Open Access Highly Accessed Research article

Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon

Ross D Houston1*, John W Davey2, Stephen C Bishop1, Natalie R Lowe1, Jose C Mota-Velasco3, Alastair Hamilton3, Derrick R Guy3, Alan E Tinch3, Marian L Thomson2,4, Mark L Blaxter2,4, Karim Gharbi2,4, James E Bron5 and John B Taggart5

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK

2 Institute of Evolutionary Biology, Ashworth Laboratories, King’s Buildings, University of Edinburgh, Edinburgh, EH9 3JT, UK

3 Landcatch Natural Selection Ltd., Alloa, Clackmannanshire, FK10 3LP, UK

4 The GenePool Genomics Facility, Ashworth Laboratories, King’s Buildings, University of Edinburgh, Edinburgh, EH9 3JT, UK

5 Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK

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BMC Genomics 2012, 13:244 doi:10.1186/1471-2164-13-244

Published: 15 June 2012

Additional files

Additional file 1:

Details of Family 1 RAD loci, number of RAD alleles and fragment counts for all individuals.

Format: TXT Size: 17.6MB Download file

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Additional file 2:

Details of Family 2 RAD loci, number of RAD alleles and fragment counts for all individuals.

Format: TXT Size: 18MB Download file

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Additional file 3:

List of RAD allele sequences containing SNPs marked using IUPAC ambiguity code.

Format: TXT Size: 422KB Download file

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Additional file 4:

List of high-throughput assay SNPs used for QTL mapping and population-wide association analysis.

Format: TXT Size: 6KB Download file

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Additional file 5:

Table S1. Details of the primers and SNPs for the BAC contig fps378.

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Additional file 6:

Perl script to identify the most frequent segregation patterns in the RAD loci (Additional files 1and2).

Format: TXT Size: 3KB Download file

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Additional file 7:

Perl script to merge SNP-containing bi-allelic RAD loci into a single list of sequences with IUPAC ambiguity code (Additional file 3).

Format: TXT Size: 2KB Download file

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Additional file 8:

Table S2. Population-wide association between genotype at SSA0019ECIG and mortality in a freshwater IPNV challenge (all associations significant at P<0.05).

Format: DOC Size: 35KB Download file

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