NOV 08, 2016 10:00 AM PST

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

  • Research Geneticist, NCCCWA-ARS-USDA
      Dr. Palti currently holds the positions of a research geneticist and lead scientist of the Genetics, Physiology and Genomics unit at the National Center for Cool and Cold Water Aquaculture (NCCCWA), Agricultural Research Service, USDA. He obtained a Bachelor's degree in Agricultural Economics in 1991 from the Hebrew University of Jerusalem, Israel, and in 1997 a PhD in Genetics and Cell Biology from Washington State University (Pullman, WA, USA). Dr. Palti joined the NCCCWA in 2001 following postdoctoral fellowships at the Israeli Agricultural Research Organization (1998-1999), The Israeli Institute of Technology (Technion; 1999-2000) and Thomas Jefferson University, Philadelphia (2000-2001). At the NCCCWA Dr. Palti leads efforts to develop tools and resources for genomics research in rainbow trout and other salmonids. To date he has authored 83 published papers (67 peer-reviewed) and two book chapters. The major genomics tools and resources that were developed for rainbow trout research by teams under Dr. Palti's leadership include a BAC physical map of the genome, an integrated physical and genetic map, a database of 145K RAD SNPs, a draft assembly of the rainbow trout genome sequence, RAD SNPs genetic maps for QTL mapping and a 57K SNP chip. The major focus of Dr. Palti's current research is aimed at developing and evaluating strategies for genome-enabled selection in traits that cannot be measured directly on potential breeders in rainbow trout aquaculture. Dr. Palti collaborates with other geneticists, research physiologists, immunologists, microbiologists and nutritionists to map quantitative trait loci that affect disease resistance and aquaculture production efficiency with the overarching goal of identifying genes and genetic elements that can be utilized for improving aquaculture production efficiency and sustainability.
    • Research Scientist, Fisheries and Oceans Canada, Molecular Genetics Laboratory
        Dr. Beacham has been a research scientist in Fisheries and Oceans Canada for the past 37 years, largely at the Pacific Biological Station in Nanaimo, British Columbia. He is the head of stock identification research within the Molecular Genetics Laboratory, and has examined genetic variation to evaluate population structure and associated stock identification applications across a range of Pacific salmon species. He has employed allozymes, minisatellites, microsatellites, and single nucleotide polymorphisms (SNPs) in salmon stock identification applications. His current focus is to evaluate and apply parentage-based tagging and genetic stock identification techniques for Chinook and Coho Salmon in British Columbia, particularly for hatchery populations. This work is conducted by developing panels of primers that amplify specific fragments of DNA (amplicons) in single PCR reaction, and then direct DNA sequencing of the amplicon is employed in order to genotype individuals at selected SNPs in the amplicon.

      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.

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