An apple a day

French

 

Though his background is in human genetics, Sean Myles studies the genetic composition of apples.

So how did he come to be studying apples? The Associate Professor and Faculty Research Chair at Dalhousie University’s Faculty of Agriculture pauses and says simply “I mean, I like apples.”

And then he tells the story behind his switch from mammals to plants.

“I was doing my PhD in Germany at the Max Planck Institute, working in human genetics,” Myles says, “and that’s when I realized I would be seeking a position in a pretty crowded and competitive research field if I continued with that.”

Moreover,  he’s a small-town boy — from Fredericton, New Brunswick — who was dating an even smaller-town girl from Cape Breton’s Port Hawkesbury in Nova Scotia. At the time, she was doing an apprenticeship as a winemaker in Germany’s Rheingau region and he realized she was going to have to live in a wine region for her career. So he looked for a way to make that work for him too.

“Human genetics was so far ahead of grape genetics, I thought I might have an advantage if I made the switch,” Myles explains. “I managed to get post-doctoral work at Cornell University, working with the Buckler Lab for Maize Genetics and Diversity. I spent a couple of years there and we worked on grapes, specifically how to use technology to evaluate lots of genome characteristics in the fruit.”

When his wife got a job back in Nova Scotia, he approached Dalhousie University’s Faculty of Agriculture. The faculty acknowledged that Nova Scotia had a wine industry, but said they couldn’t devote a position exclusively to grapes. Instead, they suggested he consider apples as well.

Today, he runs a program that tries to accelerate apple breeding.

“Apple trees take a very long time to grow and selecting a winning variety is a very time-consuming and expensive task,” Myles says. “One of the ways we can make that faster is by evaluating the trees when they’re just little seedlings, just sprouting out of the ground, and taking a little bit of their tissue and looking at their DNA. Using the DNA, you can see which have desirable and which have undesirable genetics.”

Of course, to accomplish that, you need to know what’s desirable and what isn’t. Enter his lab, which seeks out the parts of the apple genome that everyone wants in the apple and makes sure those pieces of DNA are in the new varieties breeders are growing. It doesn’t mean they’re making genetically modified organisms, rather, they’re helping breeders to screen the offspring of their cross-breeds to ultimately be more efficient producers.

“Instead of planting 10,000 trees and then waiting eight years for them to bear fruit and then deciding most of them are actually garbage, they can make that determination when their seedlings are a couple of centimetres tall,” Myles says. “It’s the same principle as screening for genetic diseases in humans.”

Given that there are more than one billion apples grown yearly in Canada, this can significantly advance the industry, he says. But there’s a lot of work involved in getting there. After all, the apple genome is 750 million letters long and his end goal is to look at a lot of apples to find the desirable letters. To that end, Myles has  planted more than 1,000 varieties of apples — 2,300 trees in all — in a controlled area and his lab analyzes the DNA from every one of those.

“With 750 million letters and 1,000 varieties, you can see how the numbers are starting to climb,” he says. “And you can’t only sequence each letter once — you have to do it multiple times. That results in a huge amount of data. We have on the order of about 10 terabytes of data on the Compute Canada cluster. And that’s just the DNA sequence data.”

After they sequence everything, they go and measure all the apples for acidity, sweetness and firmness. They then store them and measure their firmness-retention after storage. They also measure the molecules responsible for taste as well as the aromatics, colour and uniformity of colour.

“That all results in a multi-dimensional dataset where we try to link all these characters up with DNA and find the pieces of the genome that are responsible for the good things and the bad things about apples,” Myles says.

Asked whether he has a background in high-powered computing, he says he comes from a time when there were 10 people working at the bench in the lab and one person working at the computer.

“Now, there are 10 people at the computer and one at the bench,” he laughs, and admits he’s adjusted to that. “Coming out of human genetics gives me a big advantage because I could see that eventually, we would be able to sequence a thousand apple genomes.”

He also credits Compute Canada’s regional partner ACENET, as being critical to his lab’s success.

“Establishing and maintaining a local server in our lab would have been an enormous waste of our resources. I credit a significant portion of our success to ACENET and its incredibly helpful support staff. Our goal is to have an impact on the agricultural sector in Canada that benefits Canadians, and I count ACENET as a crucial partner in our pursuit of this goal.”

Myles says they haven’t sequenced the genomes of all 1,000 varieties, but he is getting a very comprehensive look at the genome-wide variation across all of the varieties. In addition to this data analysis, his lab is also responsible for taking care of the 2,300 apples trees planted on a five-acre plot of land in Nova Scotia.

“It’s a Herculean effort and it involves a lot of collaborators,” he said. “We do it as a team with organizations like Agriculture and Agri-Food Canada.”

In their spare time, he and his wife Gina have founded the Annapolis Cider Company, giving him a chance to get away from the computers, get his hands dirty, and giving them both an after-hours alternative to wine.

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