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Citation

Taggart J, Bron J, Martin SAM, Seear PJ, Hoyheim B, Talbot RT, Carmichael SN, Villeneuve L, Sweeney GE, Houlihan DF, Secombes CJ, Tocher DR & Teale AJ (2008) A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray. Journal of Fish Biology, 72 (9), pp. 2071-2094. http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8649.2008.01876.x/abstract; https://doi.org/10.1111/j.1095-8649.2008.01876.x

Abstract
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.

Keywords
Atlantic salmon; DNA microarray; gene expression; lipid metabolism; immune response; smoltification

Journal
Journal of Fish Biology: Volume 72, Issue 9

• taggart et al 2008.pdf
• Taggart et al TRAITS paper.pdf