An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha).
Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
G J
GJ
McKinney
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
L W
LW
Seeb
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
W A
WA
Larson
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
D
D
Gomez-Uchida
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
M T
MT
Limborg
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
M S O
MS
Brieuc
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
M V
MV
Everett
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
K A
http://orcid.org/0000-0002-3275-8778
KA
Naish
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
R K
RK
Waples
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.
J E
JE
Seeb
D000220:Adaptation, Biological; D000818:Animals; D002874:Chromosome Mapping; D020224:Expressed Sequence Tags; D014644:Genetic Variation; D005828:Genetics, Population; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D012474:Salmon / Q000145:classification* / Q000235:genetics*
RAD sequence; adaptation; duplicated genome; linkage mapping; population differentiation