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 improv...
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Published in | Molecular ecology resources Vol. 16; no. 3; pp. 769 - 783 |
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Main Authors | , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Blackwell Pub
01.05.2016
Blackwell Publishing Ltd Wiley Subscription Services, Inc |
Subjects | |
Online Access | Get full text |
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Summary: | 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. |
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Bibliography: | http://dx.doi.org/10.1111/1755-0998.12479 Pursuant to National Oceanic and Atmospheric Administration Washington Sea Grant Program, University of Washington - No. RMLE/1 Graduate Research Fellowship Program Grant from the US National Science Foundation - No. DGE-0718124 FONDAP - No. 15110027 Gordon and Betty Moore Foundation - No. 1453 Fig. S1. Genetic resources overlaid onto the genetic map.Fig. S2. Plot of linkage groups showing centromere span in this study (green) as well as estimated minimum (red) and maximum (black) centromere span based on marker synteny with Brieuc et al. ().Fig. S3. Plot of locus relationships between male and female maps.Fig. S4. Marker density for RAD tags that were present on the consensus linkage map and also alignment to the Atlantic salmon genome.Fig. S5. Plot of locus alignments between the Chinook salmon linkage map (x axis) and Atlantic salmon chromosome assemblies (y axis).Table S1.1 Consensus female linkage map produced by LepMap. Table S1.2 Male linkage map produced by LepMap. Table S1.3 Combined female haploid map produced using MergeMap.Table S2.1. Alignments of Atlantic salmon draft genome scaffolds to the linkage map. Table S2.2. Alignments of Atlantic salmon draft genome scaffolds to Atlantic salmon chromosomes (ICSASG_v2: GenBank accession GCA_000233375.4).Table S3. Alignments of ESTs to the Atlantic salmon genome scaffolds placed on the map.Table S4. ESTs and annotations for ESTs that are located within 0.1 cM of outlier loci from Larson et al. ().File S1. Relevant settings used in programs for analyses.File S2. FASTA file containing contigs for mapped loci assembled from paired-end data. Danish Council for Independent Research's Career Programme Sapere Aude - No. 12-126687 ArticleID:MEN12479 istex:BDB6E15585DD747D646DF1B76E3BBF79F51F6EE4 Alaska Sustainable Salmon Fund - No. 44812; No. 44913 ark:/67375/WNG-TCZP7GJ9-3 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 1755-098X 1755-0998 |
DOI: | 10.1111/1755-0998.12479 |