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

item Palti, Yniv
item LUO, MING-CHEN - University Of California
item GENET, CARINE - Institut National De La Recherche Agronomique (INRA)
item HU, YUGIN - University Of California
item YOU, FRANK - University Of California
item Vallejo, Roger
item Rexroad, Caird

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/2/2009
Publication Date: 1/9/2010
Citation: Palti, Y., Luo, M., Genet, C., Hu, Y., You, F., Vallejo, R.L., Rexroad Iii, C.E. 2010. A first generation integrated physical and genetic map of the rainbow trout genome. Plant and Animal Genome Conference XVIII. Paper No. 102.

Interpretive Summary:

Technical Abstract: The rainbow trout physical map was previously 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 (~80% of the genome). Large BAC contigs from the physical map were anchored to the genetic map chromosomes using ~200 microsatellites from BAC end sequences that were added to the genetic map by linkage analysis. The integrated 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 efficiency. This resource will also facilitate efforts to assemble a whole-genome reference sequence for this species.