Originally published as Genetics Published Articles Ahead of Print on February 1, 2006.

Genetics, Vol. 172, 2405-2419, April 2006, Copyright © 2006
doi:10.1534/genetics.105.048330

A Linkage Map for Brown Trout (Salmo trutta): Chromosome Homeologies and Comparative Genome Organization With Other Salmonid Fish

Karim Gharbi^*,,1, Angélique Gautier^*,2, Roy G. Danzmann, Sonia Gharbi^*, Takashi Sakamoto, Bjørn Høyheim, John B. Taggart^**, Margaret Cairney^**, Richard Powell, Francine Krieg^*, Nobuaki Okamoto, Moira M. Ferguson, Lars-Erik Holm and René Guyomard^*

^* Laboratoire de Génétique des Poissons, INRA, 78352, Jouy-en-Josas, France, Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada, Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Minato, Tokyo 108, Japan, Department of Morphology, Norwegian School of Veterinary Science, N-0033 Oslo, Norway, ^** Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, United Kingdom, Department of Microbiology, National University of Ireland, Galway, Ireland and Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Tjele DK-8830, Denmark

¹ Corresponding author: Division of Environmental and Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
E-mail: k.gharbi{at}bio.gla.ac.uk

We report on the construction of a linkage map for brown trout (Salmo trutta) and its comparison with those of other tetraploid-derivative fish in the family Salmonidae, including Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and Arctic char (Salvelinus alpinus). Overall, we identified 37 linkage groups (2n = 80) from the analysis of 288 microsatellite polymorphisms, 13 allozyme markers, and phenotypic sex in four backcross families. Additionally, we used gene–centromere analysis to approximate the position of the centromere for 20 linkage groups and thus relate linkage arrangements to the physical morphology of chromosomes. Sex-specific maps derived from multiple parents were estimated to cover 346.4 and 912.5 cM of the male and female genomes, respectively. As previously observed in other salmonids, recombination rates showed large sex differences (average female-to-male ratio was 6.4), with male crossovers generally localized toward the distal end of linkage groups. Putative homeologous regions inherited from the salmonid tetraploid ancestor were identified for 10 pairs of linkage groups, including five chromosomes showing evidence of residual tetrasomy (pseudolinkage). Map alignments with orthologous regions in Atlantic salmon, rainbow trout, and Arctic char also revealed extensive conservation of syntenic blocks across species, which was generally consistent with chromosome divergence through Robertsonian translocations.

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