| Summary: | Background: Most teleost species, especially freshwater groups such as the Esocidae which are theclosest relatives of salmonids, have a karyotype comprising 25 pairs of acrocentric chromosomes and 48–52 chromosome arms. After the common ancestor of salmonids underwent a whole genome duplication,its karyotype would have 100 chromosome arms, and this is reflected in the modal range of 96–104 seenin extant salmonids (e.g., rainbow trout). The Atlantic salmon is an exception among the salmonids as ithas 72–74 chromosome arms and its karyotype includes 12 pairs of large acrocentric chromosomes, whichappear to be the result of tandem fusions. The purpose of this study was to integrate the Atlantic salmon'slinkage map and karyotype and to compare the chromosome map with that of rainbow trout.Results: The Atlantic salmon genetic linkage groups were assigned to specific chromosomes in theEuropean subspecies using fluorescence in situ hybridization with BAC probes containing genetic markersmapped to each linkage group. The genetic linkage groups were larger for metacentric chromosomescompared to acrocentric chromosomes of similar size. Comparison of the Atlantic salmon chromosomemap with that of rainbow trout provides strong evidence for conservation of large syntenic blocks in thesespecies, corresponding to entire chromosome arms in the rainbow trout.Conclusion: It had been suggested that some of the large acrocentric chromosomes in Atlantic salmonare the result of tandem fusions, and that the small blocks of repetitive DNA in the middle of the armsrepresent the sites of chromosome fusions. The finding that the chromosomal regions on either side ofthe blocks of repetitive DNA within the larger acrocentric chromosomes correspond to different rainbowtrout chromosome arms provides support for this hypothesis.
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