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A description of the origins, design and performance of the TRAITS–SGP Atlantic salmon Salmo salar L. cDNA microarray
Author(s) -
Taggart J. B.,
Bron J. E.,
Martin S. A. M.,
Seear P. J.,
Høyheim B.,
Talbot R.,
Carmichael S. N.,
Villeneuve L. A. N.,
Sweeney G. E.,
Houlihan D. F.,
Secombes C. J.,
Tocher D. R.,
Teale A. J.
Publication year - 2008
Publication title -
journal of fish biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.672
H-Index - 115
eISSN - 1095-8649
pISSN - 0022-1112
DOI - 10.1111/j.1095-8649.2008.01876.x
Subject(s) - biology , salmo , suppression subtractive hybridization , microarray , genetics , complementary dna , gene , microarray analysis techniques , computational biology , transcriptome , genome , expressed sequence tag , cdna library , gene expression profiling , gene chip analysis , dna microarray , gene expression , fish <actinopterygii> , fishery
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 1·2×) 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.