A comparative study of gene expression in wild and domesticated Atlantic salmon (Salmo salar L.)

• Main Author: Bicskei, Beatrix
• Other Authors: Taggart, John B, Bron, James E, Glover, Kevin A, Norwegian Research Council
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: University of Stirling 2015
• Subjects: Atlantic salmon; Salmo salar; microarray; transcript; wild; farmed; domestication; aquaculture; gene expression; escapee; Salmon
• Online Access: http://hdl.handle.net/1893/22932; http://dspace.stir.ac.uk/bitstream/1893/22932/1/Thesis%20corrected.pdf

Atlantic salmon (Salmo salar L.) has been domesticated since the 1960s and has undergone over 10 generations of artificial selection for economically important traits. As a result, domesticated salmon have diverged with respect to a number of phenotypic, genotypic and behavioural traits from their wild counterparts. Since the selection pressures that are present in the wild differ greatly from the ones that shape salmon under culture conditions, domesticated salmon stocks are considered to be maladapted to natural conditions. Despite strict regulations, insoluble issues pertaining to large-scale cage rearing of farmed fish mean that there is a continuous presence of farm escapees in the wild. Gene flow from escapees has been perceived as a factor in the decline of wild populations, suggested to occur through disruption of local adaptation. This study aims to improve understanding of the genetic differences between wild and domesticated stocks by comparing the transcriptomes of Figgjo (wild) and Mowi (domesticated) strains. A series of common garden experiments have been performed, utilizing pure and reciprocal hybrid crosses of the wild and domesticated stocks, reared under two different conditions and sampled at four time points and three distinct life stages (embryo, sac-fry and feeding fry). Microarray interrogations were performed employing a 44K custom microarray design to identify genes and gene pathways that are differentially expressed between the stocks. KEGG-based functional analyses have been implemented using different gene set enrichment packages, and dominance and additive parameters were calculated from normalized expression values to predict the mode of heritability of the genes identified as differentially expressed between stocks. Most biological functions represented in wild and domesticated crosses were consistent across life stages and environments. The transcriptomic differences detected between stocks in multiple developmental stages likely reflected adaptations to selection pressures ...