Post on 27-Jun-2015
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Caroline StorerSAFS GSS 2010
Genetic and epigenetic variation in sockeye salmon
“Variation is the spice of life”
Kruglyak & Nickerson. 2001.Nature Genetics.
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
Types of variation
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Types of variation
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Types of variation
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Epigenetic variation
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA sequence
Epigenetic variation
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Epigenetic mechanisms can alter gene expression and phenotypes without any change in the DNA sequence
CH3
A C T C G A
A C T C G A
Epigenetic variation
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Epigenetic marks are: Heritable Naturally occurring Can be altered by the
environment
CH3
A C T C G A
A C T C G A
“Variation is the spice of life” …
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
“Variation is the spice of life” …
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
for sockeye salmon
Phenotypic variation in sockeye salmon
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Beach (top) and stream (bottom) spawning ecotypes
Genetic variation in sockeye salmon
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Ackerman et al. In reviewGenetically similar spawning populations
Genetic variation in sockeye salmon
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
Our ability to detect variation is dependent on the number of markers we have
Currently there are 42 SNP markers for sockeye salmon
Epigenetic variation in sockeye salmon
Bossdorf, Richards, & Pigliucci. 2008. Ecology Letters
?
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
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
Describing genetic variation
Methods: Genotype
populations range-wide at SNP loci
Assess genetic variation
Describing genetic variation
Methods: Genotype
populations range-wide at SNP loci
Assess genetic variation
Population 1
A C T C G
Population 2
A C A C G
SNP locus
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
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
SNP discovery
Methods:1. Identify candidate SNPs2. Validate candidate SNPs
Results: 73 new SNPs validated 115 SNPs total
Describing genetic variation
Russia
Bristol Bay
Alaska Peninsula
South-central Alaska
British Columb
ia
Washington
Genotyped 12 populations, 61- 93 fish per population, representing 6 regions
Genetic variation
Russia
Principal Coordinate 2 (15.5%)
Bristol Bay
Alaska Peninsula
South-central AlaskaBritish
Columbia
WashingtonPri
ncip
al C
oord
inate
1
(44.5
%)
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
Describing epigenetic variation Detect population specific methylation
(Me) patterns
Describing epigenetic variation Detect population specific methylation
(Me) patterns
Russia
Bristol Bay
Alaska Peninsula
South-central Alaska
British Columbia
Washington
Populations:
Describing epigenetic variation Optimize methods for detecting
population specific methyaltion patterns in sockeye salmon Me-AFLP MeDIP-CHIP
Describing epigenetic variation
Population 1
A C T C G
Population 2
A C A C G
Me locus
Me Patterns:
CH3
Conclusions
Discovered and validated new SNPs Range wide variation; following
geographic patterns Established a threshold of variation for
comparison with epigenetic variation
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
Acknowledgements
Alaska Department of Fish and Game Alaska Sustainable Salmon Fund Bristol Bay Regional Seafood
Development Association University of Washington School of
Aquatic & Fishery Sciences The Gordon and Betty Moore Foundation Applied Biosystems Foster City, CA The Seeb and Roberts Labs
Thank you.
Questions?