A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray

• Published in: Journal of Fish Biology
• Main Authors: Taggart, John, Bron, James, Martin, Sam A M, Seear, Paul J, Hoyheim, Bjorn, Talbot, Richard T, Carmichael, Stephen N, Villeneuve, Laure, Sweeney, Glen E, Houlihan, Dominic F, Secombes, Christopher J, Tocher, Douglas R, Teale, Alan J
• Other Authors: Institute of Aquaculture, University of Aberdeen, Cardiff University, Norwegian School of Veterinary Science, Roslin Institute, University of Edinburgh, University of Stirling, orcid:0000-0002-3843-9663, orcid:0000-0003-3544-0519, orcid:0000-0002-8603-9410
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley-Blackwell / The Fisheries Society of the British Isles 2008
• Subjects: Atlantic salmon; DNA microarray; gene expression; lipid metabolism; immune response; smoltification; Salmo salar
• Online Access: http://hdl.handle.net/1893/2468; https://doi.org/10.1111/j.1095-8649.2008.01876.x; http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8649.2008.01876.x/abstract; http://dspace.stir.ac.uk/bitstream/1893/2468/2/taggart%20et%20al%202008.pdf; http://dspace.stir.ac.uk/bitstream/1893/2468/1/Taggart%20et%20al%20TRAITS%20paper.pdf

The origins, design, fabrication and performance of an Atlantic salmon microarray are described. The microarray comprises 16 950 Atlantic salmon-derived cDNA features, printed in duplicate and mostly sourced from pre-existing expressed sequence tag (EST) collections [SALGENE and salmon genome project (SGP)] but also supplemented with cDNAs from suppression subtractive hybridization libraries and candidate genes involved in immune response, protein catabolism, lipid metabolism and the parr–smolt transformation. A preliminary analysis of a dietary lipid experiment identified a number of genes known to be involved in lipid metabolism. Significant fold change differences (as low as 1.2x) were apparent from the microarray analysis and were confirmed by quantitative real-time polymerase chain reaction analysis. The study also highlighted the potential for obtaining artefactual expression patterns as a result of cross-hybridization of similar transcripts. Examination of the robustness and sensitivity of the experimental design employed demonstrated the greater importance of biological replication over technical (dye flip) replication for identification of a limited number of key genes in the studied system. The TRAITS (TRanscriptome Analysis of Important Traits of Salmon)–salmon genome project microarray has been proven, in a number of studies, to be a powerful tool for the study of key traits of Atlantic salmon biology. It is now available for use by researchers in the wider scientific community.