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BackgroundSelection programs for growth and stress traits in cultured fish are fundamental to the improvement of aquaculture production. The gilthead sea bream (Sparus aurata) is the main aquacultured species in the Mediterranean area and there is considerable interest in the genetic improvement of this species. With the aim of increasing the genomic resources in gilthead sea bream and identifying genes and mechanisms underlying the physiology of the stress response, we developed a cDNA microarray for gilthead sea bream that is enriched by suppression substractive hybridization with stress and immunorelevant genes. This microarray is used to analyze the dynamics of gilthead sea bream liver expression profile after confinement exposure.ResultsGroups of confined and control juvenile fish were sampled at 6, 24, 72 and 120 h post exposure. GeneSpring analyses identified 202 annotated genes that appeared differentially expressed at least at one sampling time (P < 0.05). Gene expression results were validated by quantitative PCR of 10 target genes, and K-means clustering of differently expressed genes identified four major temporal gene expression profiles. Set 1 encompassed a rapid metabolic readjustment with enhanced uptake and intracellular transport of fatty acids as metabolic fuels. Set 2 was associated with a wide variety of tissue repair and remodeling processes that were mostly mediated by the stress response of the endoplasmic reticulum (ER). Sets 3 and 4 encompassed the re-establishment of cellular homeostasis with increased intracellular trafficking and scavenging of reactive oxygen species (ROS), accompanied by a bidirectional regulation of the immune system and a general decline of ROS production.ConclusionsCollectively, these findings show the complex nature of the adaptive stress response with a clear indication that the ER is an important control point for homeostatic adjustments. The study also identifies metabolic pathways which could be analyzed in greater detail to provide new insights regarding the transcriptional regulation of the stress response in fish.

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A purpose-designed microarray platform (Stressgenes, Phase 1) was utilised to 21 investigate the changes in gene expression within the liver of rainbow trout during 22 exposure to a prolonged period of confinement. Tissue and blood samples were collected 23 from trout at intervals up to 648 h after transfer to a standardised confinement stressor, 24 together with matched samples from undisturbed control fish. Plasma ACTH, cortisol, 25 glucose and lactate were analysed to confirm that the neuroendocrine response to 26 confinement was consistent with previous findings and to provide a phenotypic context to 27 assist interpretation of gene expression data. Liver samples for suppression subtractive 28hybridization (SSH) library construction were selected from within the experimental 29 groups comprising "early" stress (2-48h) and "late" stress (96-504h). In order to reduce 30 redundancy within the four SSH libraries and yield a higher number of unique clones an 31 additional subtraction was carried out. After printing of the arrays a series of 55 32 hybridisations were executed to cover 6 time-points. At 2h, 6h, 24h, 168h and 504h 5 33 individual confined fish and 5 individual control fish were used with control fish only at 34 0h. A preliminary list of 314 clones considered differentially regulated over the complete 35 time course was generated by a combination of data analysis approaches and the most 36 significant gene expression changes were found to occur during the 24h to 168h time 37 period with a general approach to control levels by 504h. Few changes in expression were 38 apparent over the first 6h. The list of genes whose expression was significantly 39 altered comprised predominantly genes belonging to the biological process category 40