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Open Access Highly Accessed Research article

A second generation genetic map for rainbow trout (Oncorhynchus mykiss)

Caird E Rexroad*, Yniv Palti, Scott A Gahr and Roger L Vallejo

Author Affiliations

USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia, USA

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BMC Genetics 2008, 9:74  doi:10.1186/1471-2156-9-74

Published: 19 November 2008

Additional files

Additional file 1:

Marker and Mapping Information. Additional Files are included as numbered spreadsheets in a MS Excel file:

1 Marker PCR Information (PCR primers, conditions, etc...)

2 ESTs – Comparative Assignments (identification of homologs of OMM5000 markers, developed from ESTs, in the zebrafish, medaka, tetraodon, and fugu genomes)

3 ESTs – BLASTx Annotation (Functional annotation for EST markers assigned through blastx of the GenBank nr database)

4 ESTs – RTGI and Unigene (Identification of Rainbow Trout Gene Index and Unigene Assemblies for which EST markers belong)

5 Comparative Info – BACs (Comparative information for OMM3000 markers derived from BACs containing genes of interest)

6 Inf Mei and Allele#s (informative meiosis and number of alleles for markers screened on the NCCCWA reference families)

7 Markers for Map Integration (Markers used to integrate NCCCWA linkage groups and the rainbow trout cytogenetic map)

8 Linkage Group Translation (identifying names of common linkage groups between published rainbow trout genetic maps)

9 Chromosome Info (Linkage analysis information broken down by chromosome)

10 2pt Info for loci informative but not mapped (Reporting loci which were informative in the NCCCWA reference families but not able to be placed on the map)

11 Maps (Genetic map data which can be used to recreate map figues in MapChart)

Format: XLS Size: 1.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Genetic Map. This Adobe PDF file includes figures representing the 29 linkage groups/chromosomes of the NCCCWA rainbow trout genetic map. Recombination distances are presented as total Kosambi cM for each map on the left, marker names and comparative assignments are on the right. Loci names in red bold font are ordered at LOD 4.0, loci in blue font at LOD 3.0, loci in green font at LOD 2.0, loci in black font at LOD 1.0 and loci in black italic at LOD 0.0. Paralogous assignments within the rainbow trout genome are presented in orange in the format Omy_1:10.0 where Omy is the three letter species designation for rainbow trout (Oncorhynchus mykiss), 1 is the chromosome number of the paralogous locus and 10.0 is its map position. Comparative assignments are similarly presented next to loci names in the format species abbreviation_chromosome number:homolog start nucleotide:homolog end nucleotide. Comparative assignments for zebrafish are presented in purple, for medaka in brown, for tetraodon in light blue, and fugu in maroon.

Format: PDF Size: 167KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Genetic Map. This Adobe PDF file includes figures representing the 29 linkage groups/chromosomes of the NCCCWA rainbow trout genetic map. Recombination distances are presented as total Kosambi cM for each map on the left, marker names are on the right. Loci names in red bold font are ordered at LOD 4.0, loci in blue font at LOD 3.0, loci in green font at LOD 2.0, loci in black font at LOD 1.0 and loci in black italic at LOD 0.0.

Format: PDF Size: 73KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Sex Recombination Ratios. This Adobe PDF file includes figures representing the 29 linkage groups/chromosomes of the NCCCWA rainbow trout genetic map and figures representing the differences in recombination rate between the sexes along each chromosome. The map length is presented in terms of Kosambi cM, the pairwise recombination fractions (theta) between each marker pair along the length of the chromosome map is presented.

Format: PDF Size: 194KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data