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. 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.ResultsThe 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.ConclusionThe 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.
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
After editing with FPMiner software (BioinforSoft, Beaverton, OR) 82% bacterial artificial chromosome (BAC) fingerprints from the 10X library and 50% from the CHORI-220 library were assembled into physical contigs using FPC software http://www.agcol.arizona.edu/software/fpc/ with a tolerance of 0.5 bp and an initial cutoff of 1 E-70 (1 × 10-70), followed by DQer and several rounds of endto-end merging and single-to-end merging at progressively lower cutoff stringencies
The number of contigs in this assembly is similar to the first generation Atlantic salmon physical map, which resulted in 4,354 contigs and 37,285 singletons with an average contig length of 590 kb from fingerprinting of a 12.5X library [2]
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. 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 facilitate efforts to obtain and assemble a whole-genome reference sequence for this species. It is likely that the vast majority of the duplicated loci contain enough sequence variation to allow correct assembly of a physical map using BAC DNA fingerprinting
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