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

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.

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

“…(2012); “EU” means the position on the European Atlantic salmon female linkage map by Lien et al. (2011). …”

“…DNA was extracted from all fin clip samples using 96‐well plate format Qiagen ™ DNeasy blood and tissue kits, according to the protocol recommended by the manufacturer. A custom Atlantic salmon Illumina iSelect ™ 6K bead array (Brenna‐Hansen et al., 2012; Lien et al., 2011) was used to perform SNP genotyping. Once all fish were genotyped, all genotype clusters were assigned using Illumina Genome Studio© software and subsequently checked manually.…”

“…Only diploid loci identified by GenomeStudio as (i) showing Mendelian inheritance in our population and (ii) not significantly deviating from Hardy–Weinberg equilibrium were used for subsequent analyses. Nearly all SNP loci used in our analyses had been located on a North American Atlantic salmon female linkage map (Brenna‐Hansen et al., 2012) or a European linkage map (Lien et al., 2011). …”

“…Once a p ‐value for a given QTL had been assigned to a SNP, subsequent QTLs for other traits from the same study would be assigned to adjacent SNPs. We then used each chromosome on the North American linkage map (Brenna‐Hansen et al., 2012) or the corresponding chromosome segments for each bin on the European linkage map (Lien et al., 2011) as a “bin”. We then determined whether each SNP in each bin: (i) was an F CT outlier locus and (ii) was a marker with a significant p value for a published QTL for weight or for sexual maturity.…”

“…Application of genome scans to Atlantic salmon populations has been facilitated by the greatly increased availability of SNPs for Atlantic salmon (Houston et al., 2014; Lien et al., 2011) and the publication of the genome (Lien et al., 2016). Recent outlier locus studies of salmonid fishes have primarily compared wild populations at different spatial scales (Freamo, O'Reilly, Berg, Lien, & Boulding, 2011; Vasemägi & Primmer, 2005) or have correlated outlier loci of wild populations with specific environmental variables (Bourret, Kent, et al., 2013; Bourret, Dionne, Kent, Lien, & Bernatchez, 2013; Narum, Campbell, Kozfkay, & Meyer, 2010; Perrier, Bourret, Kent, & Bernatchez et al., 2013).…”