AquaBreeding Project title: “Towards enhanced and sustainable use of genetics and breeding in the European aquaculture industry”

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6. Molecular tools and protection strategies

Figure a:

Molecular fingerprinting for parentage assignment is implemented by 15 out of 16 breeding organisations making use of molecular tools in their breeding program. When such a technique is implemented, about half of them use that information for genetic traceability.

Even if marginal, alternative approaches are also used to protect the genetic progress obtained: restriction of the genetic variation in selected batches sold to clients, contract agreements on the use of seeds or introduction of reducing fitness recessive genes in the genetic pattern of production fish.
Figure b:

The use of molecular fingerprinting is spread over eight species. Only two salmonid programs have implemented a marker assisted selection.

The possibility to implement genetic traceability is better considered on marine fish species.

7. Type of selection and alternative genetic improvement

7. Type of selection and alternative genetic improvement


- Crossbreeding: mating of individuals coming from two different populations, most often consisting in crossing unrelated inbred lines.

- Individual selection: breeding strategy which acts upon individuals within a population without considering their family relationship

- Within family selection: breeding strategy based on the selection of the best individuals within each family.

- Combined selection: breeding strategy based on the selection of the best individuals across the best families.
Figure a:

The combined selection is preponderant among the polled breeding programs (21 out of 37), followed by 13 individual based breeding programs.

Figure b:

All the Atlantic salmon and Atlantic cod breeding programs are based on combined selection. Gilthead seabream and common carp are each improved following 3 different kinds of selection.

Among the alternative improvement strategies, triploidisation is the most popular and is implemented on 9 programs among shellfish, freshwater and marine fish species.

8. Eggs and spats production

8. Eggs and spats production

The seeds production volumes are expressed in millions of eggs or spats for different fish species and the Pacific oyster respectively. They represent the activity performed in Europe, plus Israel, during the 2006-2007 season.

Figure a:

A balanced number of programs is observed among the six proposed categories of seed production numbers, from less than 2 million up to the maximum range 200-500 million.

Figure b:

Both Pacific oyster programs supply, together with 2 salmonid programs between 200 and 500 million “seeds” per year.

Trout programs are present in all categories while each of the Atlantic salmon programs supply more than 20 million eggs per year.
Seabass and gilthead seabream programs providing fry are also seller of eggs.

9. Fry production

9. Fry production

The seeds production volumes are expressed here in millions of fry for all the polled species except oyster. They represent the activity performed in Europe, plus Israel, during the 2006-2007 season.

Figure a:

The majority of production volumes are located in the lower category (< 20 million per year) while the maximum of fry produced by a single breeding organisation do not exceed 100 million per year.

Figure b:

Most of the programs supplying less than 2 million fry per year are also supplier of eggs. The others are minor species not having reached yet big production volumes at the European level (< 10.000 tons in 2006, FEAP source). Thus, most of the commercial activity of fry suppliers range from 2 to 100 million fry per year.

The main providers of fry are seabass and seabream producer organisations.

10. Share of the market of spats, eggs or fry

Fig. a: share of the national market

(nb of breeding programs)

Fig. b: share of the European market

(nb of breeding programs)

Fig. c: share of the world market

(nb of breeding programs)

10. Share of the market of spats, eggs or fry

The share of the markets covered by breeding companies are estimates provided by the polled organisations and as such are subject to uncertainty.

Figure a:

14 breeding companies over 34 are dominant on their national market. Situations close to the monopoly (category > 75%) are observed in countries where a unique breeding program is implemented for a given species (data not shown).

Figure b:

At the European level, the majority of polled breeding companies cover less than 15% of the market. The salmon market is supplied most exclusively by selected animals (data not shown). Four out of the six breeding companies covering more than 30% of the European market are performed on minor species (European production < 10.000 tons in 2006, FEAP source).

Figure c:

Most of polled breeding companies cover less than 15% of the world market. Above that level, breeding programs are either implemented on minor species or concern species primarily produced in Europe.

11. Breeding programs and trade of “seeds”

11. Breeding programs and trade of “seeds”
This figure reports single selective breeding programs sorted according to the number of countries where the genetic material is sold.
It demonstrates the prevalence of the transnational dimension for the trade of seeds of most breeding programs implemented in Europe.
This document is the result of a work financed by the European Commission and conducted by the AquaBreeding project partners: Hervé Chavanne (Istituto Sperimentale Italiano “Lazzaro Spallanzani”, Italy), Ashie Norris (Marine Harvest Ireland, Ireland), Anna Sonesson (NOFIMA, Norway), Pierrick Haffray (SYSAAF, France), Marc Vandeputte, Béatrice Chatain, Pierre Boudry (INRA-Ifremer GDR, France), and the decisive contribution of the following organisations:

• Aarhus University (DK)

• Agricultural Research Organization (IL)

• Akvaforsk Genetics Center (NO)

• Andromeda (GR)

• Aquaculteurs Bretons (FR)

• AquaGen (NO)

• Aquark (GR)

• AquaSearch (DK)

• Ardag (IL)

• Bodø University (NO)

• Ecloserie de Guyenne (FR)

• Ecloserie Marine de Gravelines (FR)

• Ferme Marine du Douhet (FR)

