Projects per year
Abstract / Description of output
Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array.
Results
SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex.
Conclusions
This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.
Original language | English |
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Article number | 90 |
Journal | BMC Genomics |
Volume | 15 |
Issue number | 1 |
DOIs | |
Publication status | Published - 6 Feb 2014 |
Fingerprint
Dive into the research topics of 'Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)'. Together they form a unique fingerprint.Projects
- 4 Finished
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ISP1: Analysis and prediction in complex animal systems
Tenesa, A., Archibald, A., Beard, P., Bishop, S., Bronsvoort, M., Burt, D., Freeman, T., Haley, C., Hocking, P., Houston, R., Hume, D., Joshi, A., Law, A., Michoel, T., Summers, K., Vernimmen, D., Watson, M., Wiener, P., Wilson, A., Woolliams, J., Ait-Ali, T., Barnett, M., Carlisle, A., Finlayson, H., Haga, I., Karavolos, M., Matika, O., Paterson, T., Paton, B., Pong-Wong, R., Robert, C. & Robertson, G.
1/04/12 → 31/03/17
Project: Research
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Development of a high density Atlantic salmon SNP chip
Blaxter, M., Archibald, A., Bishop, S., Houston, R. & Gharbi, K.
UK central government bodies/local authorities, health and hospital authorities
1/08/11 → 31/07/14
Project: Research
Datasets
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Atlantic salmon Illumina Sequencing
Houston, R. (Creator), Edinburgh DataVault, 2016
DOI: 10.7488/8f6c3792-d79f-4dcd-88ff-150646fc59d1, https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP017393 and 4 more links, https://www.ncbi.nlm.nih.gov/bioproject/PRJEB4796, https://www.ncbi.nlm.nih.gov/bioproject/PRJEB4783, https://www.ncbi.nlm.nih.gov/bioproject/PRJEB4785, https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP003968 (show fewer)
Dataset
Press/Media
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Genetic chip will help salmon farmers breed better fish
Ross Houston
13/02/14
1 item of Media coverage
Press/Media: Research