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An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon ( Oncorhynchus tshawytscha )
Author(s) -
McKinney G. J.,
Seeb L. W.,
Larson W. A.,
GomezUchida D.,
Limborg M. T.,
Brieuc M. S. O.,
Everett M. V.,
Naish K. A.,
Waples R. K.,
Seeb J. E.
Publication year - 2016
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12479
Subject(s) - biology , oncorhynchus , candidate gene , genetics , genome , quantitative trait locus , genetic linkage , population , genotyping , genomics , gene , computational biology , evolutionary biology , genotype , fishery , demography , sociology , fish <actinopterygii>
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 EST s. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP 70, 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 EST s 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.