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.2011 Apr 7:12:180.
doi: 10.1186/1471-2164-12-180.

A first generation integrated map of the rainbow trout genome

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A first generation integrated map of the rainbow trout genome

Yniv Palti et al. BMC Genomics..

Abstract

Background: 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. 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.

Results: The 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.

Conclusions: The 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.

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Figures

Figure 1
Figure 1
Chromosome 2 from the new NCCCWA linkage map is shown as an example. Annotation of genes linked to the marker or BAC contig from the 1stgeneration physical map are connected to the marker name by underscore (e.g. OMM3080_TAP1_ctg260). Annotation of "or_?" means that the marker is duplicated and only one of two BAC contig was identified for the marker. Blue, Green, Red, Black and Italicized font markers were mapped to their specific location on the linkage group at LOD scores of 4, 3, 2, 1 and 0, respectively. Sex average distances between markers are shown in cM.
Figure 2
Figure 2
A schematic illustration of a BAC fingerprinting contig anchored to the rainbow trout Chr. 2 using microsatellites isolated from BACs. The four microsatellite markers from Ctg260 (224 clones; 1,584 CB or approximately 2.7 Mb) were mapped to Chr. 2 and the TAP1 positive BACs (highlighted in green) were previously identified by probe hybridization and confirmed by PCR and direct sequencing. The microsatellites order shown is based on the FPC map (not the genetic map). Markers in bold blue (OMY4005 and 4006) were localized on the linkage group at LOD4 and markers in regular font at LOD0. The genetic distance between the LOD4 markers is marked by a solid-line arrow and between markers that were localized at lower confidence by broken-line arrows.
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References

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