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Apples of the future take root in the nation’s strategic fruit repository

Climate change will require breeders to develop apples that can withstand harsher conditions. But can they do that while keeping the fruit crisp and sweet?

The apple, grape, and tart cherry collections at the US Department of Agriculture's Plant Genetic Resources Unit in Geneva, N.Y.Martin Hooker/US Department of Agriculture

You don’t have to be at the US Department of Agriculture’s Plant Genetic Resources Unit very long to discover that an apple tree casts a shadow the perfect size for hiding from the sun. Each tree is a little taller than a person, and at 3 p.m. on a blazing late summer day, that cool lozenge of darkness feels like a cave. Ben Gutierrez, 39, is in the cave too. He has sweat glistening on his forehead, an impish smile on his lips, and the hair and beard of a Dumas musketeer. He is the nation’s curator of apples.

Here, in a field in the Finger Lakes region of New York State maintained by the Department of Agriculture, the apples stretch toward the horizon. It feels like a pick-your-own orchard, except that it goes on and on, and rather than possessing three or four varieties — Macoun, Cortland, Gala, etc. — in this orchard, nearly all the trees are different. There are knobbly French apples, of a variety shown in a Monet still life; there are Spanish apples and Virginia cider apples and hundreds of trees marked “Malus sieversii.” These are Kazakh apples, most grown from scionwood collected decades ago by a former curator in the ancestral heartland of the apple, the mountains of Eastern Kazakhstan. Many of their fruits are purple or yellow and plum-like in shape. I try one; it tastes like death.


These apples show russeting, a pattern on the skin caused by the interaction of genetics and environmental conditions. Common enough in nature, russeting is rarely seen in the apples that make it to the grocery store.Veronique Greenwood

Actually, it turns out that the native state of apples generally is that they taste like death. Gutierrez and his molecular biologist colleague Tori Meakem lead me through a gauntlet of apple tasting that illuminates the many qualities of the unimproved apple: It’s a tart, sometimes bitter thing. As I retch and spit a cherry-sized little number out, Gutierrez insists that there’s something there, behind the unbelievable bitterness, some trait that might be interesting to explore.


That’s part of why this collection exists: The breeders of the apples that wind up in our fruit bowls need raw materials. When they take an apple and try to make it crisper, or sweeter, or, as may soon be necessary, more able to stand up to the looming trials of climate change, that new trait needs to come from somewhere. It needs to come from a tree like these I’m standing among. If the fruit tastes awful now, it might not matter in the long run: Over the course of many generations, breeders can make some surprising things happen.

As I bite my way through the field, I start to recognize the many ways that an apple can be unlike the fruit that we buy: There are dry apples, fiercely astringent apples, chalky apples, even a tiny beautiful thing like a Rainier cherry that tastes of vanilla but has no acid. Ever since Cornell University first set up an apple breeding center in Geneva in the 1890s — the USDA facility, which opened in 1983, drew on Cornell’s apples to get started — breeders have crossed and backcrossed these trees in their quest to make the next blockbuster fruit.

Acid, it turns out, is key to what humans want from apples. Sweetness, too. But one of the most important traits these days, the grail of 21st century pomology, is crispness. Susan Brown, Cornell’s giant of apple breeding and co-inventor of the SnapDragon apple, ranks it about even with flavor, in terms of what consumers want. And giving consumers what they want, in the form of a crisp, gleaming, sweet-tart apple, can change a university’s fortune, at the same time that it benefits growers. The Honeycrisp, released in 1991 by David Bedford and Jim Luby at the University of Minnesota, has netted millions.


Apples come in all shapes, sizes, colors and flavors.Veronique Greenwood

Beyond their culinary qualities, apples have a romance that sometimes baffles even Gutierrez, who used to be the curator of grapes. Of all the items in the USDA’s holdings — this location includes tomatoes, onions, and asparagus, among others — it’s the apples that draw the most attention from non-scientists. The collection was featured in Michael Pollan’s book “Botany of Desire,” a star turn that led motorcyclists to roll up at the facility hoping to take a look. Gutierrez would like to direct everyone’s attention to the USDA’s stash of tart cherries, which are full of interesting traits like the ability to make melatonin. “We have other stuff!” he says.

But apples, for all their charm, are fragile. In 2020, the repository saw a vicious outbreak of fire blight, a bacterial disease that thrives in humid conditions. The strain was resistant to the usual antibiotic. The trees had their limbs amputated by the hundreds, as the team worked to keep their library alive. As climate change continues to trigger weather that’s different from what trees are used to, disease outbreaks may become more frequent.

