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United States Department of Agriculture

Agricultural Research Service

Research Project: UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

Title: A first generation integrated map of the rainbow trout genome

Authors
item Palti, Yniv
item Genet, Carine -
item Luo, Mingcheng -
item Charlet, Aurelie -
item Gao, Guangtu
item Hu, Yugin -
item Castano-Sanchez, Cecilia -
item Yao, Jianbo -
item Vallejo, Roger
item Rexroad, Caird

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 22, 2011
Publication Date: April 7, 2011
Repository URL: http://handle.nal.usda.gov/10113/56828
Citation: Palti, Y., Genet, C., Luo, M., Charlet, A., Gao, G., Hu, Y., Castano-Sanchez, C., Yao, J., Vallejo, R.L., Rexroad III, C.E. 2011. A first generation integrated map of the rainbow trout genome. Biomed Central (BMC) Genomics. 12:180. DOI: 10.1186/1471-2164-12-180.

Interpretive Summary: Rainbow trout is one of the most important aquaculture species in the United States and around the world, but little is known about its genetic makeup. To this end we report the first integrated map of the rainbow trout genome which combines genetic information on the inheritance of chromosomes throughout generations with the physical DNA sequences that contain genes that control biological processes. This resource will facilitate the identification of genes affecting important aquaculture production traits and enhance strategies targeting the genetic improvement of this species for production efficiency.

Technical Abstract: Background 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. Results 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 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 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. Conclusions The integrated map described here provides a frame work for a robust composite genome map for rainbow trout. This resource is needed for genomic analyses in this research model and economically important species. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species.

Last Modified: 8/21/2014
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