The genetics of aquaculture: Genotyping with GBS and arrays for species identification and trait improvement

DATE: November 8, 2016
TIME: 10:00am PT, 1:00pm ET

Stock and individual identification of Coho and Chinook Salmon in British Columbia via amplicon sequencing

We have assembled a panel of primers for Coho Salmon that produces 305 amplicons (about 250 derived from Coho–origin primers and about 55 from Chinook–origin primers) containing approximately 380 single nucleotide polymorphisms (SNPs), with all sequences amplified via a single polymerase chain reaction. We have also developed a panel of primers that amplify approximately 350 amplicons (280 derived from Chinook–origin primers and about 70 from Coho–origin primers) containing approximately 450 SNPs that we are currently tracking. Application of the panels to Coho and Chinook Salmon from hatchery populations in southern British Columbia (BC) has indicated substantial differentiation among populations, as well as differentiation among brood years and individuals within hatcheries. We have sampled all hatchery broodstock used in major hatcheries operating in southern BC (Coho 2014–2015, Chinook 2013-15), thereby achieving 100% ‘genetic tagging’ of hatchery production.  Adipose fin clipping of juveniles upon hatchery release provides a visual marker to identify hatchery-produced Coho and Chinook Salmon.  Individual Coho and Chinook Salmon (clipped and unclipped) that fail to assign to sampled parents will be identified to hatcheries and wild populations of origin through genetic stock identification using the SNP loci. Preliminary analysis has indicated very high resolution in stock composition estimates among populations. Assignment of individual Coho Salmon to parents using the SNP panels in a multi-generation, tracked population has provided accurate assignments, thus confirming the correct assignment to both hatchery and brood year (and therefore providing age of the individual). Amplicon sequencing will be the routine method of choice for Coho and Chinook Salmon stock identification in BC in the near future, as high-resolution estimates of stock composition, age, and family structure will be available.  

Genetic and Genome Analyses Using the Rainbow Trout 57K SNP Array

In this webinar I will briefly describe the single nucleotide polymorphism (SNP) content of the array. I will also discuss various research applications including the use of genomic selection for important economic traits like disease resistance; genome-wide association studies (GWAS); and the generation of a dense genetic linkage map for the trout reference genome.