An Apple Is An Ovary: The Science of Apple Breeding

Summary

Short Wave Podcast Summary

Episode: An Apple Is An Ovary: The Science of Apple Breeding
Date: November 18, 2025
Hosts: Emily Kwong, Hanna Chin
Featured Experts: Dr. Susan Brown (Cornell Agritech), Ben Gutierrez (USDA Plant Geneticist)

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Overview

This episode dives into the mind-bending science of apple breeding, revealing why your favorite apples are essentially clones, how entirely new varieties like the Honeycrisp or Rosalie are painstakingly created, and why preserving apple diversity could shape the future of what we eat. The hosts mix playful banter with a look behind the scenes at Cornell’s world-renowned apple breeding lab and the USDA’s “Noah’s Ark” of apple diversity.

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Key Discussion Points & Insights

Apple Cloning and Propagation

• All commercial apples are clones: Whether you pluck a Rosalie in Maryland or buy one in New York, it’s genetically identical to every other Rosalie.
  • “Those Rosalie apples that you saw, they’re the same Rosalies that I might see apple picking in New York. They’re clones.” — Hannah Chin [00:42]
  • This is accomplished by grafting cuttings (buds) from one tree onto the rootstock of another, ensuring that every tree grows apples with identical DNA.
• Botanist’s take:
  • “Every leaf has the genetic potential to make a tree.” — Dr. Susan Brown [01:16]

How New Apples Are Born

• Cross-breeding apples: To make a new apple variety, scientists like Dr. Susan Brown manually control apple pollination:
  • Remove petals and anthers from the 'seed parent' flower to prevent pollination by bees, then apply pollen from a chosen 'pollen parent.'
  • Comparing the process to reality TV:
    • “And apparently there's several rounds of testing. It's like the American Idol, but of apple tasting.” — Hannah Chin [11:33]
    • “And she’s Simon Cowell.” — Emily Kwong [11:39]
• Labor-intensive magic:
  • Each prospective apple is hand-pollinated, apples are grown, seeds extracted, and seedlings planted—then comes the taste test.
  • “I create thousands of these hybrids, and then, yes, I must eat them... I can be brutal. I have two wonderful children. I had to keep them. My apples, I don't have to keep.” — Dr. Susan Brown [10:44]

The Science: Apples as Ovaries & Genetic Goldmines

• Biology 101:
  • “When an apple tree is still in flower, bees visit... that apple flower becomes an apple, which you can kind of think of like a fertilized ovary.” — Hannah Chin [05:47]
  • Every apple seed is unique—just as you are a mix of both parents, so is each apple seed a mix of two apple trees.
• Genetics complexity:
  • “There are 54,000 genes in apples, more than in humans.” — Hannah Chin [12:45]
  • This genetic complexity is both a challenge (makes selective breeding slower) and an opportunity (more variety and potential).

Modernizing Apple Breeding

• DNA Marker-Assisted Selection:
  • Researchers are developing methods to identify desired traits earlier, by reading gene markers at the sapling stage.
  • “Let’s see, on the genetic level, whether we can find a strand of DNA that matches whether it’s red or yellow... You can use that marker to select at the seedling stage so before they even fruit.” — Dr. Susan Brown [12:14]
  • Full reliance on this technology awaits further research due to apples’ genetic complexity.

Preserving Apple Diversity for the Future

• “Noah’s Ark” of apples: The USDA runs a unique orchard with 5,000 different, wild, and rare apple varieties to safeguard genetic diversity.
  • “Each one of them is totally unique. Some... huge and round and green... some tiny... so red that they were almost purple.” — Hannah Chin [14:08]
  • Apples can’t be preserved merely as seeds—their next generation will always be genetically different.
  • “Apples need to be preserved as trees because... the seed... is going to be something different.” — Ben Gutierrez [14:20]
• Long-term vision: Breeders and geneticists are seeking unique genes that may not taste good today but could ensure disease resistance or other future traits.
  • “This is maybe 50 to 60 years away from becoming optimistic... But it could have an interesting trait for, again, disease resistance...” — Ben Gutierrez [15:06]

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Notable Quotes & Memorable Moments

• On the odd truth about apples:
  • “Oh, an apple is an ovary.” — Emily Kwong [06:12]
• Joking about lineage:
  • “It’s like a Maury Povich episode up in these apples.” — Emily Kwong [06:40]
• On the patience needed:
  • “On average, it takes maybe 20 years to develop a new apple. There’s a lot of waiting and patience and work involved.” — Hannah Chin [09:57]
• The genetic lottery:
  • “I want that one really bright child, the shining star of apples... My apples, I don’t have to keep.” — Dr. Susan Brown [10:44]
• On bad apples:
  • “I’m sure that there are some that are not good.” — Hannah Chin [11:16]
  • “Oh, there’s many. They’re called spitters because you spit them out.” — Dr. Susan Brown [11:26]
• On apple genome complexity:
  • “Wait, more than in humans?” — Emily Kwong [12:55]
  • “Yeah.” — Susan Brown [12:57]
• The vision for the future:
  • “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, you know, almost unlimited potential.” — Ben Gutierrez [13:29]

