Dr. Ben Koop

Canada Research Chair in Genomics and Molecular Biology
Principal Investigator, consortium on Genomics Research on All Salmon Project (cGRASP)
Professor, Biology Department
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Phone: (250) 472-4071
Department Page
Research area: genetics and evolution
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Research profile:

Bringing the power of genomics to aquaculture

It’s rare to go a week in B.C. without a fight about salmon. News stories about collapsing stocks in the Fraser River compete with those about sea lice in the Broughton Archipelago, and if people are not arguing about which tastes better, farmed or wild, they are arguing about which is more ethical. To quote a recent Globe and Mail article “salmon is not just a menu option; it's part of the British Columbian identity.”

Given salmon’s significance, Dr. Ben Koop felt it was important to bring the power of genomics to salmon aquaculture and fisheries. Koop has enjoyed considerable success as a geneticist, with a history of leadership roles in several multidisciplinary, large-scale research projects, including the Human Genome Project. His latest venture is the consortium for Genomic Research on All Salmon Project (cGRASP).

The consortium pools the resources of geneticists world-wide to study fish health by focusing on Atlantic salmon as a model species. The group chose Atlantic salmon because of its importance in aquaculture, but also because of its similarity to other salmon species. The research is already providing genetic tools to learn about such diverse areas as aquaculture conditions, sea lice, salmon evolution and salmon development.

Koop co-founded cGRASP (which is both a Genome Canada and Genome BC project) with Dr. Willie Davidson from Simon Fraser University in 2001. They were soon joined by a third principal investigator, Stig Omholt, from The Centre for Integrative Genetics (CIGENE) in Norway. Nine other labs are part of the consortium.

The project has several goals, the first being to identify and map all of the expressed genes of Atlantic salmon. The group has identified most expressed genes and is now mapping them. Another large part of the project is studying salmon gene expression through DNA microarrays.

DNA microarrays help tackle sea lice problem

DNA microarrays are a common way to monitor how organisms express different genes depending on their surrounding conditions (like temperature, food supply or exposure to chemicals). Dr. Koop’s lab is using this technology to understand sea lice, which are an expensive problem for fish farms around the world. Sea lice attach to a salmon’s surface, leaving them susceptible to disease and reducing a fish’s market value. In B.C., there are several raging controversies surrounding sea lice. One is fish farms’ use of the drug SLICE to control sea lice in their farms and the possible effect of SLICE on ocean ecology and human health. The second controversy is whether sea lice are spreading from fish farms to wild juvenile salmon as they swim past the farms, affecting their survival, especially in the Broughton Archipelago.

DNA microarrays can help tackle these questions from several angles. For instance, microarrays can show how salmon and sea lice react to each other at the genetic level. (A DNA microarray is a series of thousands of microscopic spots of DNA fixed to a glass slide or silicon chip. In a microarray experiment, the DNA spots will light up to varying degrees to tell you at what level genes are being expressed in an organism.) Most DNA microarrays contain a few thousand genes; Dr. Ben Koop's are much larger. Recently, lab members created three massive microarrays: one containing all 32,000 genes of Atlantic salmon and two microarrays containing 9,000 genes from two important species of sea lice.

Koop’s lab hopes to use these microarrays get clues on how to best design aquaculture to suit salmon – and not sea lice. The microarrays can also help with designing new drugs against sea lice, by allowing researchers to screen chemicals to see their affect on both lice and salmon.

Beyond the sea lice issue, the Atlantic salmon microarray is a powerful tool for countless studies. For instance, members of Koop’s lab plan to use the microarray to identify salmon genes that control growth and regulate salmon immune systems.

Proof for rapid evolution

Throughout his varied genomic projects, Dr. Ben Koop has had an abiding interest in evolution and the ways nature creates genetic diversity. Salmon species are perfect for this interest because they’ve evolved so recently (relatively speaking). In fact, they seem to be currently in the midst of an evolutionary mechanism: gene re-organization following a whole genome duplication event.

Gene duplication is often cited as the most important factor in evolution. There are several mechanisms by which short sections of DNA (or, more rarely, whole genomes) are duplicated by mistake during cell division. Duplications are followed by a burst of evolution, possibly because duplicated genes are free from selective pressure and start to vary, giving rise to new functions.

It appears that a salmon ancestor duplicated its whole genome between 25 and 100 million years ago. The genome duplication was followed by a time of rapid evolution, where the ancestor diverged into whitefish, grayling and about 30 species of salmon and trout. All these species still have four copies of their genome, but it is thought that, over time, their genomes will reorganize and settle down to the standard two copies normally seen in vertebrates. Koop and his cGRASP colleague Dr. Johan de Boer are analyzing salmon DNA sequence to track this evolutionary event (see BMC Genomics 2007, 8:422). More