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

Background: 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. Results: 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. Conclusion: 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. Background Genome research in agriculturally important species is facilitated by the availability of species-specific molecular genetic tools and resources such as chromosome maps and large volumes of sequence data. Recently such resources have been developed for important aquaculture species including rainbow trout, which are also widely used as a model system for carcinogenesis, toxicological, and comparative immunological research [1]. Several genetic maps [2-4] consisting primarily of type II markers [5] (amplified fragment length polymorphism simple sequence repeats) have been utilized in the identification of qualitative and quantitative trait loci (QTL) [6] associated with rainbow trout production traits. This includes QTL for natural killer cell-like activity, temperature tolerance, spawning date, body weight, resistance to infectious pancreatic necrosis virus (IPNV), resistance to infectious hematopoietic necrosis virus (IHNV), embryonic development rate, and albinism [7-19]. Although the Published: 18 April 2005 BMC Genomics 2005, 6:54 doi:10.1186/1471-2164-6-54 Received: 20 December 2004 Accepted: 18 April 2005 This article is available from: http://www.biomedcentral.com/1471-2164/6/54 © 2005 Rexroad et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BMC Genomics 2005, 6:54 http://www.biomedcentral.com/1471-2164/6/54