich episode up in these apples. A mori what? Mori-po. No, it's like the parentage detective of the aughts. Don't worry about it. Okay. Back to apples. Let's talk about Apple Willie Wonka land. Susan Brown and her team at Cornell Agritech are inventing brand new varieties of apples all themselves. How are they doing that? So in order for Susan to create this brand new apple, this cross between these two different apple trees, she has to be able to choose the parents. And that means she has to beat the bees. So in an orchard, a tree is there and bees are going to bring pollen. But if I take off the petals and the anthers, that's the part of the flower that attracts the bee.

You probably know what the petals look like already, but the anthers are the little almost antenna-looking things in the middle of the flower. They're tipped by pollen. So she takes those off. And so that process is called amasculation, which gets a lot of laughs during dogs. That's intense. Susan's emasculating these trees. So the tree is not like appealing to the bee. Yes.

So that apple tree is what they call the seed parent. And then they pick the other apple they're going to cross it with, which is called the pollen parent. Okay. So what then do they do? So a pollen parent, we select the flowers before they open. And we use a screen or a comb and we comb out the a others. So they collect that pollen in little plastic vials about the size of like, a film canister. Susan actually showed me some. It basically looked like maybe a teaspoon,

maybe two of this really, really fine yellow powder. And this is enough pollen to pollinate a ton of flowers. Wow. Okay. And then once the flowers are ready, Susan and her team go through all the trees and Emily, get this. They have to pollinate each individual flower by hand. Wow. So if we had a flower here, I'd be like gently touching the stigma, which is the receptive surface that the pollen grains grow down. Right. So she hand-pollinates that stigma in the center of the flower. And it's a ton of work.

She brings in her kids. She brings in her grad students. They have to pollinate each flower on each tree twice. It all takes place over the span of two weeks because they have to do it in the span of time where the apples are flowering. it's totally exhausting. Wow, so they're racing around like bees. They're impersonating these bees flying all about, hand-pollinating these apple flowers.

Then what happens? Time passes. The trees bear apple fruit, which have seeds inside. And then we collect the seeds. Right this time of year, we're collecting the fruit. And then by hand we extract the seeds, which are then propagated. Are these the seeds inside the apple?

Fruits? Yes. They have to cut up all the apples and then extract the seeds by hand and then plant them. This is so labor intensive. Yeah. So this is also why on average it takes maybe 20 years to develop a new apple. There's a lot of waiting and patience and work involved. Anyway, Susan will then plant these newfangled seeds in a giant greenhouse. Okay. And the seeds grow into apple trees. Not quite. They become apple seedlings, these toddler trees, which Susan and her team transplant onto tree bases, called rootstocks, because it speeds up the process of them bearing fruit. Okay. So each seedling becomes like an apple branch and produces two, three apples, which Susan and her team then have to taste test.

So what I do is I create thousands of these hybrids. and then, yes, I must eat them. I kind of use the human example that as a breeder, I get to do thousands because I want that one really bright child, the shining star of apples. And I can be brutal. I have two wonderful children. I had to keep them.

My apples, I don't have to keep them. She throws out the literal bad apples. She does. And sometimes they're always, all bad. Can I ask, you said you have to eat all of these thousands of apples. I'm sure that there are some that are not good. Oh, there's many. They're called spitters. Because he spit them out? Oh, yeah. And apparently there's several rounds of testing. It's like the American idol, but of apple tasting. And she's Simon Cowell. She is. But this whole process, hand pollinating,

seed extraction, seedling growth, taste testing. It's pretty inefficient. So Susan is researching a different way to do it through Apple DNA testing. The idea behind this research is that you could look at each apple tree and read its gene markers like a book. That way, before you even have to taste each apple, you know what it'd be like.

And you could potentially select for specific markers, like whether an apple is red or yellow. Let's see on the genetic level, whether we can find a strand of DNA that matches whether it's red or yellow. And it's like marking a deck of cards. You can use that marker to select at the seedling stage. So before they even fruit. That's clever. That's really practical.

And I imagine it saves a lot of time and bad apple tasting. So has this process been implemented? Like, why isn't she doing this right now? Well, this is still an emerging area of research. And Emily, there are 54,000 genes in apples, more than in humans. Wait, more than in humans? Apples are complex. I know.

That's what I'm learning in this episode. Hey, I appreciate apples so much more now than I ever did before. So Susan says that until we have way more genetic markers, we're probably going to have to keep breeding apples the old-fashioned taste test way. Yeah. 54,000 genes, that is a lot to map. Exactly. Which, honestly, sort of overwhelming, but also means there's so much possibility for scientists to explore. What's so amazing about Apple is just its broad genetic diversity.

Like, it can't self-pollinate. So each generation of Apple is some new cross that's never been done before. So there's almost unlimited potential. This is Ben Gutierrez. He's a plant geneticist and a former student of Susan's. And his job is basically to preserve that genetic diversity of apples. In fact, the U.S. Department of Agriculture has an entire orchard just dedicated to that preservation. And Ben gave me a tour.

Nice. Emily, this orchard was huge. Like 5,000 trees, and each one of them is totally unique. Some of the apples were huge and round and green. and some of them were tiny, so cute and so red that they were almost purple. Like, I've never seen so many different types of apples. Different from other gene banks where you can store the material as seed in a vault, and it's secure and tucked away, and all you need is a fridge or a freezer that won't fail, right?

Apples need to be preserved as trees because the seed, again, the next generation is going to be something different. This work has such longevity. Like, it is about looking to the future of apple making. Yeah, it's like this huge archive, like a Noah's arc of apples from all over the world. A lot of diversity collections like in other countries like focus on Malas Domestica, the commercial apple, whereas most of our collection is wild. So we've done a lot of explorations through Kazakhstan. This one was from Turkey.

That one was really bad. That's not bad. So certainly this is not the next Snapdragon, right? This is maybe 50 to 60 years away from becoming optimistic. But it could carry some trait. It could have an interesting trait for, again, disease resistance. Maybe like, it could just be some missing link in understanding the evolution of Apple as a whole. That is such a nice way to look at it.

Yeah. These apples, Fenn says their genes could hold the key to the apples of the future. We just don't know yet. We'll find out. 50, 60 years from now, we'll all be. eating whatever you just spit out, Hannah. Thank you so much for this reporting. Thank you.

This episode was reported by Hannah Chin and produced by Rachel Carlson. It was edited by Rebecca Ramirez. Tyler Jones checked the facts. Cui Cui Lee was the audio engineer. Beth Donovan is our senior director and Colin Campbell is our senior vice president of podcasting strategy.

I'm Emily Kwong. Thanks for listening to Shorewave from NPR. Have you heard Apple by Charlie X? X. No. Okay. It's like, it goes,

I guess the apples wrapped right to the core. You haven't heard this song. No, but I'll definitely check that out.