Salmon Genomics Projects
•
•
•
•
•
•
GRASP 2000 – 2005
cGRASP 2006 – today
FishManOmics 2009 –
ICSASG 2010 –
GiLS 2009 –
Upper temperature
tolerance in Arctic charr
2009 –
Consortium for Genomic
Research on All Salmonids Project
Ben Koop
Willie Davidson
Stig Omholt
Caird Rexroad
Vanya Ewart
Chris Secombes
Patricia Gallaugher
Michael Burgess
Bill Driedzic
Bob Devlin
Graham van Aggelen
Ruth Phillips
Up Fraser
Mid Fraser
Strait of Georgia
Chinook Salmon
Creel Survey
May - Jun
Lr Fraser
N Thomp
S Thomp
Apr - May
Lr Thomp
West VI
East VI
North BC
South BC
Puget Snd
SW Vancouver
Island
Troll Fishery
Washington
Apr
Columbia
Oregon
Aug
June
May
From Kristi Miller
and colleagues at DFO
QTL Mapping of Resistance to ISA
LG8
Moen et al. (2007) BMC Genetics 8:53
Syntenic Sequence Analysis
Ssa0821BSFU
BHMS177 Ssa0130ECIG
Ssa0578BSFU
Candidate gene
Candidate gene for ISA resistance
cDNAs and ESTs allow “Gene chips” or microarrays to be built
Atlantic salmon Rainbow trout
cDNA Microarray Application: Environment
work of
Kristi Miller
and colleagues at DFO
FishManOmics Project: From Genomics to the Generation of New
Fisheries Models
DFO Header
Functional Genomics to Identify Biomarkers
Predictive of Salmon Condition
Out-migrating smolts
Bioinformatics
Return migrating adults
Conditional Biomarkers
Mortalities
Social Sciences
Survivors
Expected
Number of fish returning
PSC
Number of fish returning
Developing the first models with physiological/environmental variables
returns
Date
DFO
Fisheries and Oceans Canada
Project Lead
Co-PI’s
Gar
Lepisosteidae
Sardine
# Species
Clupeomorpha
Zebrafish Ostariophysi
357
6375
Carp
Catfish
Salmon
Protacanthopterygii
312
Trout
Cod
Paracanthopterygii
1212
Medaka
Atherinomorpha
1283
Halibut
Pleuronectiformes
570
Stickleback Gasterosteiformes
Need to have a reference
genome for salmonids
Tilapia
Perciformes
Fugu
Tetraodontiformes
Tetraodon
ICSASG: Norway, Chile and BC
257
9293
339
Ben Koop, Simon Jones,
Willie Davison, Grant Murray
Louse Genome
Salmon Genome
Chalimus on Atlantic salmon fin 20 DPI -S. Johnson NRC
Genetic analyses of
sea lice populations
6 populations, 3 from Atlantic and 3 from Pacific.
14 microsatellites, 80 individuals from each pop.
Different species in Atlantic and Pacific.
No population structuring within an Ocean.
14 populations from Pacific
32 microsatellite markers
Sequencing 500 bp of mtDNA
Sequencing 30 EST loci
Identifying genes associated with
Upper Temperature Tolerance (UTT) in salmonids
Same region found on Atlantic
salmon linkage group 23
Funded by NSERC strategic grant
Genomics of Smolt Out-migration: Can we identify conditional states
DFO Header
associated with poor feeding and growth?
Sampled white muscle from wild Chinook salmon smolts
June 2007
Four groups resolved
Environment only a minor role
40% of the fish in “slow growth”
Trend towards higher growth
in the north
rapid growth,
exercise
moderate
growth/
early adaptation,
exercise
sedentary,
slow growth
slow
growth
Better prey quality in the north
Over-represented
Exclusive to
SE Alaska
Vancouver Island
No SE
Alaska
Fisheries and Oceans Canada