Open Access Research article

A first generation integrated map of the rainbow trout genome

Yniv Palti1*, Carine Genet2, Ming-Cheng Luo3, Aurélie Charlet2, Guangtu Gao1, Yuqin Hu3, Cecilia Castaño-Sánchez14, Kamila Tabet-Canale25, Francine Krieg2, Jianbo Yao4, Roger L Vallejo1 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 INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France

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

4 West Virginia University, Animal and Nutritional Sciences, Morgantown, WV, 26506, USA

5 INRA, UMR 444 ENVT Génétique Cellulaire, 31326 Castanet-Tolosan, France

For all author emails, please log on.

BMC Genomics 2011, 12:180  doi:10.1186/1471-2164-12-180

Published: 7 April 2011



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. An integrated physical and genetic map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) programs for improving rainbow trout aquaculture production.


The first generation integrated map of the rainbow trout genome is composed of 238 BAC contigs anchored to chromosomes of the genetic map. It covers more than 10% of the genome across segments from all 29 chromosomes. Anchoring of 203 contigs to chromosomes of the National Center for Cool and Cold Water Aquaculture (NCCCWA) genetic map was achieved through mapping of 288 genetic markers derived from BAC end sequences (BES), screening of the BAC library with previously mapped markers and matching of SNPs with BES reads. In addition, 35 contigs were anchored to linkage groups of the INRA (French National Institute of Agricultural Research) genetic map through markers that were not informative for linkage analysis in the NCCCWA mapping panel. The ratio of physical to genetic linkage distances varied substantially among chromosomes and BAC contigs with an average of 3,033 Kb/cM.


The integrated map described here provides a framework for a robust composite genome map for rainbow trout. This resource is needed for genomic analyses in this research model and economically important species and will facilitate comparative genome mapping with other salmonids and with model fish species. This resource will also facilitate efforts to assemble a whole-genome reference sequence for rainbow trout.