RT Journal Article
T1 Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome
A1 Tsai, Hsin Y.
A1 Robledo Sánchez, Diego
A1 Lowe, Natalie R.
A1 Bekaert, Michaël
A1 Taggart, John B.
A1 Bron, James E.
A1 Houston, Ross D.
K1 Salmo salar
K1 Linkage map
K1 SNP array
K1 Recombination
K1 RNA-Seq
AB High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, andcharacterization of the recombination landscape of a species’ genome. Genomic resources for Atlanticsalmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism(SNP) arrays. Our aim was to create a high density linkage map, and to align it with the referencegenome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using apedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the ‘ssalar01’ highdensity SNP array. The number of SNPs per group showed a high positive correlation with physical chromosomelength (r = 0.95). While the order of markers on the genetic and physical maps was generallyconsistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped referencegenome sequence was assigned to chromosomes using the linkage map. Male recombination rate waslower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions.Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorizedaccording to their predicted function, including annotation of  2500 putative nonsynonymous variants.The highest density SNP linkage map for any salmonid species has been created, annotated, and integratedwith the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy ofsalmon, and provides a useful resource for salmonid genetics and genomics research
PB Genetics Society of America
YR 2016
FD 2016
LK http://hdl.handle.net/10347/16319
UL http://hdl.handle.net/10347/16319
LA eng
NO Hsin Y. Tsai, Diego Robledo, Natalie R. Lowe, Michael Bekaert, John B. Taggart, James E. Bron and  View ORCID ProfileRoss D. Houston G3: GENES, GENOMES, GENETICS July 1, 2016 vol. 6 no. 7 2173-2179; https://doi.org/10.1534/g3.116.029009
NO The University of Edinburgh. Edinburgh Genomics is partly supported through core grants from the Natural Environment Research Council (NERC) (R8/H10/56), Medical Research Council (MRC) (MR/K001744/1),and the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/J004243/1). This research was supported by BBSRC grants (BB/H022007/1, BB/F002750/1, BB/F001959/1) awarded to The Roslin Institute and University of Stirling, and by BBSRC Institute Strategic Funding Grants to The Roslin Institute (BB/J004235/1, BB/J004324/1, BB/J004243/1). D.R. was funded by a postgraduate grant from Fundación Barrié. The authors also acknowledge the support ofthe MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) in the completion of this study. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions
DS Minerva
RD 25 abr 2026