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Impact of aquaculture on the immune response genes of natural salmonid populations: Spatial and temporal genetic signatures and potential fitness consequences.

Extensive farming or rearing of salmonid fishes, both in fresh- and sea water, has inherent associated risks for natural populations. We identify two major risk factors, which can impinge on the genetic integrity of natural populations of salmonids (Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)). These are:
Hybridisation (intra- and interspecific) between cultured fish and natural populations through deliberate or inadvertent release of cultured stocks.
Genetic effects of disease transmission from aquaculture stocks to natural populations.
Many previous and ongoing studies have attempted to assess the effect of the former, but to date there has been no such attempt to assess the importance of the latter.
In SALIMPACT the impact of aquaculture will be directly examined by comparison of present-day populations which are known to have been impacted by aquaculture with either adjacent populations that have no history of impact (spatial analysis), or with samples from the same population taken before any impact of aquaculture (temporal analysis). Samples for temporal analysis are available as archived scale samples and ethanol-preserved juveniles.
The project will address these issues by using molecular genetic techniques to screen selected (CO1 and CR3) and neutral markers (CR2 and CR4) and to examine seven case studies. Field experiments will be designed to test the role of MHC polymorphism on fitness-related traits.
SALIMPACT will generate samples from case studies and field experiments. The case studies will be identified in two distinct geographical regions (Ireland and Norway). Two field experiments will be conducted at appropriate facilities provided by two partners (CR4 and CR5). The samples collected from the case studies and field experiments will be analysed by a large proportion of the consortium using different molecular techniques according to their expertise.

The objective of this project is to assess the extent to which disease transmission has, or has had, an impact on genetic variation in natural populations of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). This will be achieved by a novel comparison of patterns of genetic variation at loci that are critically involved in the immune response (i.e., major histocompatibility complex (MHC) genes) with variability at a number of selectively-neutral loci (non-MHC microsatellites) in focused case studies.
1. Refinement of molecular tools for screening of neutral and MHC markers.
Assess relationships between MHC class I and class II alpha alleles and embedded microsatellite markers.
Establish an agreed panel of neutral microsatellite markers chosen from those currently available according to a carefully designed set of criteria.
These markers will be used in the analysis of both case studies and of field experiments.
2. Spatial and temporal analysis of the impact of aquaculture using case studies.
Compare populations with histories of deliberate (ranching, stocking) and/or inadvertent (farm escapes) introductions of cultured fish with adjacent unaffected populations.
Analyse samples obtained from populations before, during and after disease epidemics (furunculosis and sea-lice) associated with the development of aquaculture.
3. Field experiments designed to assess fitness differences among MHC genotypes.
Examine patterns of mate choice in relation to MHC genotype in Atlantic salmon. WP5
Determine the relationship between individual fitness and MHC variability in Atlantic salmon under natural and semi-natural conditions.
Test the selective neutrality of the non-MHC microsatellite markers.
These objectives will be met through an integrated collection of workpackages (WP) which will result in the following expected achievements:
Identification and quantification of the impact of aquaculture on genetic variation at immune response genes in natural salmonid populations.
Validation of MHC polymorphisms as molecular markers of fitness and tests of the assumption of selective neutrality of the non-MHC microsatellite markers.
The outcome of these studies will have implications for further development of fish farming, sea ranching, local stocking and management of natural salmonid populations. In addition, SALIMPACT can serve as a model study for other aquaculture species (e.g. seabass, seabream, cod), where cultured and natural populations may interact.

Validated protocols and techniques for the detection of microsatellite markers from archived scales and extant fish populations.
Collection of DNA samples from selected populations.
Marker analyses of DNA samples and evaluation of the results.
Identification and quantification of the effect of fish farming on fitness-related traits.


Scientist responsible for the project

Marijkeweg Box 338
6709 PG Wageningen
Netherlands (The) - NL

Phone: +31 317 48 39 22/67
Fax: +31 317 48 39 55


Project ID QLRT-2000-01185
Area 5.1.2
Start date 01 October 2001
Duration (months) 36
Total cost 1 964 196 €
Total EC contribution   1 425 382 €
Status in progress
Web address of the project

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