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Gene expression profiling of soft and firm Atlantic salmon fillet

ABSTRACT: Microarray analyses revealed strong correlations between firmness of fillet (most important quality parameter) and a large number of genes. Highly similar expression profiles were observed in several functional groups. Positive regression was found between firmness and genes encoding proteasome components (41 genes) and mitochondrial proteins (129 genes), proteins involved in stress responses (12 genes) and lipid metabolism (30 genes). A weaker though highly significant negative regression was seen in sugar metabolism (26 genes) and myofiber proteins (42 genes). Among individual genes that showed a strong association with firmness, there were extracellular matrix proteins (negative correlation), immune genes and intracellular proteases (positive correlation). Several genes can be regarded as candidate markers of flesh quality (coiled-coil transcriptional coactivator b, AMP deaminase 3 and oligopeptide transporter 15) though their functional roles are unclear.

ORGANISM(S): Salmo salar Oncorhynchus mykiss

PROVIDER: GSE36475 | GEO | 2012/03/14

SECONDARY ACCESSION(S): PRJNA153505

REPOSITORIES: GEO

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Project description:Sexual maturation causes loss of fish muscle mass and deterioration of fillet quality attributes that prevent market purpose. We recently showed that fillet yield and flesh quality are recovered in female trout after spawning. To gain insights into the molecular mechanisms regulating flesh quality recovery we conducted a time-course analysis of large-scale gene expression in trout muscle from spawning to 33 weeks post-spawning. Using an Agilent-based microarray plate-form, we identified about 5500 unique genes that were differentially expressed during the post-spawning period. These genes segregated into four major clusters with distinct temporal expression profile and functional categories. A first cluster containing around 2000 genes down-regulated after 4 weeks after spawning was enriched in genes linked to mitochondrial ATP synthesis, fatty acid catabolism and proteolysis. A second cluster comprising about 1200 genes with early and transient induction between 2 to 8 weeks post-spawning was enriched in genes involved in RNA processing, translation, ribosome biogenesis and protein folding. A third cluster containing about 700 genes up-regulated from 4 weeks post-spawning onwards was enriched in genes encoding ribosomal subunits or regulating translation and cell cycle. At last a fourth cluster which contained about 1000 genes with late up-regulation from 13 weeks post- spawning onwards, was dominated by genes encoding myofibrillar proteins and matricial components and genes involved in glycolysis. On the whole our study indicates that muscle tissue restoration and flesh quality recovery occurring after spawning is mainly associated with anaerobic ATP production, muscle fibre hypertrophic growth, fatty acid metabolism and extracellular matrix remodelling. The generation of the first database of genes associated with post-spawning muscle recovery will allow future mechanistic studies and facilitate identification of genetic markers for fish muscle yield and quality traits.

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Gene expression profiling of soft and firm Atlantic salmon fillet

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