IDENTIFICATION AND CHARACTERIZATION OF GENES AFFECTING COOL AND COLD WATER AQUACULTURE PRODUCTION
Location: Cool and Cold Water Aquaculture Research
Title: A first generation BAC-based physical map of the Rainbow trout genome
Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 2, 2009
Publication Date: October 8, 2009
Citation: Palti, Y., Luo, M., Hu, Y., Genet, C., You, F., Vallejo, R.L., Thorgaard, G., Wheeler, P., Rexroad Iii, C.E. 2009. A first generation BAC-based physical map of the Rainbow trout genome. Biomed Central (BMC) Genomics. 10:462.
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. ARS scientists in Leetown, WV, and cooperators in UC Davis, California, and France teamed up to produce detailed maps of the trout genome. The genome is the sum of all the genetic material for any given species. As part of this international collaboration we produced an integrated physical and genetic map for rainbow trout. A physical map shows the specific locations of a species genes and/or markers on each chromosome; genetic maps reveal how genes are inherited in relationship to each other. Integrating these maps will facilitate the indentification of genes that affect aquaculture production traits and can be exploited to improve production efficiency of this important source of nutritious protein and healthy unsaturated oil.
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. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and selecting positional candidate genes for incorporation in marker-assisted selection (MAS) schemes. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species.
The 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.
The 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.