Using a genomic approach to identify individual Chinook Salmon

Description

The data needed to allow an estimation of mortality rates on individual populations of Pacific salmon species currently depends on the Coded-Wire Tag (CWT) program. However, concern is now growing as the current form of the program conducted by Fisheries and Oceans Canada (DFO) for Chinook Salmon assessment is not financially sustainable and the quality of information delivered by the program is not sufficient for certain fishery management decisions. Next generation sequencing (i.e. determining the genetic sequence) of DNA to obtain the genotype of an individual, a method that can be used to ‘mark’ the offspring of hatchery broodstock (breeding stock), will radically change the techniques used in stock identification applications to monitor the migration patterns and returns of Chinook Salmon. This form of parental based tagging may be a possible replacement of current coded wire tag program for Chinook Salmon, potentially resulting in significant cost savings to DFO.

Using the code of certain genetic markers (single nucleotide polymorphisms or SNPs) has been very useful in genetically identifying individuals among salmon stocks. Sampling of Chinook Salmon broodstock at all hatcheries where coded wire tags are applied (approximately 10,000 individuals from 10 facilities) was conducted successfully in 2013 and again in 2014 (with a total sample of 300 SNPs each year). The initial objective of the project is to develop a single molecular test to screen all available SNPs. The next objective will be to apply this test to screen for SNPs for the hatcheries sampled. Accuracy of identification will be evaluated by sampling Chinook that return to hatcheries in 2015, as well as older fish in subsequent years. If demonstrated to be successful, it would no longer be necessary to collect heads of CWTed salmon in order to determine year and location of release, providing benefits to the industry. It would also allow the production of specific parental crosses to be evaluated, and this can be linked to the health status of parents in the broodstock.

Scientific title for this project:

Parental-Based Tagging (PBT) of Chinook Salmon

Program Name

Genomics Research and Development Initiative (GRDI)

Year(s)

2014 - 2017

Principal Investigator(s)

Dr. Terry Beacham
lead

Dave Willis

Cheryl Lynch
Fisheries and Oceans Canada