Chromosomal differences between European and North American Atlantic salmon discovered by linkage mapping and supported by fluorescence in situ hybridization analysis

Abstract

BackgroundGeographical isolation has generated a distinct difference between Atlantic salmon of European and North American Atlantic origin. The European Atlantic salmon generally has 29 pairs of chromosomes and 74 chromosome arms whereas it has been reported that the North American Atlantic salmon has 27 chromosome pairs and an NF of 72. In order to predict the major chromosomal rearrangements causing these differences, we constructed a dense linkage map for Atlantic salmon of North American origin and compared it with the well-developed map for European Atlantic salmon.ResultsThe presented male and female genetic maps for the North American subspecies of Atlantic salmon, contains 3,662 SNPs located on 27 linkage groups. The total lengths of the female and male linkage maps were 2,153 cM and 968 cM respectively, with males characteristically showing recombination only at the telomeres. We compared these maps with recently published SNP maps from European Atlantic salmon, and predicted three chromosomal reorganization events that we then tested using fluorescence in situ hybridization (FISH) analysis. The proposed rearrangements, which define the differences in the karyotypes of the North American Atlantic salmon relative to the European Atlantic salmon, include the translocation of the p arm of ssa01 to ssa23 and polymorphic fusions: ssa26 with ssa28, and ssa08 with ssa29.ConclusionsThis study identified major chromosomal differences between European and North American Atlantic salmon. However, while gross structural differences were significant, the order of genetic markers at the fine-resolution scale was remarkably conserved. This is a good indication that information from the International Cooperation to Sequence the Atlantic salmon Genome, which is sequencing a European Atlantic salmon, can be transferred to Atlantic salmon from North America.

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).…”

“…nChromosome containing SNP inferred from European map (Lien et al., 2011) after known translocations were accounted for (Brenna‐Hansen et al., 2012); consequently, the exact position on the chromosome is unknown.…”

“…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.…”