The changing climate poses other risks to apples. In the Northeast, winters will be warmer and springs wetter, and the weather is expected to become more erratic. But many apples need an autumn chill to turn red and grow sweet. A warm fall makes them mealy and pale. Other dangers come with a cold spring. If a late freeze comes after a tree has already bloomed — and in the warmer temperatures occurring in the Northeast, that’s expected to happen — the cold will destroy the flowers. No flowers, no fruit. In fact, people looking for pick-your-own-apples this year in Massachusetts will find that many familiar orchards won’t be open. On May 18, a sudden freeze devastated fruit blossoms across the state, wiping out the crop.


Growers worried about the future might start planting apples from warmer places like Italy, apples whose needs could match better with the future climate. At a fruit conference in February, an industry group called the Hot Climate Partnership and fruit company VentureFruit released an apple called Tutti, billed as the world’s first specially bred heat-resistant apple variety.

Do traits that could make apples resilient lie in the repository’s collection of wild apples? I ask Jason Londo, a Cornell fruit physiologist based in Geneva.

In his office, he traces a circle in the air with a pen. Each apple has a comfort zone, a range of conditions in which it can reasonably survive, he says. With a wild apple, that range might indeed be larger. They are generally hardier than their domesticated kin. And if scientists can identify the genes associated with such traits, they can start a program of crosses to bring them over to the vulnerable varieties.


Identifying such traits is a monumental task, however. How do you test for something as vague as “resilience”?

You break it down into pieces, like standing up to flooding or blooming late enough to escape frosts, says Chris Gottschalk, a USDA geneticist at the Appalachian Fruit Research Institute. He studies wild apples with an eye toward using them for breeding, and he is particularly interested in Malus fusca, a wild North American relative of domesticated apples that can resist fire blight. The Geneva collection’s M. fusca was grown from a tree found on an Alaskan beach, suggesting it can survive challenging conditions.

“If I can find really durable, strong resistance to fire blight, and if I can combine that with an extremely late-blooming phenotype,” Gottschalk explains, “I could have an apple that could resist frost damage, but also not be affected by the pathogen that’s present in those hot humid spring days.”

Nearly every tree in the Geneva field is different: There are 3,355 trees, representing 2,939 different genotypes. These are Lady Ilgen apples, a German crab apple given to the USDA in 1954, with distinctive, multi-lobed structures at the base of the fruit.Veronique Greenwood

These are long-term projects, though: It takes years, often decades, to bring such traits into trees that university and commercial breeders could then use in their breeding efforts. We might need these traits sooner than we can have them.

So far, growers are still mainly focused on producing a picture-perfect apple that will enchant grocery shoppers, says Londo. Breeding for climate change resilience could introduce qualities that consumers don’t like or value as much. It is still profitable to plant apples that may not fare well in the future, as long as that fruit commands high prices today.

What will cause a sea change? Perhaps the first fall that every apple crop in the United States fails —Washington has a frost, New York has a drought, Michigan has floods — and the price of apples skyrockets, there may be a change of heart, says Londo. Then if people ask why apples are so expensive, there will be an answer, he says: “We are growing apples that need help, and we can’t fix them fast enough.”

For now, Gutierrez and Meakem are finding new ways to record what their apples can do. Meakem is learning to analyze the volatile compounds in apples — the things that often impart flavor and aroma — and plans to upload each plant’s profile to the repository’s online database. Gutierrez and other colleagues published a paper about the fire blight outbreak, with detailed data on its effects. Gutierrez reminds visitors that the goal of that broad field of trees is to contain multitudes, oddities — not necessarily tasty individuals. “I love to be shocked,” he says, when I ask him what he loves about apples. “And I’m always shocked out there.”

The next morning, in the cooler hours after dawn, I walk from row to row to row. Some trees, replanted after the fire blight, are just sticks. Others have dense batons of orange fruit. Some have sprays of tiny, perfectly formed fruit no larger than a dime. A pale yellow globe the size of a toddler’s head peeks out from the leaves of its tree. The label nearby reads “Surprise.”

Look at all the things the apple can do, if we let it.

This story was updated on Oct. 16 to correct the description of Jason Londo’s speciality.

Veronique Greenwood is a science writer who contributes frequently to Ideas.