Identification issues in marine species Identification issues in marine species

In contrast to salmonids there are various challenges to identifying marine fish as originating from aquaculture or wild populations and even more when considering their hatchery of origin:
• Due to the recent domestication of many marine fish, allele frequencies of broodstock and their offspring remain similar to natural populations.
• The lack of targeted selective breeding for cod and especially sole, lowers the likelihood to find "domestication" markers, unambiguously identifying fishes originating from a farm or hatchery. Many fish farms are only at the first generation of breeding, coinciding with the genetic background of offspring similar to that of natural populations. However, several new developments and peculiarities of marine fish aquaculture, aid in the identification of a farmed individual.
• Due to the use of mass spawning in breeding tanks and the very high variance in reproductive success of parents in hatcheries (Porta et aI., 2006 a,b, 2007), genetic diversity of offspring is usually much lower than parental populations and natural population offspring in the wild. As such first generation escapees or restocking material will exhibit a very low individ ual heterozygosity level (MLH) compared to outbred natural populations.
• Additionally, based on recent results of natural population genotyped for 450+ (sole) and 1300+ (cod) SNPs, farmed offspring would be easily identified if exported outside their region of origin, using genetic assignment tools.
• For both species, a large panel of individuals from natural populations, potential sources for aquaculture purposes, is available genotyped for a large number of SNPs and microsatellites. As such simulation studies can be applied to assess the power of both marker types in assigning aquaculture vs natural origin, besides tracing individuals to the hatchery of origin.
• Finally, the rate of fixation of neutral markers depends on the effective population size of breeding populations, but SNPs under positive/negative selection can increase the rate of fixation and thus form ideal candidate domestication markers. Additionally, such markers may introgress more rapidly/slowly than selectively neutral markers, providing crucial insights into the fitness and molecular consequences of restocking/escapees in natural populations.


These issues combine to form several lines of research to be addressed within AquaGen. Collectively, this work presents an excellent opportunity to develop a research framework and set of management tools required for an expansion of marine fish aquaculture in the EU.

The stated aims of AquaGen are to:

1. Evaluate the feasibility of distinguishing genetically between farmed and wild common sole and Atlantic cod;
2. Evaluate the feasibility of genetically tracing individual fish back to a farmed origin, - ideally to the farm of origin -, in common sole and Atlantic cod;
3. Develop appropriate identification methodologies, including a comparison of population assignment methods with parentage identification techniques, to provide the greatest power for correctly identifying farmed individuals;
4. Develop traceability assays within a forensic framework (standard operating procedures) in order to ensure that the assays can be applied in a legal context;
5. Examine the applicability of the approach to other marine aquaculture species, particularly farmed in the Mediterranean, e.g. European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata).
AquaGen will achieve these aims by utilizing the genetic resources developed during the EU's FP7 project FishPopTrace (EC: 212399), combined with samples of farmed fish from the two target species. Methods of assignment will be evaluated using real and simulated genetic data to optimise the design of robust traceability assays. The work will be placed in a broader context of marine fish aquaculture management through the delivery of a critical literature review to ensure that conclusions regarding genetic traceability tools are applicable across species.