When Jude Schuenemeyer picked the apple up off the ground in December 2017, he wondered whether his two-decade search was over. It was a firm winter apple, orange in colour with a distinctive ribbed shape and wider than it was tall. “We knew right away that we had never seen it before,” Schuenemeyer says.

He and his wife, Addie, started the Montezuma Orchard Restoration Project in 2008 to find and revive endangered heirloom apple varieties. The horticulturalists, based in Cortez, Colorado, had made a few discoveries, but there was one coveted variety that had eluded them: the Colorado Orange. Once a popular apple in the western United States, it had essentially disappeared by 1900. And although the Schuenemeyers had chased a few false leads in the past, this apple — from an almost-dead tree on a private piece of land near Cañon City — looked promising.

Months of careful consultation followed. The couple compared the specimen with the US Department of Agriculture’s pomological watercolour collection of some 7,000 historical fruit images as well as with century-old wax apple models stored at Colorado State University in Fort Collins. Their search paid off — the Colorado Orange apple had survived and could possibly be preserved.

Today, a young sapling grafted from the tree in Cañon City is growing in a unique research orchard on the outskirts of Boulder. It was planted alongside 30 or so trees, resurrected from old, unvisited spaces — abandoned homesteads, overgrown fields and hidden canyons. Some came from trees growing in places where no one would expect an apple tree to grow.

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Amy Dunbar-Wallis, a plant ecologist at the University of Colorado Boulder has been collecting these lost or half-forgotten apples in the hope of finding genetic variants that will unlock the flavour and texture profile of the next blockbuster fruit¹. Apple-conservation efforts are continuing in other parts of the world and the specimens that they are reviving reflect the cultural and ecological history of their place in the world.

The genes might also encode traits that make the trees more resistant to disease, climate change and other environmental pressures. These genes could then be incorporated into other apple varieties through careful breeding strategies or potentially through genetic engineering.

“They might have really great gene variants,” says Cameron Peace, a fruit geneticist at Washington State University in Pullman. Peace has been working with Dunbar-Wallis and others to catalogue the apple genes that contribute to traits such as cold hardiness, heat tolerance, flavour and aroma. And as they wait for the saplings — each now around 5 feet tall — to bear fruit, the effort to find out what makes these varieties unique has already begun.

The road to domestication

All cultivated varieties (or cultivars) of eating apple belong to the same species, Malus domestica. Currently, there are around 7,500 recognized cultivars worldwide. Some are well-known: Fuji, Gala, Granny Smith and Honeycrisp to name a few. But at the end of the short list of widely marketed varieties is a much longer list of obscure apples. Each has its own distinct origins and characteristics, some of which go back centuries. Pippins, Spys, Russets and Smiths. All are different.

The flesh of the Autumn Glory, named in 2011 in Washington state, for example, imparts a subtle cinnamon flavour. The Winter Banana (Indiana, 1876), has a taste reminiscent of its incomparable tropical namesake. The skin of the Bloody Ploughman (Carse of Gowrie, UK, around 1800) is so darkly empurpled that it looks almost black. And in 1785, when the Pitmaston Pineapple was introduced in Worcester, UK, most of the locals had probably never even seen the fruit after which it was named.

“Apples are wildly heterozygous,” says Dunbar-Wallis, which is to say that many apple genes have variants that can produce drastically different characteristics. This presents a challenge for cultivation. To bear fruit, apple trees must cross-pollinate. They must rely on insects — typically bees — to transport pollen from a flower on one tree to a flower on another. Although the genes (and traits) of the borne fruit match the plant on which they grow, the seeds in the apples contain a random mixture of the parents’ genomes.

“Say you had an apple for lunch, and you planted eight seeds from that apple,” says Dunbar-Wallis. From the trees that would result, “you’re going to get eight very different tasting fruits”.

This is why apple growers propagate apples by grafting a flowering branch from a specific cultivar to the rootstock of another tree, rather than planting seeds. The resulting limbs, leaves and fruit are all genetic clones of the tree from which they were grafted. It’s a process that dates back thousands of years, to when apples spread across central Asia westward along the Silk Road to Europe.

But without careful and constant maintenance, things can quickly unravel for the cultivars. Apple trees have an average lifespan of 80–140 years. So without human involvement, all known apple varieties would be gone in just a few centuries. In the United States, people have also intentionally reduced the list of commercially available varieties to those with attributes that benefit mass production, casting away hundreds of lesser-known regional varieties. The main winner of this winnowing down was Red Delicious, a juggernaut of an apple.

