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SALSEA-Merge Project

SALSEA-Merge was a three year, multi-agency €5.5 million scientific project to investigate the migration and distribution of Atlantic salmon in the North-East Atlantic. The project was supported by the European Commission under the 7th Framework Programme for Research and Technological development.

SALSEA-Merge aimed to deliver innovation in the areas of: genetic stock identification techniques; the development of new genetic markers; fine scale estimates of salmon growth; the use of novel high-seas pelagic trawling technologies; individual stock-linked estimates of food and feeding patterns; and novel stock specific migration and distribution models.  By merging genetic and ecological investigations, the project sought to advance understanding of stock specific migration and distribution patterns and overall ecology of the marine life of Atlantic salmon and to gain an insight into the factors resulting in recent increases in marine mortality.

The team at Exeter were part of the genetics working group and undertook two main tasks within the project:

  • Calibration of microsatellite scoring by all laboratories involved in the project
  • Characterisation of salmon populations included in the database from England and Wales

Microsatellite Calibration

Microsatellite standardization was undertaken for 16 loci across twelve laboratories. A panel of test samples from across the European range of the species, together with samples from North America, were included on two 96-well plates which were sent to all 12 participating laboratories. Each laboratory then typed and scored the control plates on their in-house sequencing machine. The results were then sent to Exeter and data were compared and standardised. The standardisation process included a detailed analysis of the degree of genotyping error, the partitioning of the causes of this error and the distribution of this error across laboratories using differing genotyping platforms and methods, and across loci of different size ranges and repeat motifs. Ultimately, this allowed us to formulate a set of rules by which to standardise data from all partners. These rules were developed in collaboration with John Gilbey at the FRS Marine Scotland laboratory in Pitlochry, where all data for entry into the SALSEA database were subsequently deposited and stored. The lead postdoctoral researcher on the calibration project at Exeter was Jon Ellis (now at Plymouth University).

This work is published as:

Gilbey et al. (in press) A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.). ICES Journal of Marine Science

Ellis, J.S., Gilbey, J. et al and Stevens, J.R. (2011) Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.). Genetica, 139: 353–367. 


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