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Caroline Storer<br />SAFS GSS 2010<br />Genetic and epigenetic variation in sockeye salmon<br />
“Variation is the spice of life”<br />Kruglyak & Nickerson. 2001.<br />Nature Genetics. <br />
Everybody’s talking about variation<br />“Variation is the spice of life”; it is required for evolution<br />Genetic varia...
Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Epigenetic variation <br />Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA se...
Epigenetic variation <br />CH3<br />A C T C G A <br />A C T C G A  <br />Epigenetic mechanisms can alter gene expression a...
Epigenetic variation <br />CH3<br />A C T C G A <br />A C T C G A  <br /><ul><li> Epigenetic marks are:
Heritable
 Naturally occurring
 Can be altered by the environment</li></ul>Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
“Variation is the spice of life” …<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
“Variation is the spice of life” …<br />for sockeye salmon<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Phenotypic variation in sockeye salmon <br />Beach (top) and stream (bottom) spawning ecotypes<br />Bossdorf, Richards, & ...
Genetic variation in sockeye salmon <br />Ackerman et al. In review<br />Genetically similar spawning populations<br />Bos...
Genetic variation in sockeye salmon <br /><ul><li> Our ability to detect variation is dependent on the number of markers w...
Currently there are 42 SNP markers for sockeye salmon </li></ul>Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Epigenetic variation in sockeye salmon <br />?<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic var...
Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic var...
Describing genetic variation <br />Methods:<br />Genotype populations range-wide at SNP loci<br />Assess genetic variation...
Describing genetic variation <br />Methods:<br />Genotype populations range-wide at SNP loci<br />Assess genetic variation...
Describing genetic variation <br />Methods:<br />Genotype populations across the range at SNP loci<br />Assess genetic var...
Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic var...
SNP discovery<br />Methods:<br />Identify candidate SNPs<br />Validate candidate SNPs<br />Results:<br />73 new SNPs valid...
Describing genetic variation<br />South-central Alaska<br />Bristol Bay <br />Russia<br />British Columbia<br />Alaska Pen...
Genetic variation<br />Bristol Bay <br />Russia<br />Alaska Peninsula<br />South-central Alaska<br />Principal Coordinate ...
Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic var...
Describing epigenetic variation <br />Detect population specific methylation (Me) patterns<br />
Describing epigenetic variation <br />Detect population specific methylation (Me) patterns<br />Populations:<br />South-ce...
Describing epigenetic variation <br />Optimize methods for detecting population specific methyaltion patterns in sockeye s...
Describing epigenetic variation <br />Population 1<br />Population 2<br />Me Patterns:<br />CH3<br />A C T C G<br />A CAC ...
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Genetic and Epigenetic Variation in Sockeye Salmon

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Presentation for the UW School of Aquatic and Fishery Sciences Grad Student Symposium 2010

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Genetic and Epigenetic Variation in Sockeye Salmon

