Abstract
BackgroundRainbow 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.ResultsThe 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.ConclusionsThe 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.
Highlights
Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas
Rainbow trout are cultured on every continent except Antarctica, with 2008 global production estimated at 576,289 metric tons and valued at $2.39 billion [2]
It is estimated that 50% to 60% of the rainbow trout genome contains interspersed repeat sequences (Genet et al.: Analysis of bacterial artificial chromosome (BAC)-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes, submitted)
Summary
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. 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. Rainbow trout (Oncorhynchus mykiss) are the mostwidely cultivated cold freshwater fish in the world and are considered by many to be the “aquatic lab-rat”. Coupling great interest in this species as a research model with the need for genetic improvement for aquaculture production efficiency and product quality justifies the continued development of genome resources facilitating selective breeding. It is estimated that 50% to 60% of the rainbow trout genome contains interspersed repeat sequences (Genet et al.: Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes, submitted)
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