1. Garrett McKinney University of Washington Seeb Lab
An Improved Linkage Map Reveals Candidate Genes for Adaptive Variation in Chinook Salmon (Oncorhynchus tshawytscha)
Garrett McKinney
University of Washington
Seeb Lab
Pat Clayton

2. Genomics of Adaptation
Finding the genes involved in adaptive variation is a central theme in evolutionary ecology
Steps involved:
Identify regions of the genome associated with trait variation
Identify candidate genes within these regions
Determine if genotypes for these genes are associated with trait variation
Multiple studies have identified regions of the genome associated with trait variation and population differentiation in Chinook salmon
Genotypes
Barson et al. 2015

3. Our lab has identified regions of the Chinook salmon genome associated with population differentiation and with variation in thermotolerance and body size

4. Population Differentiation in Chinook Salmon
This slide shows regions of elevated divergence between populations identified in Larson et al Regions of differentiation are color coded by the number of pairwise populations that showed divergence.

5. Trait Variation in Chinook Salmon
Our lab has also identified regions of the genome associated with variation in thermotolerance and body size. These figures were taken from Everett and Seeb, 2014.

6. Chinook Salmon Linkage Map
14,620 Loci
2,336 duplicated loci
This shows the updated linkage map. Linkage groups (chromosomes) are oriented vertically and separated on the x-axis, cM distance along each linkage group is given on the y-axis. Non-duplicated markers are shown in blue, duplicated markers are shown in red, and centromere regions are shown in green.

7. Adding the Atlantic Salmon Genome
This shows alignment of the Atlantic salmon genome to one of the Chinook salmon chromosomes.
Linkage Map

8. Adding Chinook Salmon Gene Sequence
Chinook salmon Transcriptome
Atlantic salmon genome
This shows alignments of Chinook salmon transcriptome sequence to linkage map through direct alignment to markers on the linkage map, and by alignment to Atlantic salmon genome sequence that was placed on the linkage map.
Linkage Map

9. Regions of Trait Variation
QTL regions
Chinook salmon Transcriptome
Atlantic salmon genome
This shows placement of regions associated with trait variation (QTL) on the linkage map.
Linkage Map

10. Regions of Population Differentiation
QTL regions
Chinook salmon Transcriptome
Atlantic salmon genome
This shows regions of population differentiation placed on the linkage map
Outlier Loci
Linkage Map

11. Results from the alignment of all resources to each chromosome in the new linkage map

12. Thermotolerance Candidate Genes
BAG
Genes that are good candidates for explaining variation in thermotolerance were found within regions previously associated with variation in thermotolerance.
HSP70
Everett and Seeb, 2014

13. HSP70 and BAG
HSP70 and BAG (HSP70 inhibitor) underlie QTL for thermotolerance identified by Everett and Seeb (2014)
HSP70
Associated with thermal response
(Ojima et al. 2005, Rebl et al. 2013)
Associated with thermotolerance
(Narum and Campbell, 2015)
Known relationship with thermotolerance in other taxa
(King et al. 2002, Zhang et al. 2002
BAG
Inhibitor to HSP70 (Nollen et al. 2001)
Desert
Hybrid
Montaine
Narum and Campbell, 2015

14. Population Divergence
HSP47
HSP74
Multiple genes associated with thermotolerance were also found within regions of elevated differentiation between Western Alaska Chinook salmon populations.
Desert
Hybrid
Montaine
Narum and Campbell, 2015

15. Conclusions
Placing gene locations on linkage maps is critical to identifying candidate genes
Re-examining and combining archived data can yield new insights

16. Acknowledgements Coauthors Lisa Seeb Wes Larson Daniel Gomez-Uchida
Morten Limborg
Marine Brieuc
Meredith Everett
Kerry Naish
Ryan Waples
Jim Seeb