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Timestamps for Important Segments

• Apple varieties and cloning explained: [00:28]–[02:18]
• Introduction to apple breeding and Susan Brown: [02:44]–[04:00]
• How apples breed, apples as ovaries: [05:36]–[06:27]
• Manual cross-breeding process: [07:04]–[10:17]
• Taste testing and selection: [10:44]–[11:39]
• Apple genetics and DNA marker research: [11:42]–[12:58]
• Apple diversity preservation with Ben Gutierrez: [13:29]–[15:32]
• Closing reflections on the future: [15:32]–[15:41]

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Tone & Style

The episode mixes witty banter (“It’s like a Maury Povich episode up in these apples.”), friendly analogies, and deep-dive scientific reporting to make apple genetics and breeding accessible and fun for a general audience.

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Conclusion

This Short Wave episode delivers a vibrant, hands-on look at the science and art of apple breeding. Listeners come away with a newfound appreciation for every crunchy bite—knowing the genetics, history, and dedicated work behind their favorite varieties, and the ever-evolving search for the apples of tomorrow.

Transcript

[Announcer]

This message comes from Memorial Sloan Kettering Cancer center working to change the story of pancreatic cancer. And during Pancreatic Cancer Awareness Month, your support goes twice as far to accelerate breakthrough treatments. Donate [e-mail] give.

[Emily Kwong]

You're listening to Short Wave from NPR. Hey, Short Wavers. Emily Kwong here with producer Hanna Chin.

[Hannah Chin]

Hey, Emily.

[Emily Kwong]

And a fridge full to the brim.

[Hannah Chin]

Of apples that I picked with my.

[Emily Kwong]

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.

[Sponsor Voice]

Ooh.

[Hannah Chin]

You know, Emily, what's really cool is that those Rosalie apples that you saw, they're the same Rosalies that I might see apple picking in New York. They're clones.

[Emily Kwong]

They're clones?

[Hannah Chin]

Yeah. Basically, if I buy a Rosalie in a grocery store in New York and you buy a Rosalie in an orchard in Mar, our Rosalie apples are going to be genetically the exact same because they're all from the same original plant.

[Emily Kwong]

So you're telling me all apples are copies of each other?

[Hannah Chin]

Exactly. Well, in botanist terms, they're propagated.

[Susan Brown]

Every leaf has the genetic potential to make a tree.

[Hannah Chin]

So this is Susan Brown, and she 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.

[Susan Brown]

So we take a leaf from the tree that we want to propagate. So in this case, let's say honeycrisp, 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.

[Emily Kwong]

Oh, this is what people do with houseplant cuttings. When they propagate them, they, like, snip off a bit, put it in water. You're telling me this that the new plant is genetically the exact same as the old plant?

[Hannah Chin]

Yeah. When people do that, they're basically cloning their houseplants. So when Susan propagates apple trees, she's basically just copy and pasting them. And that means all of the apples on that honeycrisp tree are going to be genetically identical.

[Emily Kwong]

So then if that's the case, Hannah, how do you create a new kind of apple like that Rosalie apple? I know it's a cross between a Honeycrisp and a Fuji, but I got to admit, I have no idea how that happens.

[Hannah Chin]

It's science. And the science of apple breeding is fascinating. Like Emily, there's 7,500 varieties of apples grown around the world.

[Emily Kwong]

That is so many. I thought I knew a whole bunch of types of apples, but I didn't realize there were thousands.

[Hannah Chin]

Yeah, most of them, like Rubyfrost or Snapdragon, are invented by breeders like Susan. She's basically the Willy Wonka of apples.

[Emily Kwong]

Wait, I think I've eaten snapdragons in New York. They're really crunchy.

[Hannah Chin]

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.

[Susan Brown]

Honeycrisp is a wonderful apple. Great name, great marketing, really popular with people. But only about 40% of the Honeycrisp makes it from the orchard to the grocery store.

[Hannah Chin]

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.

[Emily Kwong]

So today on the show, the science.

[Hannah Chin]

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 in hopes they'll lead us to the fruit of the future.

[Emily Kwong]

You're listening to Shorewave, the science podcast from npr.

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[Emily Kwong]

Okay, Hannah, 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?

[Hannah Chin]

Totally. Let's start with 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.

[Emily Kwong]

Oh, an apple is an ovary.

[Hannah Chin]

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.

[Emily Kwong]

And its two parents are like the apple tree and then the pollen from some other tree.

[Hannah Chin]

Exactly. But the bees are really busy, Right. So they bring a lot of different pollen from a lot of different trees.

[Emily Kwong]

Okay, so it's like a Maury Povich episode up in these apples.

