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

1. Caroline Storer SAFS GSS 2010 Genetic and epigenetic variation in sockeye salmon

2. “Variation is the spice of life” Kruglyak & Nickerson. 2001. Nature Genetics.

3. Everybody’s talking about variation “Variation is the spice of life”; it is required for evolution Genetic variation enables a population to evolve in response to environmental change on a long time scale Epigenetic variation enables a population to evolve in response to environmental change on a short time scale Genetic and epigenetic mechanisms work in concert

4. Types of variation Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

5. Types of variation Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

6. Types of variation Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

7. Epigenetic variation Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA sequence Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

8. Epigenetic variation CH3 A C T C G A A C T C G A Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA sequence Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

10. Heritable

11. Naturally occurring

12. Can be altered by the environmentBossdorf, Richards, & Pigliucci. 2008. Ecology Letters

13. “Variation is the spice of life” … Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

14. “Variation is the spice of life” … for sockeye salmon Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

15. Phenotypic variation in sockeye salmon Beach (top) and stream (bottom) spawning ecotypes Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

16. Genetic variation in sockeye salmon Ackerman et al. In review Genetically similar spawning populations Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

18. Currently there are 42 SNP markers for sockeye salmon Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

19. Epigenetic variation in sockeye salmon ? Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters

20. Research objectives What is the molecular basis of phenotypic variation in sockeye salmon? Describe genetic variation across the species’ range Describe epigenetic variation across the species’range

21. Research objectives What is the molecular basis of phenotypic variation in sockeye salmon? Describe genetic variation across the species’ range Describe epigenetic variation across the species’ range

22. Describing genetic variation Methods: Genotype populations range-wide at SNP loci Assess genetic variation

23. Describing genetic variation Methods: Genotype populations range-wide at SNP loci Assess genetic variation Population 1 Population 2 A C T C G A CAC G SNP locus

24. Describing genetic variation Methods: Genotype populations across the range at SNP loci Assess genetic variation Problem: Only 42 nuclear SNPs available for sockeye salmon Solution: Discover more SNPs

25. Research objectives What is the molecular basis of phenotypic variation in sockeye salmon? Describe genetic variation across the species’ range SNP discovery Describe epigenetic variation across the species’range

26. SNP discovery Methods: Identify candidate SNPs Validate candidate SNPs Results: 73 new SNPs validated 115 SNPs total

27. Describing genetic variation South-central Alaska Bristol Bay Russia British Columbia Alaska Peninsula Genotyped 12 populations, 61- 93 fish per population, representing 6 regions Washington

28. Genetic variation Bristol Bay Russia Alaska Peninsula South-central Alaska Principal Coordinate 1 (44.5%) British Columbia Washington Principal Coordinate 2 (15.5%)

29. Research objectives What is the molecular basis of phenotypic variation in sockeye salmon? Describe genetic variation across the species’ range SNP discovery Describe epigenetic variation across the species’range

30. Describing epigenetic variation Detect population specific methylation (Me) patterns

31. Describing epigenetic variation Detect population specific methylation (Me) patterns Populations: South-central Alaska Bristol Bay Russia British Columbia Alaska Peninsula Washington

32. Describing epigenetic variation Optimize methods for detecting population specific methyaltion patterns in sockeye salmon Me-AFLP MeDIP-CHIP

33. Describing epigenetic variation Population 1 Population 2 Me Patterns: CH3 A C T C G A CAC G Me locus

34. Conclusions Discovered and validated new SNPs Range wide variation; following geographic patterns Established a threshold of variation for comparison with epigenetic variation

35. Possible implications Often, genetic variation alone has not been able to explain observed phenotypic diversity Epigenetics may be part of that missing link Current management strategies are based on measures of genetic variation Epigenetics could be used as an additional, more sensitive measure of variation

37. Alaska Sustainable Salmon Fund

38. Bristol Bay Regional Seafood Development Association

39. University of Washington School of Aquatic & Fishery Sciences

40. The Gordon and Betty Moore Foundation

41. Applied Biosystems Foster City, CA