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How About Them Apples? Research Orchards Chart a Fruit’s Future.

Imagine reaching up to a tree branch and plucking an apple that’s unusually tall and narrow — a variety called Kandil Snap, native to the Black Sea region. In an adjacent arboreal row, 11 trees to the north, you’ll find the equally exotic dark purple Black Oxford apples, resembling large plums.

Add 1,000-plus more varieties of the fruit genus Malus, which isbursting with an autumn-themed rainbow of red, orange, yellow, green and even purple, to this scene, and you’re in the Apple Biodiversity Collection in the Annapolis Valley of Nova Scotia, Canada.

The apples won’t end up in pies or the baskets of autumn leaf peepers. Instead, scientists there are working on understanding the genetics that result in this bonanza of apple diversity, with the ultimate goal of improving the fruit in different ways — tastier, heartier, more disease-resistant and with longer shelf-life in the face of changing climates.

“It’s tremendous to be able to walk through what is essentially the United Nations of apples and see the world’s genetic diversity all in one place,” said Sean Myles, who started the orchard in 2011, “and that feeling is quickly replaced with a tremendous urgency to get all this work done.”

You might not realize it, but many popular apples in grocery stores in recent years — Cosmic Crisps from Washington State, SnapDragons from New York and Honeycrisps, originally from Minnesota — originated with the efforts of scientists examining the qualities of different apple types and crossbreeding them. With some 7,500 varieties of apple in the world, there’s plenty to discover. Future generations of apples in grocery stores may come from research orchards like the one in Nova Scotia, which is among the newest.

Dr. Myles did not start out as an apple genes aficionado — he has an allergy to raw apples, which make his mouth itch unless they’re cooked. He had previously worked on human genetics at the Stanford University School of Medicine. Rather than a love of the fruit, his love of his now-wife prompted a move to the Annapolis Valley, where she makes wine. Because the region’s main crop was apples, Dr. Myles got into the business of apple genes. He joined Dalhousie University’s Faculty of Agriculture in 2011 and got a Canada Research Chair position with funding to start the Apple Biodiversity Collection.

From left, a multitude of apple varieties from the Nova Scotia orchard; Dr. Myles navigating the collection; a striped apple. Credit…Paul Atwood for The New York Times

There is no global census of all efforts to preserve apple diversity. A 2019 report published by the Global Crop Diversity Trust found 40 apple diversity collections around the world, with seven established during the 21st century, but because it was not a complete list, the Nova Scotia orchard was not included. The report also notes that more than half of the 40 surveyed orchards are in North America or Europe. Only three are in Central Asia and the Caucasus Region, where scientists believe many contemporary apple varieties originated.

To ensure greater security of long-term conservation of the world’s apple diversity, the report calls for a global organization of those who cultivate these collections. But today, “we are certainly a long way away from having any sort of international coordination of apple diversity maintenance,” Dr. Myles said.

In the United States, the U.S. Department of Agriculture manages the country’s most diverse apple collection in Geneva, N.Y., which is also among the world’s largest, said Ben Gutierrez, the collection’s curator (the site includes grapes and cherries, too). Most of the more than 5,000 apple varieties are planted in an orchard across 30 acres. Tissue from each kind of apple is stored in a giant freezer so that if weather or disease harms a particular tree, researchers can reintroduce that variety to the orchard.

More than half of the apple materials in the U.S.D.A. collection, are wild, with nearly 4,000 samples, including trees and seeds.

“Though not immediately appealing from a fruit quality perspective, these wild apples have tremendous potential for disease resistance, climate adaptability or other unexpected high-value traits and are critical for understanding the evolution of Malus species and the domestication history of modern apples,” Dr. Gutierrez said.

In Nova Scotia, creating the Apple Biodiversity Collection was a painstaking six-year process. It involved planting 4,000 little trees, ripping them up after a year, preserving them in moist sawdust in a giant fridge during the winter, replanting them during the next summer, then waiting for them to mature. Dr. Myles and his colleagues affixed labels with names to every tree and waited.

The Canadians collaborated with the U.S.D.A. orchard in Geneva, where the focus is conservation, to obtain the raw materials. Having a lot of the same types in both places “gives some insight into how the trees would perform in additional sites,” Dr. Gutierrez said. He added that because the Nova Scotia orchard has more of a research focus, it was designed with randomization, replication and other factors in mind, “to make their data more relevant.”

Ben Gutierrez, curator of the U.S.D.A.’s Apple Collection in Geneva, N.Y., which boasts more than 5,000 apple varieties.Credit…Heather Ainsworth for The New York Times

By conserving a diverse variety of apples and studying the genetic underpinnings of various traits, sites like the one in Nova Scotia help to broaden the scope of possible future apples.

