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Open Access Research article

A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts

René Guyomard*, Mekki Boussaha, Francine Krieg, Caroline Hervet and Edwige Quillet

Author Affiliations

INRA, UMR1313, Animal Genetics and Integrative Biology, Domaine de Vilvert, 78350 Jouy-en-Josas, France

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BMC Genetics 2012, 13:15  doi:10.1186/1471-2156-13-15

Published: 16 March 2012

Additional files

Additional file 1:

Raw INRA, ARS and UoG genotype files (worksheets 2 to 7); loci discarded in each data set (worksheet 8); loci located at the same linkage group and showing two different positions in two data sets (worksheet 9); new loci added in the updated INRA map (worksheet 10); full legends are given in worksheet 1.

Format: XLS Size: 3.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

Accession numbers for loci used in the INRA and synthetic maps (worksheet 2); data files to produce the INRA and consensus graphical maps with MAPCHART (worksheets 3, 4 and 5); comparison of marker orders in the INRA and synthetic maps for each linkage group (worksheets 6 to 34); oxford grid showing homeologous affinities between rainbow trout chromosome arms (worksheet 35); full legends are given in worksheet 1.

Format: XLS Size: 1.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Graphic representation of the updated INRA map; duplicated loci are in red bold type; underlined bold type marker names localize centromeric regions.

Format: PDF Size: 168KB Download file

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Additional file 4:

Graphic representation of the synthetic map (same captions as in Additional file 3).

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Additional file 5:

Significant blast results found in this study, in Danzmann et al. [22]and Rexroad et al. [23]; see worksheet 1 for full legends.

Format: XLS Size: 1.2MB Download file

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Additional file 6:

Conserved syntenies from between rainbow trout and, respectively, medaka, stickleback and zebrafish (worksheets 2, 5 and 9); Oxford grids showing chromosome homologies within stickleback and zebrafish (worksheets 6 and 10); files used to generate map alignments between rainbow trout and each of the three model species (worksheets 3, 8 and 11); Oxford grids showing homologous affinities between the rainbow trout arm chromosomes and the chromosomes of each model species (workheets 4, 7 and 12); full legends in worksheet 1.

Format: XLS Size: 1.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 7:

Map alignments between chromosomes of rainbow trout and zebrafish; underlined blue bold type marker names approximately localize centromeric regions; green and red lines distinguish between the two arms in acrocentric rainbow trout chromosomes; homologous marker positions in model species chromosomes are identified by Gene ID and sequence start position when blastx hits and blastn hits are used respectively.

Format: PDF Size: 338KB Download file

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Additional file 8:

Map alignments between chromosomes of rainbow trout and medaka, stickleback and zebrafish; underlined blue bold type marker names approximately localize centromeric regions; green and red lines distinguish between the two arms in acrocentric rainbow trout chromosomes; homologous marker positions in model species chromosomes are identified by Gene ID and sequence start position when blastx hits and blastn hits are used respectively.

Format: PDF Size: 352KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9:

Map alignments between chromosomes of rainbow trout and medaka, stickleback and zebrafish; underlined blue bold type marker names approximately localize centromeric regions; green and red lines distinguish between the two arms in acrocentric rainbow trout chromosomes; homologous marker positions in model species chromosomes are identified by Gene ID and sequence start position when blastx hits and blastn hits are used respectively.

Format: PDF Size: 346KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data