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Abstract: A simulation study was conducted to investigate the potential advantage of two-step selection for dissemination of genetic gains in salmon production through a system with a nucleus breeding population, a multiplier tier and a grow-out tier. Results demonstrated that profit (measured in the grow-out tier in generation 8) can be substantially increased through production and dissemination of specialised stocks suited for e.g. specific production environments or markets. Truncation selection alternatives in two steps with varying selection proportions were compared to random sampling of parents in both dissemination steps: from the nucleus to the multiplier and from the multiplier to the grow-out tier. Strategies where truncation selection was used in one step and random sampling of parents in the other step were also tested. The selection alternatives with truncation selection in both steps gave on average between 31% and 26% higher profit than random selection. The selection alternative with an extremely low truncation selection proportion in two steps would on average give 2% higher profit than the selection alternative with extremely low truncation selection proportion from the nucleus to the multiplier (1st step), and a normally low truncation selection proportion from the multiplier to the grow-out (2nd step). However, the former alternative yielded five times fewer eggs. The study also showed that one step of truncation selection and one of random sampling of parents, irrespective of the order, would give on average about 19% higher profit compared to random selection in two steps. The effect of the correlation between the nucleus/multiplier breeding goal and the breeding objective of the grow-out was that profit was highest when the correlation was high. With a negative genetic correlation between the traits, profit was still high if the trait with the highest heritability (i.e. the trait measured on candidate itself) had the highest economic value. It was concluded that selection of specialised stocks for specific breeding objectives in two steps from the nucleus via the multiplier and to the grow-out could increase profit by 24%. Specific breeding objectives would also give more flexibility for a final product when the grow-out producers could ask for unique trait-combinations for their fish. [Copyright &y& Elsevier]

Abstract: A simple selection scheme is proposed that facilitates the selection for a growth trait (GROWTH) with heritability of 0.25 and one disease trait (SURVIVAL) with heritability of 0.1 or 0.4 using a two step selection procedure. First, the scheme applies phenotypic selection for SURVIVAL among all the 10,000 candidates per generation, assuming that Nsurvival=2500, 5000 or 7500 survived a disease challenge test. Survivors were measured for GROWTH, and the (Ngenotyped=1000 or 2000) highest ranked were DNA genotyped for parentage testing. Second, parents were selected for GROWTH on their BLUP breeding values using optimum contribution selection, which restricted the rates of inbreeding to 1% per generation. At this second selection step, no selection for SURVIVAL was possible, because all survivors had the same phenotype for this trait and the pedigree of the dead individuals were not known. Results show that selection for SURVIVAL was very efficient for schemes with high heritability of SURVIVAL (0.4) and positive genetic correlation between the traits (0.3), and more efficient with decreasing survival rate, because of the higher intensity of selection. However, for schemes with negative correlation between the traits (−0.3), the heritability of 0.1 of SURVIVAL was too low to get positive genetic response for SURVIVAL. Genetic gain for GROWTH and SURVIVAL was not significantly improved by increasing Ngenotyped=1000 to 2000 for the schemes used here, i.e. genotyping 1000 individuals allowed the best possible parents to be selected for breeding when using optimum contribution selection. In conclusion, this is an efficient and very simple selection scheme for aquaculture species which can be used for specific cases where a whole production system is limited by a disease that is not transmitted from parent to offspring. The scheme may be worth considering also for vertically transmitted diseases for which the breeding candidates or their gametes can be reliably disinfected and screened before being transferred to the nucleus and the industry. [Copyright &y& Elsevier]

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. [Copyright &y& Elsevier]

Abstract: We have compared rate of inbreeding (ΔF) and genetic gain (ΔG) in truncation selection schemes for fish on best linear unbiased prediction (BLUP) estimated breeding values (EBVs; BTS) or phenotypic values (PTS) with one constraint on the number of tanks (100 or 200) to rear the families, e.g., until tagging size, and one constraint on the total number of selection candidates (3200 or 6400). Single trait selection was practiced for a trait with heritability of 0.1, 0.4 or 0.7 and 5, 10, 20, 50, 100 or 200 selected sires and dams were selected. When going from PTS to BTS, we found an overall increase of ΔG and ΔF of a factor of 0.07 and 1.45, respectively; that is, the increase of ΔG was moderate and accompanied by a dramatic increase of ΔF. In general, ΔF was reduced by increasing the number of tanks at a given number of selection candidates and by decreasing the number of selection candidates at a given number of tanks. ΔF was also reduced for schemes with high heritability because BLUP breeding value estimation then increases the weight on the individual''s phenotype, which leads to a reduced correlation between BLUP estimated breeding values within a family, and fish from more families become selected. In practical fish breeding schemes, PTS seems preferable over BTS because BTS generally give unacceptable high ΔF (≫0.01) for these schemes with few but large families. PTS can, however, only be used for traits measured on the selection candidate, which makes PTS less valuable for schemes with comprehensible breeding goals, including, for example, growth, disease resistance, maturity and fillet quality traits. Several traits are measured today on sibs only. [Copyright &y& Elsevier]