Developing a genomics tool (FIT-CHIP) for in-season information on Salmon health

Description

Climate change, genetic challenges, ecological inconsistency, and disease can all be listed as potential stressors to wild populations of salmon on Canada’s west coast. This project is addressing the physical states of wild populations through the development of a series of “salmon FIT-CHIPs” which will be used as a predictor of salmon condition. The system offers extreme flexibility, allowing biological markers to be easily customized for stress or other conditional states to different life-history stages, environments, and in different tissues. There are a number of potential end-user groups (fisheries management, aquaculture, hatcheries, environmental non-government organizations and university research labs) and these FIT-CHIPs can be customized to meet their needs. This tool will provide the first in-season method to incorporate information on salmon condition into fisheries management decision making.

A text search will be conducted on abstracts or full papers for key protein (biomarkers) word associations that have been linked to a given stressor. The project will then continue by data-mining the huge in-house microarray ^{Footnote 1} databases produced from dozens of studies that encompass more than 4,900 microarrays and three salmon species (Chinook, Sockeye, and Coho) as well as over 60 stress-challenge microarray studies conducted across a broad range of salmon species available in public databases. The ultimate aim is to discover biomarkers predictive of the presence of specific stressors or conditions and to translate these into a tool (FIT-CHIP) that can inexpensively and rapidly identify the presence of multiple stressors or conditions in a group of fish at once. Tests will be developed that should work across all three species, and preferentially across Atlantic Salmon and Rainbow Trout as well. In all, it is anticipated that five FIT-CHIPS will be developed through this project.

Scientific title for this project:

Bioinformatic Support to Develop FIT-CHIP for Industry and Salmon Management Applications

Program Name

Genomics Research and Development Initiative (GRDI)

Year(s)

2014 - 2017

Principal Investigator(s)

Dr. Kristi Miller-Saunders
lead – Fisheries and Oceans Canada

Paul Pavlidis
University of British Columbia