Development and assessment of oligonucleotide microarrays for Atlantic salmon (Salmo salar L.)

The cDNA microarrays have played a major role in functional genomics of fish and contributed substantially to different areas of aquaculture research. However at present these platforms are gradually substituted with oligonucleotide microarrays (ONM), which represent the most cost-efficient, flexible, powerful and accurate tool for multiple gene expression profiling, especially in species with rich genomic resources. This paper describes the development and assessment of ONM platforms for Atlantic salmon. The process started with the establishment of a bioinformatic system, selection of a low redundancy set of nucleotide sequences providing coverage of transcriptomes of several fish species, their identification by protein products and annotations. Pilot experiments were performed to address issues that are essential for development of ONM: gene composition, quality assessment, hybridization success of homologous and heterologous probes, optimum numbers of spot replicates and processing, management and mining of gene expression data. Performance of microarrays was evaluated in two experiments with Atlantic salmon. Comparison of peripheral blood leukocytes with a mixture of other tissues was conducted for characterization of the leukocyte transcriptome. Analyses of salmon infected with different viral diseases identified virus-responsive genes that can be used as markers for diagnostics of infected status of fish. Data mining with functional annotations confirmed the relevance of these findings.