Laura Sieger takes clippings from a Jefferis apple tree for DNA testing at Maine Heritage Orchard in Unity. Shawn Patrick Ouellette/Staff Photographer

When John Bunker first moved to Palermo 50 years ago, he was struck by the lack of street name signs in town.

“None of the roads had (name) signs, because after all, everybody knew what all the roads were,” said Bunker, Maine’s foremost apple historian, who also runs the orchard at Palermo’s Super Chilly Farm. “So I didn’t even know what road I lived on.”

Compounding the confusion, he recalled, was that segments of the same road sometimes had different names.

Palermo’s lack of formal street-naming conventions was interesting and a little confusing, but not alien to Bunker. Because before the 20th century, important information about each particular apple variety was often passed along by oral tradition. Unique varieties migrated from region to region along with the people who cherished those particular apples, sometimes getting renamed along the way without any documenting of the change.

“Those apples were like folks songs that traveled around and had different lyrics in different states,” Bunker said.

Some apple trees planted in Maine since the end of the Civil War – and throughout the country –  are in fact well documented with names and descriptions of their phenotypes, or observable characteristics. But for most of what we now call heirloom apples, “descriptions are either nonexistent or rudimentary,” Bunker said, for the same reason nobody needed street name signs in Palermo – everybody at the time knew what they were.


Today, most people eat just a handful of commercial cultivars. Meanwhile, the huge holes of data in apple horticulture regarding the old varieties have confounded scientists, historians and apple explorers for decades. Now, genetic testing may be able to fill in the blanks. The best news? The data being gathered has the potential to make Maine’s apple landscape almost unimaginably more diverse and delicious.

Since 2019, Bunker has been working with College of the Atlantic history professor Todd Little-Siebold, Laura Sieger, orchard manager for the Maine Organic Farmers and Gardeners Association and MOFGA intern Lydia Pendergast to collect samples from hundreds of Maine’s unidentified apple trees. They send the samples clear across the country to their partner in the project, Cameron Peace, a horticulture scientist at the University of Washington who runs tests to reveal the DNA.

“It’s almost like 23andMe, but for apples,” Sieger said, referring to the popular human genetic testing web service,

Peace logs test results into the massive apple DNA database he and his University of Washington colleagues are compiling, which now contains more than 3,000 unique, named apple varieties from around the world.

Peace’s hypothesis – so far supported by evidence since his DNA project began a few years ago – is that all apple varieties worldwide are related within a handful of generations. “My vision is to put everything into one big, happy family tree,” Peace said.

MOFGA’s Laura Sieger labels a test tube containing clippings from an American Summer Pearmain, a type of heirloom apple tree, for DNA testing. Shawn Patrick Ouellette/Staff Photographer



Today’s average consumer may be familiar with five or 10 apple varieties, tops. Those popular cultivars, like Honeycrisp, Gala, McIntosh and Golden Delicious, are dominant nationwide. Commodity farming of the 20th century drastically culled America’s available apple varieties, focusing almost entirely on 20 or so apples chosen for hardiness, large size and high yields rather than the actual reasons people buy apples – for flavor or how they hold up when cooked or baked.

But in the decades before modern farming practices took hold in the United States, the market for apples was much different.

Bunker said between the end of the Civil War and the turn of the 20th century, “Almost every county from here to Georgia had its own special apples that were unique to that area. And certainly every town had its own unique mix of apples people would grow.

“I think more and more Americans are seeing that the one-size-fits-all approach is a worn-out model,” Bunker continued. “I like to think apples in Maine should be like cheeses in France, where you go 10 miles and you get a whole new cheese. In Maine there should be a different cider and apple in every town or county.”

The push for greater diversity in the market begins with identifying old apple trees and their heirloom fruit. Since Maine’s team of hardcore apple advocates started working with Peace three years ago, they’ve completed about 350 DNA tests on the state’s apple trees, Little-Siebold said. Test results sometimes showed duplication among the samples, but were highly illuminating nonetheless.

Little-Siebold said, for example, that they collected test samples from what seemed like three different apples, snipped from trees in Washington, Hancock and Kennebec counties.


