Genomics investments provide new tools to salmon enhancement program


- Ottawa, Ontario

As Fisheries and Oceans Canada (DFO) research scientist Ruth Withler points out, when it comes to judging whether a fish hatchery is doing its intended job, "You have to know who your fish are and where they're going."

With the help of funding from the Government of Canada's Genomics Research and Development Initiative (GRDI), Ms. Withler and her colleagues at the DFO Pacific Biological Station in Nanaimo have developed the tools and gathered the data to answer those questions with greater confidence than ever before.

The Chinook

Ms. Withler's recent research has focused on Chinook salmon populations that spawn in rivers along the west coast of Vancouver Island. The Chinook, which can grow to more than 50 kilograms, is by far the largest of the Pacific salmon species. It supports an important commercial and recreational fishery, and has been an integral part of the diet and culture of coastal First Nations for centuries. Like virtually all species of Pacific salmon, while abundance varies from year to year, the overall population of wild Chinook has followed a generally downward trend over the past 30 to 40 years.

Along with habitat restoration and engaging communities in stewardship activities, hatcheries are one of the key elements in DFO's Salmonid Enhancement Program, which has been operating in the Pacific and Yukon regions for more than 40 years. Every year, tens-of-millions of juvenile salmon are released from hatcheries, helping to sustain salmon populations and provide harvest opportunities in the commercial, recreational and Aboriginal fisheries.

Genomics-based tools key to understanding hatcheries impact

"There is no question the hatcheries are contributing to the fishery in terms of making more fish available for harvesting," says Ms. Withler, "But we are less sure about their impact on the wild salmon population in terms of maintaining the biodiversity that's essential to sustaining that population—fish that are well-adapted to surviving and reproducing in the wild."

Part of the problem is identifying which salmon are wild and which are from a hatchery. Traditionally, hatchery salmon have been marked with what's known as a coded-wire tag (CWT) but, in large part due to tagging costs and the sheer number of fish involved, the CWTs are applied to only about 10 percent of the juvenile salmon released from hatcheries each year.

"GRDI provided the resources we needed to identify and record genetic markers for both hatchery and, in some cases, wild salmon, enabling us to develop a pedigree for these fish—so we don't need tags, their DNA tells us where they came from," explains Ms. Withler. "Now, as we collect fish when they come up-river to spawn, we can make a much more accurate assessment of the numbers of hatchery and wild fish that are successful in making it to the spawning grounds, and how many of each actually spawn successfully."

Just a beginning

Mateo Juan, a member of a DFO Stock Assessment Division tagging crew, holds an adult Chinook salmon. (Photo by Allan Moreau)

Ms. Withler notes that this kind of research is only just getting started. "We initially developed these pedigrees for a few river systems using just a dozen genetic markers. Now, starting with the 2013 brood year, we have characterized the broodstocks of all southern BC hatcheries where CWTs are applied to juvenile Chinook salmon, using hundreds of genetic markers. Their offspring are just starting to return from the ocean to hatcheries and natural spawning grounds," says Ms. Withler.

"This will be the first time we will have tracked an entire generation of hatchery fish and had an opportunity to study the numbers, see what kind of diversity exists in the returning fish, and how well they spawn in the natural environment. This information will help our assessment and enhancement biologists determine not only how hatchery Chinook contribute to fisheries, but also whether they are beneficial or detrimental in the process of rebuilding natural spawning populations."

GRDI a key element

Ms. Withler says none of this work would have been possible without the GRDI. "In many ways, GRDI support for this and other projects here at the Pacific Biological Station have kick-started the application of genomics to salmon enhancement," says Ms. Withler. "It's provided the impetus for a range of research projects that may help us understand why, for example, hatchery fish become poor natural spawners after just a few generations, how that might affect diversity in wild populations—and what we might be able to do about it."