Ruby red, with an easily stackable shape, a long shelf life and a tough skin that protects the fruit against damage, Red Delicious became the quintessential US apple, part of every school lunchbox and a staple in cafeterias and supermarkets. Between 1968 and 2018, it was by far the most widely grown cultivar in the United States. In the 1980s, Red Delicious accounted for around 75% of the apple crop in Washington state, the country’s top grower of apples.

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Dunbar-Wallis calls the popularity of Red Delicious a product of 1950s US food culture. “It’s just like getting canned vegetables,” she says. Convenient, but not very good: “It’s so mealy.”

Since the late 1990s, growers have begun to replace Red Delicious with other cultivars. ‘Big Red’ was overtaken by Gala in 2018; in 2023 Honeycrisp hurtled into third place and is rapidly closing the gap.

But many of the thousands of varieties that once grew in the western United States and elsewhere are in danger of disappearing. Jude Schuenemeyer has compiled a list of around 500 old varieties from Colorado alone. “Half are extinct,” he says. When the Schuenemeyers and others find an old tree growing an unfamiliar fruit, the race begins to see if they can revive another heirloom. One of the first steps is identifying the variety.

Apple ID

For a long time the only way to identify a cultivar was to show the fruit and leaves to someone with an encyclopaedic knowledge of apples. This person — known as a phenotyper — can identify a cultivar from its observable characteristics, or phenotype. They might look at the pre-bloom colour of the flower; or the distribution of russeting (brown patches) on the skin of the fruit. In other words, someone must read the fruit. This is imperfect.

“We found that even our most knowledgeable phenotypers can be wrong,” says Dunbar-Wallis. That is why she relies on geneticists such as Peace to read the DNA of specimens in her collection instead. Before her apple trees even bear fruit, she can get a reasonable idea of, not just of what cultivar they are, but what characteristics the fruits might have, by sending a sample of its fresh green leaves to Peace.

The apple genome contains 750 million letters, or nucleotides. That’s not particularly long, says Etienne Bucher, a plant scientist at Agroscope, an agricultural research centre in Bern, who led the team that first sequenced the apple genome², in 2017.

For reference, the human genome is about 4 times the size of the apple genome, the wheat genome is more than 20 times larger.

But apples are particularly interesting, Bucher says, because there are so many genetic mutants. There are about 25 million known single nucleotide polymorphisms (SNPs): letter changes at a single point on the genome. These genetic variations — along with less common mutations, such as deletions and duplications — can differentiate a Golden Delicious from, say, a Kentucky Longstem or a Bascombe Mystery.

By comparing the SNPs, researchers can begin to chart the relationships between two cultivars, says Sean Myles, a plant geneticist at Dalhousie University in Halifax, Canada. “You’d be able to tell whether an apple was a parent or a sibling of Golden Delicious, and in some cases even further relationships — a first cousin, a second cousin and so on.”

As well as constructing detailed family trees, researchers can run a comparison known as a genome-wide association study (GWAS), comparing multiple apple genomes at once to determine which SNPs are linked to particular traits.

“One classic example is Gala,” says Bucher. Although all Gala apples are essentially clones, some boast an intense red colour, others are yellow, or mottled or striped. These differences come from rare random mutations that have accumulated over the years. Sequence and compare their genomes, says Bucher, “and you can find the genetic change that is responsible for the colour difference”.

Using this and other approaches, researchers have begun to identify the genes involved in traits such as ripening period, apple quality and flesh browning. In 2021, a group led by Liao Liao, a plant scientist at the Chinese Academy of Sciences in Wuhan, identified several candidate genes for manipulating the taste of apples³. By conducting a GWAS of nearly 500 apple varieties, they identified around 6,000 SNPs associated with the relative concentration of compounds such as malate, citrate, fructose, sucrose, glucose and sorbitol, all of which contribute to an apple’s flavour and its crucial ratio of sugar to acid.

These are the sorts of findings that interest Peace, and they are the reason that he genotypes apple trees. Peace processes thousands of leaf clippings at his laboratory in Pullman through a service called MyFruitTree. They come in bulk from commercial growers, but also in singletons and pairs from hobbyists and curious landowners who have found a mystery tree. The simple test, which costs US$50, targets 48 SNPs across the apple genome, allowing Peace to identify specific cultivars and provide limited information about some fruit traits. A more costly test gives much more detail and provides genetic information that can help in the development of new cultivars.

