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SuperSAGE digital expression analysis of differential growth rate in a European sea bass population

Louro, Bruno, Martins, Rute S.T., Pinto, Patricia I.S., Reinhardt, Richard, de Koning, Dirk-Jan, Canario, Adelino V.M., Power, Deborah M.
Aquaculture and fisheries 2019 v.4 no.1 pp. 17-26
Dicentrarchus labrax, bass, brain, gene expression, genes, hatcheries, liver, messenger RNA, muscles, selective breeding
One of the goals of the aquaculture industry is to understand and control growth associated traits through selective breeding. In the present study the molecular basis of growth heterogeneity in the European sea bass (Dicentrarchus labrax) was addressed. To establish growth heterogeneity in a group of hatchery bred sea bass individuals were tagged and their specific growth rates (SGR) determined at monthly intervals. Gene expression in the brain, liver and white muscle from fish with the most divergent sustained SGR (6 individuals of the first and last quartile) was assessed using SuperSAGE (Serial Analysis Gene Expression) combined with next generation SOLiD4 sequencing. A total of approx. 11 million edited tags (26 bp), on average 2 million tags per SAGE library, that represented 47.071 unique transcripts were identified. Comparison of transcripts in fish with high and low SGR yielded 344, 698 and 601 differently expressed tags (0.01% false discovery rate and 4-fold change) in brain, liver and muscle, respectively. The tags were mapped onto the sea bass genome and approximately one third of the tags could be assigned to annotated genes. Pathway enrichment analysis revealed in liver, muscle and brain intricate gene expression changes in endocrine regulatory pathways involved in growth, metabolic and the stress axis, underlying divergent SGR in sea bass.