Forging careers in Atlantic Canada, thanks to genomics

Published: February 13th 2019

Forging careers in Atlantic Canada, thanks to genomics

Three highly trained scientists, one from Brazil and two from Canada, attribute their ability to forge careers in Atlantic Canada partly to their experiences as doctoral students or as postdocs working on Genome Atlantic-supported projects.

“Well, the CGP quite literally changed my life,” said Dr. Tiago Hori, recently appointed Director of Innovation at Atlantic AquaFarms in Orwell, PEI.  He joined the CGP – shorthand for the Atlantic Cod Genomics and Broodstock Development Project – as a Memorial University doctoral student from Brazil and helped build genomic data for Atlantic cod. He also used these resources to conduct functional genomics analysis of cod’s molecular response to stress.

The $18.4 million project, developed in partnership with Genome Atlantic and roughly half-financed by Genome Canada with matching funds from other sources, worked closely with aquaculture companies to find cod genes related to economically-relevant traits such as increased growth rates, disease resistance and stress tolerance. The aim was to reduce production costs to the point that cod aquaculture could become commercially viable in Atlantic Canada.

 “For one thing, I would not have come to Canada,” said Hori, without the project’s associated stipend, most of which came from Genome Canada. “Perhaps, more interestingly, it also almost completely changed my career.”

He explained, “When I first joined CGP, my role was supposed to be centered on the generation of physiological data and the use of a few molecular tools to characterize the stress response of cod. In 2006, I was supposed to spend six months in Newfoundland at Memorial University doing one of my own physiology experiments. However, the tanks that CGP had ordered for me burnt down alongside the factory that made them. I kid you not!”

In the aftermath, he was redeployed to work on a heat shock experiment to help Dr. Matthew Rise at Memorial, a principal investigator doing stress tolerance research for the CGP. “That’s when I started doing genomics, and I really never went back,” Hori says.

Hori completed his PhD in Biology during the highly successful $6.1 million camelina project, funded through the Atlantic Canada Opportunity Agency’s Atlantic Innovation Fund, and supported by Genome Atlantic. His role there was to provide training and secondary supervision, including assisting graduate and doctoral students with their analyses and sample collection.

The study found camelina to be an excellent match to the fatty acid composition required in the diets of farmed fish, and ultimately resulted in government approval of camelina as a feed ingredient for farmed salmon and trout.

Dr. Stephanie Colombo, Assistant Professor and Canada Research Chair in Aquaculture Nutrition, Dalhousie University, is another camelina project veteran. She offered an unqualified “yes” too, when asked if the experience helped her research career.

As a Memorial University doctoral student, she recalled her part in the study provided unusually well-defined deliverables for a PhD project. That factor enabled her not only to work more purposefully, but also to develop the creative freedom to pick up on what she had learned on each round of experimentation and figure out how to apply it to the next.

“My part of the project,” Colombo said, “was to evaluate the lipid biochemistry and growth of Atlantic salmon, rainbow trout and Atlantic cod that were fed diets containing camelina oil and meal.”

She added, “I was allowed and encouraged to publish my results, which was motivating for me to produce data. The project provided this established framework which gave me a roadmap and stability to excel in my studies.”

A native of Brantford, Ontario, Colombo did her undergraduate degree at the University of Guelph in marine and freshwater biology. Later, scouting for a job, she landed one at Scotian Halibut Ltd., Clark’s Harbour, Nova Scotia, her first encounter with Atlantic Canada. The company’s collaborations with the National Research Council in fish nutrition inspired her to do graduate study at Dalhousie, and then a chance meeting, during an annual conference of the Aquaculture Association of Nova Scotia, introduced her to Genome Atlantic and the prospect of a PhD project with Dr. Chris Parrish within the camelina undertaking.

Her PhD completed, she took up a postdoc position at Ryerson University, Toronto, but kept an eye on Atlantic Canada for future opportunities. One arrived in familiar territory. During the camelina project, she spent time with Dr. Derek Anderson and his lab in the Dalhousie Faculty of Agriculture. The experience, she believed, proved an asset when a faculty position there opened.

