Open Access Highly Accessed Research article

Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: Conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss)

Ruth B Phillips12, Kimberly A Keatley1, Matthew R Morasch1, Abigail B Ventura1, Krzysztof P Lubieniecki3, Ben F Koop4, Roy G Danzmann5 and William S Davidson3*

Author Affiliations

1 Department of Biological Sciences, Washington State University, Vancouver, WA 98686-9600, USA

2 Center for Reproductive Biology, Washington State University, Pullman, WA 99164-4236, USA

3 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada

4 Department of Biology, University of Victoria, Victoria, British Columbia V8W 3P2, Canada

5 Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada

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BMC Genetics 2009, 10:46  doi:10.1186/1471-2156-10-46

Published: 18 August 2009



Most teleost species, especially freshwater groups such as the Esocidae which are the closest 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 seen in extant salmonids (e.g., rainbow trout). The Atlantic salmon is an exception among the salmonids as it has 72–74 chromosome arms and its karyotype includes 12 pairs of large acrocentric chromosomes, which appear to be the result of tandem fusions. The purpose of this study was to integrate the Atlantic salmon's linkage map and karyotype and to compare the chromosome map with that of rainbow trout.


The Atlantic salmon genetic linkage groups were assigned to specific chromosomes in the European subspecies using fluorescence in situ hybridization with BAC probes containing genetic markers mapped to each linkage group. The genetic linkage groups were larger for metacentric chromosomes compared to acrocentric chromosomes of similar size. Comparison of the Atlantic salmon chromosome map with that of rainbow trout provides strong evidence for conservation of large syntenic blocks in these species, corresponding to entire chromosome arms in the rainbow trout.


It had been suggested that some of the large acrocentric chromosomes in Atlantic salmon are the result of tandem fusions, and that the small blocks of repetitive DNA in the middle of the arms represent the sites of chromosome fusions. The finding that the chromosomal regions on either side of the blocks of repetitive DNA within the larger acrocentric chromosomes correspond to different rainbow trout chromosome arms provides support for this hypothesis.