Firmer apples. More sugary — or more tart. Apples can even have red flesh inside — a “fashionable” trend spun off from wild Kazakh apples that are too bitter to eat, said Francois Laurens at INRAE, the French national research institute for agriculture.

When it comes to cooking up new looks for a fruit that seems fully baked, apples are harder to work with than many other crops because of the five- to seven-year wait before a tree produces fruit. And before a new variety even reaches growers, researchers take about 15 years to breed and test a given apple.

“We’re easily talking 20 to 25 years from this year for those new varieties to really get to consumers in a big way,” said James Luby, professor of horticultural sciences at the University of Minnesota.

Dr. Luby’s claim to apple fame is his involvement in the Honeycrisp, developed at the University of Minnesota Horticultural Research Center in the 1960s and 1970s. He started at the center in 1982, about a decade before the Honeycrisp hit the market in the early 1990s. At that time, he said, some growers and “probably some journalists” were skeptical that new apples were needed.

“We knew when we first tasted it that it was something very different than what was on the market — you know, that kind of explosive crunchiness, breaking flesh, was very different,” Dr. Luby said of the Honeycrisp apple.

Honeycrisp and many other commercial apples originated through a technique called controlled hybridization, which includes taking pollen from one kind of apple tree and putting it on the flower of another. The cross-pollination produces a hybrid apple, just as two parents produce a child who shares both of their genetic traits, said Susan K. Brown, a professor at Cornell University’s School of Integrative Plant Science, who leads the nation’s oldest apple breeding program, also in Geneva.

Some recent apple successes from Dr. Brown, the research specialist Kevin Maloney and their large team of collaborators at Cornell have included the RubyFrost and SnapDragon types, which debuted to consumers in 2013. They were commercialized in a partnership with Crunch Time Apple Growers of New York.

Firecracker, another one of the Cornell group’s creations, “was one of many names suggested by testers and it matched the variety for having an explosion of flavor,” Dr. Brown said.

Other researchers have pursued genetic modification methods, which alter an existing apple variety by inserting genetic material. Some G.M.O.’s already being sold include the Arctic Apples, with “Arctic” versions of Fuji, Gala and Granny Smith apples.

From left, a pink-fleshed apple; Dr. Myles in the Apple Biodiversity Collection’s orchards; mist-covered apples ready for picking.Credit…Paul Atwood for The New York Times

Distinct from genetic modification is CRISPR, a technique that slices and edits genomes directly. CRISPR may become important for the future of apples and food generally. For one thing, “when you want to understand the function of a gene, you can disrupt it using CRISPR,” said David Chagne of the New Zealand Institute for Plant and Food Research.

There have been some preliminary successes — an Italian group demonstrated in a 2019 study that CRISPR could be used to reduce susceptibility to fire blight disease, for example.

But CRISPR isn’t a magic paring knife. Some countries such as New Zealand do not allow CRISPR to be used for commercial foods, Dr. Chagne said. Another difficulty for CRISPR is regenerating a woody plant from a single cell is not easy, Dr. Myles said.

The Canadian group is getting into the CRISPR game, but the challenge of the apple’s long development period also remains an obstacle: Even if Dr. Myles’s team can make an edit to a Honeycrisp plant that makes the apple a little tastier, it will take five years for the first test fruit to grow up.

“It may be a while before people are seeing these things on the grocery store shelf,” Dr. Myles said, “but it is coming down the pipeline for sure. And our group hopes to be the ones that sort of lay the foundation for that.”

To characterize apple flavors or to make sure the fruits are ready to be picked, researchers need to personally sample them. Somewhat like professional wine tasters, apple experts “bite, chew, taste and spit,” or else they’ll upset their stomachs, Dr. Myles said.

Sophie Watts, a Dalhousie University doctoral student with Dr. Myles’s group, said she had likely tasted about 800 of the orchard’s apples “in the name of research.” The orchard has, for example, some apples with “hints of banana, citrus fruits and even one called Cotton Candy that tastes exactly like cotton candy,” she said.

Samples of the 75 wild apple from the orchard “for the most part, tasted pretty bad” she said.

Ms. Watts also emphasized the Nova Scotia lab’s role in preserving biodiversity. “It’s important we keep as much crop diversity around so that we can lean on it to breed new varieties that are adapted to our changing world,” she said.

Dr. Myles’s team has done basic genetic sequencing of all of the trees in the Apple Biodiversity Collection, resulting in a flurry of publications delving into the genetic underpinnings of apple traits. The group has identified genes that regulate how much apples change while they are kept in storage, for example.

Still, Dr. Myles cautions, there’s no single genetic modification that will transform the apple world.

“I really wish I had that knock-it-out-of-the-park trait,” he said. “I wish we could make it taste like a banana and look like an avocado. And, you know, have it yield three times as much and be resistant to every disease.”

He added, “Whoa, wouldn’t that be awesome? But science doesn’t work that way.”

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