Comparative Genomic Analysis of Atlantic Salmon, Salmo Salar, from Europe and North America

Background: Several lines of evidence including allozyme analysis, restriction digest patterns and sequencing ofmtDNA as well as mini- and micro-satellite allele frequencies indicate that Atlantic salmon (Salmo salar) from NorthAmerica and Europe are genetically distinct. These observations are supported by karyotype analysis, whichrevealed that North American Atlantic salmon have 27 pairs of chromosomes whereas European salmon have 29pairs. We set out to construct a linkage map for a North American Atlantic salmon family and to compare this mapwith the well developed map for European Atlantic salmon.Results: We used microsatellite markers, which had previously been mapped in the two Atlantic salmon SALMAPmapping families from the River Tay, Scotland, to carry out linkage analysis in an Atlantic salmon family (NB1)whose parents were derived from the Saint John River stock in New Brunswick, Canada. As large differences inrecombination rates between female and male Atlantic salmon have been noted, separate genetic maps wereconstructed for each sex. The female linkage map comprises 218 markers in 37 linkage groups while the male maphas 226 markers in 28 linkage groups. We combined 280 markers from the female and male maps into 27composite linkage groups, which correspond to the haploid number of chromosomes in Atlantic salmon from theWestern Atlantic.Conclusions: A comparison of the composite NB1 and SALMAP linkage maps revealed the reason for thedifference in the chromosome numbers between European and North American Atlantic salmon: Linkage groupsAS-4 and AS-32 in the Scottish salmon, which correspond to chromosomes Ssa-6 and Ssa-22, are combined into asingle NB1 linkage group as are linkage groups AS-21 and AS-33 (corresponding to chromosomes Ssa-26 and Ssa-28). The comparison of the linkage maps also suggested some additional chromosomal rearrangements, but it willrequire finer mapping, potentially using SNPs, to test these predictions. Our results provide the first comparison ofthe genomic architecture of Atlantic salmon from North America and Europe with respect to chromosomeorganization