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

Abstract

High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (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 reference genome assembly. Over 96,000 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 subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according 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 integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research.

Keywords: RNA-Seq; SNP array; Salmo salar; linkage map; recombination.

Figure 1

Comparison of the number of SNPs in corresponding chromosomes and physical length retrieving from recent reference assembly (GenBank assembly reference GCA_000233375.4, Davidson et al. 2010). The correlation was approximately 0.95.

Figure 2

A comparison between genetic and physical maps of a representative chromosome (Chr 22), reflecting the recombination pattern difference between males and females. Details of genetic distance and physical distance for all mapped loci are given in File S1.

Figure 3

A comparison of male and female recombination level (cM/Mb) graphed according to physical distance from the nearest chromosome end (expressed as a percentage of total chromosome size in megabases).