Abstract
BackgroundThe 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.ResultsA 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.ConclusionThe 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.
Highlights
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
Linkage map construction Linkage mapping based on genotyping of 3297 Atlantic salmon from 143 families resulted in a linkage map with a total of 5650 single nucleotide polymorphisms (SNPs)
Previous studies in Atlantic salmon have reported extreme differences in recombination rates between the sexes, with female:male ratios ranging from ~5:1 to
Summary
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. The common ancestor of the salmonid fishes is suspected to have undergone a whole genome duplication (WGD) 25-100 million years ago [1]. Ohno et al [4] suggested that the genomes of salmonids have been reverting toward a diploid state through the differentiation of duplicated chromosome sets into distinct pairs of homeologs. Large-scale deletions, gene silencing and chromosomal rearrangements are all thought to be a part of this process, it is not known if these events occur randomly along different lineages or if there is a burst of activity immediately after the duplication followed by stability in the resulting genomes [5]
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