Edinburgh Research Explorer

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

Research output: Contribution to journalArticle

  • J B Taggart
  • J E Bron
  • S A M Martin
  • P J Seear
  • B Høyheim
  • R Talbot
  • S N Carmichael
  • L A N Villeneuve
  • G E Sweeney
  • D F Houlihan
  • C J Secombes
  • D R Tocher
  • A J Teale

Related Edinburgh Organisations

Open Access permissions



Original languageEnglish
Pages (from-to)2071-2094
Number of pages24
JournalJournal of Fish Biology
Issue number9
Publication statusPublished - Jun 2008


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.

Download statistics

No data available

ID: 13093123