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Kristi Miller-Saunders

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Email: MillerK@dfo-mpo.gc.ca
Phone: (250) 756-7155
Fax: (250) 756-7053
Region: Pacific
Office: Pacific Biological Station

Field(s) of Research:
  • Biotechnology/ Genomics
  • Fish Population Science

Research Description:
I have overseen a diverse molecular genetics research program within DFO for over 15 years. The overarching goal of my program is the development and application of molecular genetic tools that can be applied towards sustainable fisheries management and aquaculture development of aquatic species. Population genetics research has been applied to establish management and conservation units within species, develop stock identification databases in salmon, and in forensic identification for enforcement. Genetic studies have been conducted on a variety of marine fish and shellfish species, including salmonids, rockfish, sablefish, Atlantic cod, herring, urchins, geoduck, and abalone. While we have developed and utilized a variety of molecular markers, including minisatellite and microsatellite loci and mitochondrial DNA, my main interest is in adaptive variation. The Major Histocompatibility Complex (MHC) is the premiere adaptive gene complex in vertebrates, and my lab has conducted extensive research on MHC gene discovery in teleosts, adaptive population genetics of MHC genes in salmon, and mechanisms of selection on the MHC in teleosts. My group has also developed genetic markers and techniques for species identification and applied these in forensic analysis for enforcement, scat analysis in stellar sea lions, and identification of escaped farmed salmon. Our work on bacterial typing has been applied to the development of probiotics for aquaculture, delineation of bacterial complexity in salmon streams and lakes, and pathogen screening in fish. For aquaculture, we have developed quantitative RT-PCR assays for pathogens, identified the Kudoa thyrsites protein responsible for the post-mortem liquefication of salmon tissue, and identified ?expressed? QTLs associated with rapid muscle growth in scallops. In 2004, with the introduction of the first GRASP (Genomics Research on Atlantic Salmon Project; Ben Koop and Willie Davidson) salmon cDNA microarray, I initiated the formation of a new functional genomics program, the Marine Ecological Genomics and Adaptation Group, within the Molecular Genetics Laboratory. This new program expands my interest in adaptive evolution to the molecular control of phenotypic adaptation. Research within this program has included species-specific salmonid host response to the IHN virus, aimed at elucidating effective host responses for targeted vaccine research, salmon migration physiology, to identify physiological profiles associated with river entry timing and fate of late-run Fraser river sockeye salmon, and density stress in pen-reared salmon, to identify stress biomarkers for aquaculture. This program focuses largely, although not exclusively, on wild ecological genomics research to elucidate phenotype-environment interactions and limits to adaptability. See the MEGA tab under the Molecular Genetics Laboratory for more details.

