Evaluation of three strategies using DNA markers for traceability in aquaculture species

Hayes, Ben, Sonesson, Anna K. and Gjerde, Bjarne (2005) Evaluation of three strategies using DNA markers for traceability in aquaculture species. Aquaculture, 250 1-2: 70-81. doi:10.1016/j.aquaculture.2005.03.008


Author Hayes, Ben
Sonesson, Anna K.
Gjerde, Bjarne
Title Evaluation of three strategies using DNA markers for traceability in aquaculture species
Journal name Aquaculture   Check publisher's open access policy
ISSN 0044-8486
1873-5622
Publication date 2005-11-14
Sub-type Article (original research)
DOI 10.1016/j.aquaculture.2005.03.008
Open Access Status Not yet assessed
Volume 250
Issue 1-2
Start page 70
End page 81
Total pages 12
Place of publication Amsterdam, Netherlands
Publisher Elsevier BV
Language eng
Abstract Traceability schemes for aquaculture species are essential for tracing market product to farm of origin in the event of detection of disease or toxins in the market fish. DNA markers have been proposed as a tool for traceability. These markers can be used to genotype fish by taking a sample from live fish or fish product at any stage along the production chain. In this paper, we consider three alternate traceability schemes using DNA markers. The example of the Norwegian farmed Atlantic salmon industry was used. This industry, like many aquaculture industries, has three tiers, the nucleus, multiplier and commercial tiers. The nucleus individuals are grandparents of the commercial fish, and the multiplier individuals are the parents of the commercial fish. The traceability strategies we considered were: (1) FS, assignment of market place fish to full sib families based on the marker information (this strategy assumes all individuals from a full sib family are allocated to a single farm and a limited number of fish, representing all full sib families on that farm, are genotyped); (2) PAR, assignment of market place fish to parents (multiplier individuals) and (3) GRAND, assignment of market place fish to grandparents (nucleus individuals). Using simulation, we determined the number of DNA markers required to achieve 95% of correct assignment decisions for each strategy. The simulation included a wild population which contributed to market place fish. The wild fish were correctly assigned if they were excluded from belonging to the farmed population in each strategy, otherwise they were incorrectly assigned. Both microsatellite markers or single nucleotide polymorphism markers were considered. Seventy five, 15, and 50 microsatellites were required to achieve 95% correct assignment decisions for FS, PAR and GRAND, respectively. Four hundred, 75 and 200 SNPs were required to achieve 95% correct assignment decisions for FS, PAR and GRAND, respectively. If the cost of genotyping microsatellites is assumed to be five times as high as genotyping a SNP, GRAND using SNP markers is the cheapest strategy. The logistics of implementing each strategy are discussed. GRAND in particular and PAR in some industries requires complicated logistics. The most suitable and cost effective traceability strategy for a particular industry will depend heavily on the organisation of that industry, for example the degree of recording transfer of fish, eggs and larvae between tiers. Even if complicated logistics prevent the adoption of marker based schemes by some industries, traceability with DNA markers may still be important for verification of labelling-based schemes.
Keyword Accuracy
Aquaculture species
Microsatellites
SNP markers
Traceability
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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