Open Access Research article

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss)

Caird E Rexroad1*, Maria F Rodriguez1, Issa Coulibaly1, Karim Gharbi2, Roy G Danzmann2, Jenefer DeKoning3, Ruth Phillips3 and Yniv Palti1

Author Affiliations

1 USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia 25430 USA

2 Department of Zoology, University of Guelph, Guelph, Ontario N1G 2W1 Canada

3 School of Biological Sciences, Washington State University-Vancouver, Vancouver, WA 98686 USA

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BMC Genomics 2005, 6:54  doi:10.1186/1471-2164-6-54

Published: 18 April 2005



Comparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest. The development of microsatellite markers from expressed sequence tags will serve to increase marker densities on current salmonid genetic maps and initiate in silico comparative maps with species whose genomes have been fully sequenced.


Eighty-nine polymorphic microsatellite markers were generated for rainbow trout of which at least 74 amplify in other salmonids. Fifty-five have been associated with functional annotation and 30 were mapped on existing genetic maps. Homologous sequences were identified for 20 of the EST containing microsatellites to identify comparative assignments within the tetraodon, mouse, and/or human genomes.


The addition of microsatellite markers constructed from expressed sequence tag data will facilitate the development of high-density genetic maps for rainbow trout and comparative maps with other salmonids and better studied species.