[Hannah Chin]

Amori.

[Emily Kwong]

What? Maury Po. It's like he's like the parentage detective of the aughts. Don't worry about it.

[Hannah Chin]

Okay, back to apples. Let's talk about apple.

[Emily Kwong]

Willy Wonka Land. Susan Brown and her team at Cornell Agritech are inventing brand new varieties of apples all themselves. How are they doing that?

[Hannah Chin]

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.

[Susan Brown]

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.

[Hannah Chin]

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.

[Susan Brown]

And so that process is called emasculation, which gets a lot of laughs during dogs.

[Emily Kwong]

That's intense. Susan's emasculating these trees. So the tree is not like appealing to the bee.

[Hannah Chin]

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.

[Emily Kwong]

Okay, so what then do they do?

[Susan Brown]

So a pollen Parent. We select the flowers before they open, and we use a screen or a comb, and we comb out the anthers.

[Hannah Chin]

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.

[Susan Brown]

And this is enough pollen to pollinate a ton of flowers. Wow.

[Hannah Chin]

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.

[Ben Gutierrez]

Wow.

[Susan Brown]

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.

[Hannah Chin]

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.

[Emily Kwong]

So they're racing around like bees. They're impersonating these bees flying all about, hand pollinating these apple flowers. Then what happens?

[Hannah Chin]

Time passes. The trees bear apple fruit, which have.

[Susan Brown]

Seeds inside, and then we collect the seeds. So right this time of year, we're collecting the fruit, and then by hand, we extract the seeds, which are then propagated.

[Emily Kwong]

Are these the seeds inside the apple fruits?

[Hannah Chin]

Yes. They have to cut up all the apples and then extract the seeds by hand and then plant them.

[Emily Kwong]

This is so labor intensive. Yeah.

[Hannah Chin]

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.

[Emily Kwong]

And the seeds grow into apple trees?

[Hannah Chin]

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.

[Sponsor Voice]

Okay.

[Hannah Chin]

So each seedling becomes like, an apple branch and produces two, three apples, which Susan and her team then have to taste test.

[Susan Brown]

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.

[Emily Kwong]

She throws out the literal bad apples she does.

[Hannah Chin]

And sometimes they're 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.

[Susan Brown]

Oh, there's many. They're called spitters because you spit them out. Oh, yeah.

[Hannah Chin]

And apparently there's several rounds of testing. It's like the American Idol, but of apple tasting.

[Emily Kwong]

And she's Simon Cowell. She is.

[Hannah Chin]

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.

[Susan Brown]

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.

[Emily Kwong]

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?

[Hannah Chin]

Well, this is still an emerging area of research. And, Emily, there are 54,000 genes in apples, more than in humans.

[Emily Kwong]

Wait, more than in humans?

[Susan Brown]

Yeah.

[Hannah Chin]

Apples are complex. I know.

[Emily Kwong]

That's what I'm learning in this episode.

[Hannah Chin]

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 gonna have to keep breeding apples. The old fashioned taste test way.

[Announcer]

Yeah.

[Emily Kwong]

54,000 genes. That is a lot to map.

[Hannah Chin]

Exactly. Which honestly, sort of overwhelming, but also means there's so much possibility for scientists to explore.

[Ben Gutierrez]

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, you know, almost unlimited potential.

[Hannah Chin]

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.

[Ben Gutierrez]

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. Like, apples need to be preserved as trees because the seed, again, the next generation, is going to be something different.

[Emily Kwong]

This work has such longevity. Like, it is about looking to the future of apple making.

[Hannah Chin]

Yeah, it's like this huge archive, like a Noah's ark of apples from all over the world.

[Ben Gutierrez]

A lot of diversity collections like in other countries, like Focus on Malus 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.

[Hannah Chin]

That one was really bad.

[Ben Gutierrez]

It's not bad. So certainly this is not the next Snapdragon. Right. Like, this is maybe 50 to 60 years away from becoming optimistic.

[Hannah Chin]

But it could carry.

[Ben Gutierrez]

But it could have. 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.

[Emily Kwong]

That is such a nice way to look at it.

[Announcer]

Yeah.

[Hannah Chin]

These apples, Ben says their genes could hold the key to the apples of the future. We just don't know yet.

[Emily Kwong]

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.

[Hannah Chin]

Thank you.

[Emily Kwong]

This episode was reported by Hannah Chin and produced by Rachel Carlson. It was edited by Rebecca Ramirez.

[Hannah Chin]

Tyler Jones checked the facts.

[Emily Kwong]

Kwesi 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 Short Wave from npr.

[Hannah Chin]

Have you heard Apple by Charli xcx?

[Susan Brown]

No.

[Hannah Chin]

Okay. It's like it goes, I guess the apple's rotten right to the core. You haven't heard this song?

[Susan Brown]

No, but I'll definitely check that out.

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