“The first thing that came back is, they’re all the same,” Little-Siebold said. The DNA tests showed the apples in question were actually a single variety called Salome, which originated in central Illinois around 1860.

“We would never have been able to figure that out,” Little-Siebold said, emphasizing the advantage of the genotype approach over traditional phenotype identifications. “Salome, as far as John and I have ever seen, is mentioned once in historical records in Maine. And yet we found three of them. It is so rare, we would never have guessed it as we did the phenotypic comparisons. But the great thing about the DNA tests is that you don’t have to guess. You know they’re the same, period.”

Laura Sieger, orchard manager for the Maine Organic Farmers and Gardeners Association, takes clippings from a Jefferis apple tree for at Maine Heritage Orchard in Unity. The clipping will be sent to a lab in Washington state, where its DNA will be tested and analyzed. Shawn Patrick Ouellette/Staff Photographer

Little-Siebold considers apples and old apple trees to be one of the last living connections to the thriving farm communities that formed the basis of the early Maine economy. “The apples tell a story about who we are and where we came from,” he said. “All of a sudden, we have a brand new tool that can give us answers.”

Bunker said the Maine team also collaborates with apple historians around the country, leading them to discover that a certain apple in Sorrento – about 15 miles east of Ellsworth – was also discovered in Colorado and Washington state, for instance. “You can learn about human migration patterns by following the apples,” he said.


Apple trees planted in Maine toward the end of the 19th century are now pushing 150 years old, about their maximum lifespan, which gives the apple testing project a sense of urgency.


“There are friends and colleagues of mine all over the state now searching for the last of these old trees,” Bunker said. “We’re on this almost desperate search to find them before they die. We’re losing many of them every year now.”

Identifying and preserving old apple varieties can also help apple growers guard against against future calamity, since a limited gene pool makes a crop vulnerable to disease and decimation. “We’re looking at how we can have a safe and sustainable apple industry in the future by increasing the genetic diversity,” Bunker said.

And as more more heirloom apples become available, consumers win big, too.

“There are some excellent fresh-eating apples that are almost entirely unknown now. We need to reintroduce those to the public,” said Bunker. He cited one of his favorites, Garden Royal, which originated in Sudbury Massachusetts, and was grown all over central and southern Maine years ago.

“The Garden Royal is small, it grows poorly in the nursery, it doesn’t bear every year. And when you eat them they are like ambrosia,” Bunker said.

He also noted his two Trailman apple trees on Super Chilly Farm. “They’re like candy. People eat them and tell me, ‘My goodness, this is the best apple I’ve ever eaten.’ But they’re small, and they don’t fit that designer mode that we think the apple industry and the customer demand,” Bunker said.


Many heirloom apples that have seemingly disappeared were never meant to be eaten fresh, Bunker explained, but the fruit absolutely shined when baked in pies, cooked into sauce or juiced for cider.

“These days, people are doing more cooking for themselves,” Bunker said. “They want a good pie apple. Honeycrisp is a delicious apple, but they’re terrible for pies. McIntosh is no good in a pie, it turns into soup. But there are great pie apples out there. Most of them are these old heirlooms, because they were selected for that purpose. We need to get those back into the commercial orchards of Maine.”


Orchards like Super Chilly Farm or Cayford Orchards in Skowhegan sell scores of heirloom varieties, but the state’s apple market has a long way to go to meet Bunker’s hyper-localized vision of diversity and abundance. And the apple researchers have plenty more work ahead, too: Little-Siebold said Maine has historically hosted about 1,000 named apple tree varieties, and Bunker estimated that the apple DNA project in the state is about 20 percent complete.

A website launched earlier this year by Peace’s horticulture department at Washington State University – – might lighten their load, by taking a crowd-sourcing approach to apple gene mapping. For $120, the site’s researchers will send any apple tree owner who contacts them sampling gear and instructions for mailing the clippings back. Six months later, your apple tree mystery is solved, and the findings bolster the entire database.

