Open Access Research article

A first generation BAC-based physical map of the rainbow trout genome

Yniv Palti1*, Ming-Cheng Luo2, Yuqin Hu2, Carine Genet3, Frank M You2, Roger L Vallejo1, Gary H Thorgaard4, Paul A Wheeler4 and Caird E Rexroad1

Author Affiliations

1 National Center for Cool and Cold Water Aquaculture, ARS-USDA, 11861 Leetwon Road, Kearneysville, WV 25430, USA

2 Department of Plant Sciences, University of California, One Shields Ave., Davis, CA 95616, USA

3 INRA, UMR1313, Genetique Animale et Biologie Integrative, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France

4 School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman WA 99164-4236, USA

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BMC Genomics 2009, 10:462  doi:10.1186/1471-2164-10-462

Published: 8 October 2009



Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species.


The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map.


The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of QTL, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of MAS into rainbow trout breeding programs.