Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome

Background: High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterisation of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome and high density SNP arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly.  Results: Over 96 K SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5 % of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in sub-telomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorised according to their predicted function, including annotation of ~ 2.5 K putative non-synonymous variants.  Conclusions: The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful 36 resource for salmonid genetics and genomics research