Peace said between sample tests generated through the website and others from the dedicated teams of apple explorers around the country, “We run about 100 tests every couple of months now, and we keep finding more and more missing ancestors or pedigree filler to put everything together.” The data may eventually lead to major findings, like discovering the still-unknown “father” tree of the Golden Delicious apple, or the grandparents of the iconic Red Delicious.


“It’s a wonderful revolution in identification and preservation of the historic apples of North America, and to a large degree, around the world,” Bunker said. “It’s a win-win for everybody in the state of Maine that this is all happening now.”

“One of the things John will say is, ‘Sometimes we have an apple and we’re looking for a name, and sometimes we have a name and we’re looking for an apple,'” Little-Siebold said. “We’re tracking down old varieties that nobody has seen in a hundred years. I would say that’s going to be decades of work. But we’ve made real progress so far.”

Cardamom-Apple-Brown Butter Cake. Gregory Rec/Staff Photographer

Cardamom-Apple–Brown Butter Cake

This cake comes from Food Editor Peggy Grodinsky’s friend Mitchell Davis who, in turn, got it from Edible New Jersey magazine, which credited it to Matthew Rosenzweig, who owns The Baker’s Grove bakery in Shrewsbury, New Jersey. The original uses pears. Grodinsky switched to apples, which are traditional for Rosh Hashanah, the Jewish New Year, which starts this evening at sundown; eaten with honey, apples symbolize wishes for a sweet new year. Davis also made a few adjustments, most notably using rye flour, which Grodinsky followed – using Maine Grains’ rye flour. If you keep kosher, do not serve this cake with a meat meal (but you know that).

Makes 1 (8-inch cake), serves 8–10

¼ cup unsalted butter
½ cup brown sugar
½ teaspoon ground cardamom
2 teaspoons amaretto
3-4 apples, peeled, halved, cored and sliced (keep the halves together)


3/4 cup all-purpose flour
3/4 cup rye flour
1½ teaspoons baking powder
1½ teaspoons ground cardamom
¼ teaspoon salt
½ cup brown butter, at room temperature
¾ cup granulated sugar
1 teaspoon almond extract
2 large eggs, at room temperature
½ cup whole milk, at room temperature
¼ cup sliced almonds, toasted, to garnish
Confectioners’ sugar, for sprinkling

Ahead of time, prepare the brown butter to use in the cake batter: Melt ½ cup of unsalted butter in a light-colored saucepan over medium heat. Swirl the pan occasionally to make sure the butter is cooking evenly. As the butter melts, it will begin to foam. The color will progress to a toasty brown. Once you smell the nutty aroma and the butter is the color of graham crackers, take off the heat and transfer to a heatproof bowl. Refrigerate until solid but still soft and leave at room temperature when ready to prepare the cake batter.

Preheat the oven to 350 degrees F. Butter or spray the sides of a deep-dish 8-inch cake pan and set aside.

To make the topping, combine the butter, brown sugar, cardamom, and amaretto in a saucepan over low heat until the ingredients are melted together. Remove from heat and pour into the prepared cake pan. Arrange the apples over the brown sugar mixture, cut side down. Set aside.

To make the cake, whisk together the flour, baking powder, cardamom and salt; set aside. In a stand mixer fitted with a paddle attachment, beat together the browned butter and sugar on medium speed until the mixture is light and fluffy. Add the almond extract and eggs, 1 at a time, beating until completely incorporated. Gradually mix in half of the flour mixture. Stir in the milk followed by the rest of the flour mixture and mix until just combined.

Scrape the batter on top of the apples in the pan and smooth it into an even layer. Bake until golden brown and a toothpick inserted in the center of the cake comes out clean, about 1 hour.

Let the cake cool in the pan for about 15 minutes. Run a knife around the sides of the cake to help loosen it from the pan. Invert a serving plate or cake stand over the pan. Wearing oven mitts, grasp both the pan and the plate and turn them over together. Carefully lift off pan.

Sprinkle toasted sliced almonds over cake and dust with confectioners’ sugar. Serve the cake warm with whipped cream or ice cream.

A slice of the Cardamom-Apple-Brown Butter Cake. Gild the lily, if you like, by serving it with whipped cream or ice cream. Gregory Rec/Staff Photographer

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