Conservation genomics of Atlantic salmon towards understanding adaptive trait differences for the management of endangered populations

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Genome Canada's GRASP project has developed a new gene expression microarray containing 16,000 different genes from salmonid fishes. This has resulted in many studies that compare gene activity in different tissues of salmon subject to different environments.  However, the existing studies do not tell us how much of the observed variation in gene expression (expression level polymorphism: ELP) among different salmon populations is genetic.  Recent molecular markers have shown that 10% of the smolts from the endangered Upper Salmon River run in the Inner Bay of Fundy are F1 hybrids between salmon native to this stream and escaped salmon from a European Aquacultural strain.  In the first part of our project these F1 "Trans Atlantic" individuals will be backcrossed back to one of the parental populations to create two large full sib research families that will be segregating for the alleles that are unique to each of the original parental strains.  These backcross families will enable us to use a statistically powerful method to identify genes whose ELPs that are strongly correlated with particular values of morphological, physiological and life history traits for individuals within each of our full sib families.  In the second part of our project we will verify that these correlations have a genetic basis by comparing the DNA sequences of these genes and look for sites called SNPs (single nucleotide polymorphisms) that vary in sequence between the two parental populations.  We will then use our most promising SNP markers to genotype tail clips from endangered wild Atlantic salmon that are held in a common hatchery environment.  This will enable us to document the genetic differences in functional traits among these endangered salmon populations and may assist in their conservation. Development of these SNP genetic markers will eventually enable the aquaculture industry to practise marker-assisted selection within the St. John's Aquaculture strain that is authorized for use in New Brunswick.