  1. 1. Caroline Storer<br />SAFS GSS 2010<br />Genetic and epigenetic variation in sockeye salmon<br />
  2. 2. “Variation is the spice of life”<br />Kruglyak & Nickerson. 2001.<br />Nature Genetics. <br />
  3. 3. Everybody’s talking about variation<br />“Variation is the spice of life”; it is required for evolution<br />Genetic variation enables a population to evolve in response to environmental change on a long time scale<br />Epigenetic variation enables a population to evolve in response to environmental change on a short time scale<br />Genetic and epigenetic mechanisms work in concert<br />
  4. 4. Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  5. 5. Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  6. 6. Types of variation<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  7. 7. Epigenetic variation <br />Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA sequence<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  8. 8. Epigenetic variation <br />CH3<br />A C T C G A <br />A C T C G A <br />Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA sequence <br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  9. 9. Epigenetic variation <br />CH3<br />A C T C G A <br />A C T C G A <br /><ul><li> Epigenetic marks are:
  10. 10. Heritable
  11. 11. Naturally occurring
  12. 12. Can be altered by the environment</li></ul>Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  13. 13. “Variation is the spice of life” …<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  14. 14. “Variation is the spice of life” …<br />for sockeye salmon<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  15. 15. Phenotypic variation in sockeye salmon <br />Beach (top) and stream (bottom) spawning ecotypes<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  16. 16. Genetic variation in sockeye salmon <br />Ackerman et al. In review<br />Genetically similar spawning populations<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  17. 17. Genetic variation in sockeye salmon <br /><ul><li> Our ability to detect variation is dependent on the number of markers we have
  18. 18. Currently there are 42 SNP markers for sockeye salmon </li></ul>Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  19. 19. Epigenetic variation in sockeye salmon <br />?<br />Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters<br />
  20. 20. Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic variation across the species’ range<br />Describe epigenetic variation across the species’range<br />
  21. 21. Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic variation across the species’ range<br />Describe epigenetic variation across the species’ range<br />
  22. 22. Describing genetic variation <br />Methods:<br />Genotype populations range-wide at SNP loci<br />Assess genetic variation<br />
  23. 23. Describing genetic variation <br />Methods:<br />Genotype populations range-wide at SNP loci<br />Assess genetic variation<br />Population 1<br />Population 2<br />A C T C G<br />A CAC G<br />SNP locus<br />
  24. 24. Describing genetic variation <br />Methods:<br />Genotype populations across the range at SNP loci<br />Assess genetic variation<br />Problem:<br /> Only 42 nuclear SNPs available for sockeye salmon<br />Solution: <br /> Discover more SNPs<br />
  25. 25. Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic variation across the species’ range<br /> SNP discovery<br />Describe epigenetic variation across the species’range<br />
  26. 26. SNP discovery<br />Methods:<br />Identify candidate SNPs<br />Validate candidate SNPs<br />Results:<br />73 new SNPs validated<br />115 SNPs total<br />
  27. 27. Describing genetic variation<br />South-central Alaska<br />Bristol Bay <br />Russia<br />British Columbia<br />Alaska Peninsula<br />Genotyped 12 populations, 61- 93 fish per population, representing 6 regions <br />Washington<br />
  28. 28. Genetic variation<br />Bristol Bay <br />Russia<br />Alaska Peninsula<br />South-central Alaska<br />Principal Coordinate 1 (44.5%)<br />British Columbia<br />Washington<br />Principal Coordinate 2 (15.5%)<br />
  29. 29. Research objectives <br />What is the molecular basis of phenotypic variation in sockeye salmon?<br />Describe genetic variation across the species’ range<br /> SNP discovery<br />Describe epigenetic variation across the species’range<br />
  30. 30. Describing epigenetic variation <br />Detect population specific methylation (Me) patterns<br />
  31. 31. Describing epigenetic variation <br />Detect population specific methylation (Me) patterns<br />Populations:<br />South-central Alaska<br />Bristol Bay <br />Russia<br />British Columbia<br />Alaska Peninsula<br />Washington<br />
  32. 32. Describing epigenetic variation <br />Optimize methods for detecting population specific methyaltion patterns in sockeye salmon<br />Me-AFLP<br />MeDIP-CHIP<br />
  33. 33. Describing epigenetic variation <br />Population 1<br />Population 2<br />Me Patterns:<br />CH3<br />A C T C G<br />A CAC G<br />Me locus<br />
  34. 34. Conclusions<br />Discovered and validated new SNPs<br />Range wide variation; following geographic patterns<br /> Established a threshold of variation for comparison with epigenetic variation<br />
  35. 35. Possible implications<br />Often, genetic variation alone has not been able to explain observed phenotypic diversity<br />Epigenetics may be part of that missing link<br />Current management strategies are based on measures of genetic variation <br />Epigenetics could be used as an additional, more sensitive measure of variation <br />
  36. 36. Acknowledgements<br /><ul><li>Alaska Department of Fish and Game
  37. 37. Alaska Sustainable Salmon Fund
  38. 38. Bristol Bay Regional Seafood Development Association
  39. 39. University of Washington School of Aquatic & Fishery Sciences
  40. 40. The Gordon and Betty Moore Foundation
  41. 41. Applied Biosystems Foster City, CA
  42. 42. The Seeb and Roberts Labs</li></li></ul><li>Thank you.<br />Questions?<br />

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