Publications:
  1. Genomic signatures predict migration and spawning failure in wild Canadian salmon
  2. Mate choice for major histocompatibility complex genetic divergence as a bet-hedging strategy in the Atlantic salmon (Salmo salar)
  3. Sequence analysis of MHC class I α2 from sockeye salmon (Oncorhynchus nerka).
  4. Effects of river temperature and climate warming on stock-specific survival of adult migrating Fraser River sockeye salmon (Oncorhynchus nerka).
  5. Physiological condition differentially affects the behaviour and survival of two populations of sockeye salmon during their freshwater spawning migrations
  6. Development and application of DNA techniques for validating and improving pinniped diet estimates
  7. MHC standing genetic variation and pathogen resistance in wild 1 Atlantic salmon
  8. Population structure and stock identification of chum salmon from western Alaska determined with microsatellite and major histocompatibility complex variation
  9. Salmon Spawning Migration: Metabolic Shifts and Environmental Triggers
  10. Developing a mechanistic understanding of fish migrations by linking telemetry with physiology, behaviour, genomics and experimental biology: an interdisciplinary case study on adult Fraser River sockeye salmon
  11. Differentiating populations at broad and fine geographic scales with microsatellites and SNPs
  12. Identification, characterization, and deduced amino acid sequence of the dominant protease from Kudoa paniformis and K. Thyrsites: A unique cytoplasmic cysteine protease.
  13. Population structure of Dungeness crab (Cancer magister) in British Columbia
  14. A cDNA microarray study of Atlantic salmon (Salmo salar) response to Infectious Hematopoietic Necrosis (IHN) virus
  15. Clinal varaiation in MHC diversity with temperature: evidence for the role of host-pathogen interaction on local adaptation in atlantic salmon
  16. Development and validation of an RNA- and DNA-based quantitative PCR assay for the quantitative detection of Kudoa thyrsites (Gilchrist) in Atlantic salmon (Salmo salar).
  17. Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar)
  18. Bacterial diversity in a marine hatchery: balance between pathogenic and potentially probiotic bacterial strains
  19. Estimation of stock composition and individual identification of Chinook salmon across the Pacific Rim using microsatellite variation
  20. Major histocompatibility complex and kin discrimination in Atlantic salmon and Brook trout
  21. Pacific Rim population structure of sockeye salmon as determined from microsatellite analysis.
  22. Population structure in two marine invertebrate species (Panopea abrupta and Strongylocentrotus franciscanus) targeted for aquaculture and enhancement in British Columbia
  23. The salmonid MHC class I: more ancient loci uncovered
  24. DNA-level variation of sockeye salmon (Oncorhynchus nerka) in southeast Alaska and the Nass and Skeena rivers, British Columbia, with applications to stock identification
  25. Genetic variation within and among domesticated Atlantic salmon broodstocks in British Columbia, Canada
  26. DNA in action: Rapid application of DNA variation to sockeye salmon fisheries management
  27. Development of microsatellite loci in eulachon (Thaleichthys pacificus)
  28. Enrichment of Tetranucleotide Microsatellite Loci from Marine Invertebrate species
  29. Forensic DNA analysis of Pacific salmonid samples for species and stock identification
  30. Major Histocompatibility Complex loci are associated with susceptibility of Atlantic salmon to infectious hematopoietic necrosis virus
  31. Microsatellite loci from red sea urchins (Strongylocentrotus franciscanus)
  32. Polygamous mating and high levels of genetic variation in lingcod (Ophiodon elongatus) of the Strait of Georgia, British Columbia
  33. Stock identification of Fraser River sockeye salmon (Oncorhynchus nerka) using microsatellites and major histocompatibility complex variation
  34. Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha)
  35. Evolution of the immune system
  36. Implications of high levels of genetic diversity and weak population structure for the rebuilding of northern abalone in British Columbia, Canada
  37. The geographic basis for population structure in Fraser River chinook salmon, Oncorhynchus tshawytscha
  38. Expansion and contraction of major histocompatibility complex (MHC) genes: a teleostean example
  39. Multiple stock structure of Atlantic cod (Gadus morhua) off Newfoundland and Labrador determined from genetic variation
  40. Co-existing populations of Pacific Ocean perch, Sebastes alutus, in Queen Charlotte Sound, British Columbia
  41. Development of microsatellite loci in Pacific herring (Clupea pallasi)
  42. Development of microsatellite loci in pinto abalone (Haliotis kamtschatkana).
  43. Evaluation and application of microsatellite and major histocompatibility complex variation for stock identification of coho salmon in British Columbia
  44. Geographic heterogeneity in natural selection on an MHC locus in sockeye salmon
  45. Application of microsatellite DNA variation to estimation of stock composition and escapement of Skeena River sockeye salmon (Oncorhynchus nerka).
  46. Characterization of microsatellite loci in Sebastes alutus and their conservation in congeneric rockfish species
  47. Development of tri- and tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua)
  48. Intact genetic structure and high levels of genetic diversity in bottlenecked sockeye salmon, Oncorhynchus nerka, populations of the Fraser River, British Columbia, Canada
  49. Denaturing gradient gel electrophoresis (DGGE): A rapid and sensitive technique to screen nucleotide sequence variation in populations.
  50. The salmonid class I MHC: limited diversity in a primitive teleost
  51. Mhc diversity in Pacific salmon: Population structure and trans-species allelism
  52. Population differentiation at Mhc genes in chinook salmon Oncorhynchus tshawytscha
  53. Species identification of Pacific salmon by PCR-RFLP of a MHC gene.
  54. Minisatellite DNA variation and stock identification of coho salmon
  55. Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon
  56. Stock identification of coho salmon (Oncorhynchus kisutch) using minisatellite DNA variation
  57. Structure of an unusual minisatellite locus, Ssa1, in Pacific salmonids
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