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Open Access Research article

A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

Sigbjørn Lien1*, Lars Gidskehaug1, Thomas Moen12, Ben J Hayes13, Paul R Berg1, William S Davidson4, Stig W Omholt1 and Matthew P Kent1

Author Affiliations

1 Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432, Ås, Norway

2 Aqua Gen AS, Postboks 1240, Pirsenteret, 7462 Trondheim, Norway

3 Biosciences Research Division, Department of Primary Industries Victoria, 1 Park Drive, Bundoora 3083, Australia

4 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, V5A 1S6, Canada

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BMC Genomics 2011, 12:615  doi:10.1186/1471-2164-12-615

Published: 19 December 2011

Abstract

Background

The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD) event between 25 and100 million years ago. Existing data on the proportion of paralogous sequence variants (PSVs), multisite variants (MSVs) and other types of complex sequence variation suggest that the rediplodization phase is far from over. The aims of this study were to construct a high density linkage map for Atlantic salmon, to characterize the extent of rediploidization and to improve our understanding of genetic differences between sexes in this species.

Results

A linkage map for Atlantic salmon comprising 29 chromosomes and 5650 single nucleotide polymorphisms (SNPs) was constructed using genotyping data from 3297 fish belonging to 143 families. Of these, 2696 SNPs were generated from ESTs or other gene associated sequences. Homeologous chromosomal regions were identified through the mapping of duplicated SNPs and through the investigation of syntenic relationships between Atlantic salmon and the reference genome sequence of the threespine stickleback (Gasterosteus aculeatus). The sex-specific linkage maps spanned a total of 2402.3 cM in females and 1746.2 cM in males, highlighting a difference in sex specific recombination rate (1.38:1) which is much lower than previously reported in Atlantic salmon. The sexes, however, displayed striking differences in the distribution of recombination sites within linkage groups, with males showing recombination strongly localized to telomeres.

Conclusion

The map presented here represents a valuable resource for addressing important questions of interest to evolution (the process of re-diploidization), aquaculture and salmonid life history biology and not least as a resource to aid the assembly of the forthcoming Atlantic salmon reference genome sequence.