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To Save Apples, Look to Their Wild Roots

Making apple trees grow shorter over the years has made them easier to pick and ship, but it has also left them more vulnerable to disease.

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Workers stand on a hydraulic lift to pick fruit from the tips of trees. The lifts are equipped with floodlights to allow for night harvesting, so fruit can be picked at peak quality.


Last fall, I picked a wild apple from a tree growing in the Ile-Alatau Mountains of southern Kazakhstan. It was a Malus sieversii, wild ancestor of the cultivated apple. Biting into it, the flavor was bitter—a “spitter,” as apple aficionados call them—nothing like the sweet Fuji apples I eat from the tree on my family’s farm in Washington State.

The difference in flavor represents 2,000 years of agricultural refinement, and a journey that took the apple out of central Asia, by way of the Silk Road, to Europe and then across the Atlantic to America. Portable, slow to spoil, and packed with nutrition (around eight percent of the daily dose of fiber, vitamin C, and potassium if eaten with the skin on), it’s easy to understand why travellers went to all the trouble.

Along the way, however, apple trees lost something essential: genetic diversity.

Root Cause

“Most of the apple trees in the world are planted on M.9 rootstock,” says Gennaro Fazio, a plant geneticist with the U.S. Department of Agriculture’s Agricultural Research Service. “They’re clones of a tree that grew in the 17th century. That’s ancient technology.”

Rootstocks are used in grafting when the branch of a desirable fruit tree is spliced into the trunk of another. M.9 is used to dwarf, or shrink, the size of a fruit tree. A Gala, Fuji, or Red Delicious grown from seed will become tall and unmanageable, but if you graft their scions (branches) onto M.9 rootstock, the resulting tree will be only one-third the height. This results in a smaller canopy that allows more sunshine through, creating better and more consistent apples on each tree. And the lower height makes for more efficient harvesting.

The term M.9 is short for Malling 9, a code given to the rootstock in 1912 when it was officially cataloged at the East Malling Research Station in Kent, England.

What those early botanists were doing, unknowingly, was narrowing the apple tree’s genetic pool to the point where a mutation occurred. In this case, in the form of a the M.9’s shrimpy size. That process also eliminated genes that helped the tree fight pests and diseases.

“While M.9’s evolution was stopped in time, Mother Nature and all her pests kept on developing ways to attack it,” Fazio says.

The result is that today’s M.9 rootstocks are vulnerable to an array of maladies, such as fire blight, woolly apple aphid, and cedar apple rust.

The disease that really concerns Fazio is replant disease. Wherever multiple generations of M.9 have been replanted, the rootstock is attacked from something in the soil. Scientists don’t fully understand why.

“That’s not a problem for sieversii,” Fazio says. “They’ve been replanting themselves in the wild for thousands of years. That's a trait we want to get back.”

Out of Kazakhstan

For a long time, the sieversii’s identity was a secret hidden behind the Iron Curtain of the USSR. But with the collapse of the Soviet Union, word spread among botanists and the USDA funded a team of agricultural explorers to search the mountains of Kazakhstan for wild apples. One of the explorers, Phil Forsline, was Fazio’s predecessor at the USDA-ARS. He brought back 130,000 seeds, some of which he planted on a research farm run by Cornell University in Geneva, New York.

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Wild sieversii apple trees bloom on a horse farm bordering Ile-Alatau National Park in southern Kazakhstan. Farming and urban development cause deforestation that's made sieversii a threatened plant species. But the park’s founding in 1996 has protected a thriving population of these trees.


Michael Pollan wrote about Forsline’s work in a 1999 article for The New York Times, and again in the book The Botany of Desire. Since their publications, a sequencing of the apple genome has confirmed the sieversii’s standing as the cultivated apple’s wild ancestor.

Pollan concluded that “the story of the modern apple, which has become utterly dependent on us to keep its natural enemies at bay, suggests that domestication can be overdone.”

