ArticleBMC genomics2009
A first generation BAC-based physical map of the rainbow trout genome.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Fine scale diversity in the lava: genetic and phenotypic diversity in small populations of Arctic charr Salvelinus alpinus.BMC ecology and evolution · 2024Article
- Genome and Phylogenetic Analysis of Genes Involved in the Immune System ofFrontiers in genetics · 2019Article
- Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.BMC genomics · 2017Review
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- Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization.Marine biotechnology (New York, N.Y.) · 2016Article
- Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout.PloS one · 2015Article
- The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.Nature communications · 2014Article
- A first generation BAC-based physical map of the half-smooth tongue sole (Cynoglossus semilaevis) genome.BMC genomics · 2014Article
- Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species.BMC genomics · 2013Article
- Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements.BMC genomics · 2013Article
- Characterization of the OmyY1 Region on the Rainbow Trout Y Chromosome.International journal of genomics · 2013Article
- Article
- Article
- A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes.Marine biotechnology (New York, N.Y.) · 2012Article
- A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts.BMC genetics · 2012Article
- Genome physical mapping of polyploids: a BIBAC physical map of cultivated tetraploid cotton, Gossypium hirsutum L.PloS one · 2012Article
- Generation of the first BAC-based physical map of the common carp genome.BMC genomics · 2011Article
- Enhancing genome investigations in the mosquito Culex quinquefasciatus via BAC library construction and characterization.BMC research notes · 2011Article
- Article
- Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio.Marine biotechnology (New York, N.Y.) · 2011Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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