Today, she is a marine biologist specializing in aquatic nutrition. She uses genomics “as a tool to help answer questions related to nutrition in aquaculture. My work explores the area of nutrigenomics.”

Dr. Kyle Gardner, a research scientist with Agriculture and Agri-Food Canada, Fredericton, New Brunswick, maintains that his work on a Genome Canada project “was an important component in keeping me in the Atlantic region and fostering collaborations with local researchers from academia and government.”

A Cape Breton native he is now a quantitative geneticist with expertise in bioinformatics. As a postdoc research associate, he worked with Dr. Sean Myles at Dalhousie between 2012 and 2015 on a project that explored how new genomics technologies can help make traditional crop breeding more efficient, cost-effective and accurate. The project, Exploiting the Full Potential of the Next Generation DNA Sequencing for Crop Improvement, was led by Myles, funded by Genome Canada and supported by Genome Atlantic.

“The Genome Canada project I was involved with aligned well with my interests in bioinformatics and complemented the other work that was going on in the Myles lab, such as developing high throughput genetic markers for future tree fruit – apple –improvement,” Gardner explained.

“With the Genome Canada award, we were able to put together a team to develop some novel tools to efficiently generate more complete DNA marker data from low coverage DNA sequencing in non-model organisms, such as apples,” he said. “Essentially the method that was developed, in conjunction with Dr. Daniel Money (University of Cambridge) and Dr. Myles, allows you to get more DNA marker information out of the same DNA sequence dataset at no extra cost. This method, and associated software, has now been used in many different species study systems from wheat, corn, and grapes to house sparrows and corals.”

Fast forward to today

Today, Hori’s and Colombo ‘s expertise is focused on bettering aquaculture, while Gardner’s know-how targets improvements in potato breeding.

As a bioinformatician, Hori worked on harnessing functional genomics and structural genomic tools for the aquaculture industry, in his previous role as the Director of Genomics at the Centre for Aquaculture Technologies (CAT).  “My main role was to  figure out how genomic technologies can be applied to aquaculture in an economically feasible way,” he said. “That means testing many different approaches and algorithms and being up-to-date with technologies like sequencing and microarray. I also share the load of the bioinformatics analysis for clients.” More recently, he was appointed Director of Aquaculture Innovation with Atlantic AquaFarms, where he will focus on actively driving the application of genome-based and other innovations to improve aquaculture production and sustainability.

His participation in Genome Atlantic-supported projects has played a role in keeping him in the region. “I could have gone west,” he said, “because I worked quite a lot with salmon, but my wife is from Newfoundland, and the people I know and work with are in the Atlantic region.” Hori still works closely with many of the people he encountered on the CGP and camelina projects, especially Dr. Rise and Dr. Kurt Gamperl, professors, Ocean Sciences, Memorial University, and Dr. Mark Fast, Associate Professor of Fish Health, Atlantic Veterinary College, University of Prince Edward Island.          

Colombo’s current research at Dalhousie’s Truro, NS campus, aims to discover sustainable new ways to improve nutrition and aquaculture production.  Specifically, she is interested in developing sustainable sources of omega-3s in diets for farmed fish and discovering new ways to boost their nutrition and metabolism. The goal is to produce healthy farmed fish that supply consumers with omega-3s in ways that effectively use ocean resources. “I use genomics as a tool to help answer these nutritional questions,” she said. “It allows us to dig deeper into the synthesis and storage of these important fatty acids.” 

She now has graduate students working in her lab, and she also teaches fish nutrition as part of the B.Sc. Agriculture (Aquaculture) program.

At Agriculture and Agri-Food Canada, Gardner says he uses “genomics tools, like DNA sequence-based genotyping, in the potato breeding program, based in Fredericton, New Brunswick.” It takes 10-12 years to develop a new potato variety, he says, “so we are keen to use emerging technologies to make the variety selection process more efficient and cost effective. “

It is clear that Hori, Colombo and Gardner are applying their knowledge to help the Atlantic region prosper. For Hori especially, the journey has been an eye-opener. As a student at the Federal University of Sao Carlos, Brazil when the CGP project emerged on his radar, Atlantic Canada was well off the beaten path. “Never heard of it,” he said. Now Atlantic Canada is home.