Old trees have much to teach us

Modern apple breeders often make new cultivars by rolling the genetic dice, over and over again, cross-breeding different plants in search of the perfect combination of SNPs, and then growing the offspring until they produce apples. “You need to have thousands to find something that has the potential to become a new commercial cultivar,” Peace says.

These were the steps that led to Honeycrisp in 1991, Cosmic Crisp in 1997 and RubyFrost in 2013. But it’s a lengthy process, taking at least 25 years from the first cross-breeding to the moment an apple is placed on supermarket shelves.

Genetic engineering could potentially speed up this process. But so far, only a couple of genetically transformed apples have been approved for sale in the United States, says James Luby, an apple breeder at the University of Minnesota in Saint Paul. Luby is referring to varieties of the Arctic apple, which have an engineered gene that produces RNA designed to silence the production of enzymes that cause browning in apple flesh. When sliced, they seem to stay fresher for longer. But the modifications to create them didn’t use traits from other existing cultivars.

To borrow or blend traits through genetic engineering requires deep knowledge of existing variation, Luby says. “The first part of gene editing is gene. You need to know what your target is,” he says.

Peace is particularly interested in the trees growing in Dunbar-Wallis’s test orchard for that reason. “Many of them have already contributed to modern cultivars,” says Peace. “They’re their parents, grandparents and great grandparents; they’re the ancestors of existing cultivars.”

Varieties such as the Colorado Orange, which have been almost entirely lost for a century, would have had less of a chance than other, more widely grown varieties to contribute their genetic information. But there’s a reason that a Colorado Orange tree survived long enough for the Schuenemeyers to rediscover it. The tree has overcome drought and extreme weather — and decades of neglect. The same is true for some of the other historic cultivars that Dunbar-Wallis has resurrected.

Susan Brown, a plant breeder at Cornell University in Ithaca, New York, offers a note of caution. “I love heirloom apples,” she says. “Who doesn’t want to eat Thomas Jefferson’s favourite apple?” But she says that heirloom varieties have been known to harbour pathogens. “Let’s make sure if we’re going to put a lot of interest and emphasis on heirlooms, that they’re free of virus,” she says.

Brown’s concerns are valid, says Dunbar-Wallis. “There is a strong need and opportunity to further study what pathogens are present and where they are located nationally,” she says. And, she adds, some of the old regional cultivars are more resistant to disease and pests than varieties that were introduced more recently.

Fruit of the future

The young trees in Dunbar-Wallis’s test orchard stand in tidy rows, like fence posts against the low, brown foothills of the Colorado Rockies to the west. Their fruits could help to safeguard the future of apples while also preserving and restoring their past.

When an unknown apple variety disappears, the world it leaves behind is diminished in ways that are difficult to quantify. Apple trees don’t just materialize: humans plant them, often purposefully, and sometimes by accident. In their own way, these heirloom apple trees tell the story of the United States. The early settlers, who brought apples with them. The westward expansion. The California Gold Rush. And then later, the mass production of food.

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Inevitably, the cultivars best suited for the future might have existed and disappeared already — Jude Schuenemeyer is certain that some of them have. But perhaps Dunbar-Wallis has found others just in time, grafted them to sturdy rootstock and planted them in northeast Boulder. In the past few weeks, she says, she’s sent off a backlog of 600 tissue samples to Peace for genotyping.

She already knows the identities of some of the apples that will grow on her trees. They have historic names, such as Ben Davis and Early Strawberry. And some of the trees are mysteries — such as seedling BATP 498, named after the Boulder Apple Tree Project, a multi-institution research and education outreach group that supports the project. Its fruit will have no name, for now.

These varieties have value, says Bucher. “Modern genetic engineering can be very useful,” he says, “but it cannot be done without the information we get from wild species.”

Dunbar-Wallis checks on her Colorado Orange sapling, inspecting the undersides of its leaves and pondering its history. The tree from which it was cloned survived for more than a century in Cañon City. “It was really an old, old apple that we thought we weren’t ever going to see again,” she says.

Fruit won’t appear on its branches for a couple more years — but that’s just a moment in apple time — and Dunbar-Wallis is sure that it will be worth the wait.