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Swinging the pendulum back the other way is long and tedious work. Forsline has since retired, and Fazio has taken over working with the Kazakh trees in Geneva, New York. Whereas his predecessor aimed to improve the fruit, Fazio’s work is focused below ground, to develop a disease resistant, and drought tolerant rootstock orchards can use for growing the same apples as always.

This year, Fazio is part of a research team from Cornell who will include the sieversii in a study that aims to understand exactly how apple rootstocks function at the microbial level. This, they hope, could lead to a better understanding of how to treat replant disease.

In Fazio’s own work, though, he doesn’t want to just treat the problem, he wants to cure it for good by developing a sieversii rootstock. And he’s having success.

“We’ve grown 50 viable trees that we’re testing in Geneva,” he says.

These he’s exposed to torture chamber of tests, bombarding the plants with the apple industry’s worst pests and diseases. Already, the sieversii hybrids have proven resilient to fire blight, woolly aphid, cedar-apple rust, and blue mold.

But how will they hold up against replant disease? To find that out, Fazio distributes the rootstock to research partners in the commercial industry, where they can be planted in old orchards vulnerable to the disease. The new, sieversii-infused rootstock has been shipped for planting on commercial orchards across the U.S. and as far away as New Zealand.

In a tree generation or two, Fazio will have the answer.

Red Apple Renaissance

In the spring, I returned to the mountains of Kazakhstan because I wanted to see the wild apple trees in bloom. Traveling to Kazakhstan is a pilgrimage for apple enthusiasts.

Arsen Rysdauletov, a third-generation apple grower from the region, drove me into Ile-Alatau National Park. Swatches of light pink flowers mottled the hillsides. Forsline had collected seeds here in the 1990s. At that time, the mountains weren’t protected and the apple forests were being cut down to make way for crop and livestock farming, and housing developments for the sprawling city Almaty, Kazakhstan’s largest city with 1.3 million residents.

Ile-Alatau National Park was created in 1996, protecting the apple forests so they can propagate their way off the International Union for Conservation of Nature’s Red List of threatened species.

Descending the mountains, Rysdauletov took me to his home village of Turgen, where he is a third-generation apple grower. We visited his grandfather, who spoke of working on Soviet-era collective farms where they grew a sieversii-hybrid apple called the Aport. It was the most widely grown apple in the USSR and a mainstay of the Soviet diet. When Cosmonauts touched down in Kazakhstan after a journey to space, they were given an Aport to celebrate. I tried one. The flavor was semi-sweet, not quite the saliva gland bursting saccharine of highly cultivated varieties like Honeycrisp, but I could understand why chefs like Cherish Finden, pastry chef at the Langham Hotel in London, find it charming.

Today, the Aport is in danger of becoming extinct. Soviet apple orchards fell victim to an economic collapse that devastated all sectors of Kazakh agriculture. Aport orchards were wiped out, taking all that sieversii genetic diversity with them. As farms became privatized, new owners invariably replanted with commodity cultivars that sell well on world markets, like Gala and Red Delicious.

Rysdauletov is part of a new wave of apple growers trying to bring back the Aport. Their orchards aren’t big, but through social media they sell the apples at a premium direct to consumers in the cities.

We visited Rysdauletov’s newest stand of trees, planted on ground adjacent his father and uncle’s traditional orchard. As we walked between the rows of saplings, I realized that here was the crossroads of all the the world’s apple industries. In the foreground, Rysdauletev’s Aport, his family’s commodity apples behind them, and growing on the foothills in the background, wild sieversii. Lined up in exactly that order, the apples are like so many balls on a Newton’s Cradle, clacking one into the other.

How ironic the toy’s namesake discovered gravity after being struck on the head by an apple. Sometimes, the answers to science’s questions are right there in front of us. We just need to see them—or maybe, taste them.

(Oh yeah, that apple that supposedly hit Newton on the head? It was a Flower of Kent, the tree which was cloned at the Malling nursery in England, alongside the M.9. Our knowledge of gravity has developed over 450 years. The fruit that lent us the understanding has not.)