Apples to apples

Apples to apples

Fruit breeding gets a boost from genomics
September 10, 2013

Tucked near the back of the sprawling 200-hectare property that makes up the Atlantic Food and Horticulture Research Centre’s farm facility in Kentville, N.S., sits one of the world’s most unique orchards. It contains more than 1,000 newly planted apple trees, all neatly spaced and aligned. Unlike other orchards, each of the trees in Sean Myles’ plot is different from the rest — 1,113 distinct varieties of apples, including elite cultivars and supermarket best-sellers, heritage apples that are no longer grown commercially and even wild apples from Kazakhstan, where the fruit originated 10 millenniums ago. Each tree is carefully bar-coded and catalogued, and just to be on the safe side, the entire orchard is duplicated 100 metres away.

Myles is a professor at Dalhousie University and a Canada Research Chair in Agricultural Genetic Diversity. He’s an expert in genomics, the science of decoding how sequences of DNA create the blueprints of everything from apples to elephants. He’s also a questionable farmer. By his own admission, he’s a hopeless gardener who doesn’t even own a houseplant, and he can’t sample the apples he works with thanks to an allergy to the fruit. But Myles’ laboratory promises to revolutionize the ancient art of plant husbandry.

Since the neolithic age, farmers have crossbred plants and animals to enhance specific traits and create new varieties, a practice that is virtually unchanged today. It’s a laborious hit-or-miss process. In the case of a species like apples, it can take a quarter of a century of breeding to bring a new variety to the marketplace, with no guarantee that the end product will be a commercial hit. In fact, two of the most successful apples ever developed — McIntosh and Honeycrisp — were both the result of accidental cross-pollination.

Myles uses science to speed up the process by cataloguing how genetics activates desirable traits in farm crops such as apples and grapes. “Under normal conditions, it takes about eight years to cross-pollinate an apple, graft the seedling and grow a tree big enough to produce the fruit,” he says. “That’s eight years of waiting to see whether the new variety you’re trying to produce is any good. With our lab, we will be able to take a leaf cutting in year one, look at its DNA and tell what kinds of traits the new apple will have. It means we can potentially create hundreds of new commercial varieties in a very short period of time.”

But in order to do that, Myles and his research team first need to match the genomic sequence of apple DNA with a myriad of traits like colour, shape, firmness, flavour, starch content, weight and insect resistance. It’s a job Myles expects to be doing for the rest of his career: The combinations of genomes that influence apple traits are measured in terabytes, and cataloguing them in a database could take decades.

It’s big business. The apple is Canada’s largest fruit crop, with more than 18,000 hectares of orchards planted across the country producing over 370,000 tonnes of the fruit annually, a value of $150 million. “It costs about $40,000 to bring an [half a hectare] of apples to maturity,” says Myles. “If you’re developing an untested variety, it can end up being a very costly mistake.”

Myles was studying the emerging field of human genomics, working on his PhD at the prestigious Max Planck Institutes in Germany, when he first became interested in the genomics of agricultural plants. On weekends, he and his wife Gina Haverstock, a Nova Scotia winemaker who was studying her craft in Germany at the same time, began to explore some of Europe’s most famous and well-established vineyards. Myles became fascinated by the wide variety of grapes that humans have engineered from a single species thousands of years ago and began studying grapes and apples as a post-graduate student.

Collecting the traits, or phenotypes, found in apples is a painstaking process, one that lends itself well to what Myles calls “open source science” — encouraging the general public to feed phenotypic data to the Myles Lab database. “It would be a little like online dating meets Johnny Appleseed,” he says. Once enough data have been compiled, the lab would function as a designer seed bank where farmers and gardeners could order customized varieties of apples with a specific set of traits and growing characteristics.

One of the first things on Myles’ to-do list? Create a hypoallergenic apple that he can eat: “I’ve been giving serious thought to how I would go about doing that.”