• Finnish Game and Fisheries Research

Institute (FI)

• Fishion Breeding (NL)

• France Turbot (FR)

• Hellenic Center for Marine Research (GR)

• Institute of Fisheries and Aquaculture (BG)

• Institute of Ichthyobiology and

Aquaculture (PL)

• Kego (GR)

• Landcatch Natural Selection (UK)

• Lugo University (SP)

• Marine Harvest Norway (NO)

• MTT Agrifood Research Finland (FI)

• Murgat (FR)

• Norwegian Institute of Fisheries and

Aquaculture Research (now NOFIMA)

• Pisciculture de Font de Rome (FR)

• Poissons du Soleil (FR)

• Raumagruppen (NO)

• Research Institute for Fisheries (HU)

• SalmoBreed (NO)

• Satmar (FR)

• Selonda (GR)

• SlamoBreed (NO)

• Solea BV (NL)

• Sources de l'Avance (FR)

• South Bohemia University (CS)

• Stirling University (UK)

• Stolt Sea Farm (SP)

• Technological Educational Institute of

Messolonghi (GR)

• Vendée Naissain (FR)

• Wageningen University (NL)

    1. Development of a Vision for the aquaculture breeding sector

The aim of this document is to highlight the key objectives of present and future breeding programs supporting a vibrant aquaculture industry in Europe within the next 15 years. It depicts the world and European aquaculture production context, details the challenges for the European aquaculture breeding sector and lists the fundamentals to face such challenges.

The document will support, in the field of breeding, the EATIP Vision Paper currently under completion. It will help to shape the Strategic Research Agenda of ETPs in the same field.

All the project’s partners brought support to the build up of the survey.
The work performed is presented in the Deliverable 3.

AquaBreeding Vision


Aim of the Vision:

To highlight the key objectives of present and future breeding programs supporting a vibrant aquaculture industry in Europe.

Global aquaculture - characteristics:

Overfishing, resulting in serious catch decreases and often depletion of stocks, endangers long-term availability of fishery resources. At the same time, it is estimated that the world’s population will reach 9 billion by 2040.

Table 1: Increase in the world population, 1950-2050. Source: US Census web site.

In this context, aquaculture is expected to provide the additional fish supplies needed to meet the demand of the growing world population. Worldwide, the aquaculture sector has grown at an average rate of 8.8 percent per year since 1970, compared with only 2.8 percent for terrestrial farmed meat production systems over the same period (FAO, 2007).

As a result, the proportion of aquaculture products in global seafood consumption increased from 7% in 1970 to 45% in 2006 (FAO, 2008). In terms of food fish supply destined for direct human consumption, the world aquaculture sector produced about 52 million tonnes of farmed aquatic products in 2006, compared with 59 million tonnes from capture fisheries (FAO, 2007).

Table 2: Seafood and fish meal production in the world, 1984-2006. Aquatic plants excluded. Source: FishStat.

Simultaneously, there is an increasing demand on fisheries for fishmeal/oil, in particular to produce animal feed for carnivorous/omnivorous aquaculture species. The limited availability of these resources and the competition with human food has led to shortages and price instability of feed supplies. With technological advances in nutrition and breeding it is expected that fishmeal will be progressively replaced by vegetal ingredients.
Aquaculture in EU-27 countries plus Norway:

From the mid ‘80s till the end ‘90s, the development of European aquaculture has been characterised by a constant production of molluscs and a steady increase of finfish species production, both in terms of volume, value and variety. During the last 35 years, the number of reared aquaculture species in Europe (> 100 MT/year) increased from 17 till 57 (FishStat).

Table 3: Aquaculture production in EU-27 + Norway, 1984-2006. Aquatic plants excluded Source: FishStat.

The late ‘90s have been followed by a drop of EU catches and a stagnation of aquaculture production, resulting in increased dependence on seafood imports (Glitnir report, 2008). In 2006, EU-27 + Norway contributed 3.9% of the world aquaculture production in volume and 8.3% in value.

Table 4: World Capture & Aquaculture production, 1996-2006. Aquatic plants excluded. Source: FishStat.

Table 5: EU-27+ Norway Capture & Aquaculture production, 1996-2006. Aquatic plants excluded. Source: FishStat.

EU-27 is the world’s biggest importer of seafood products: excluding intraregional trade, it was equivalent to 23% of the world’s total seafood imports in 2006, worth $20.7 billion. Today, EU-27 imports represent approximately four times more seafood products than exports. Seafood self-sufficiency is estimated to have declined from 53% in 1997 to 36% in 2007 as per capita consumption increased. In 2006 the seafood trade balance for EU-27 was negative by nearly 4 million tonnes (worth $18 billion) for a total seafood consumption close to 14 million tonnes (Glitnir report, 2008).

In 2006, the EU aquaculture sector represented 18.5% of the EU’s total seafood production. The development of the sector is highly dependant on political will at local and national level (licences, exports etc). Based on a multispecies production system, it is driven by a high quality production policy and high sanitary level criteria. It plays a crucial role in the activity and development of remote rural and coastal areas (≈ 65,000 jobs).
Current status of aquaculture breeding in EU:

The current status of commercial aquaculture breeding in EU shows a variegated picture across species, countries and strategies implemented (AquaBreeding survey, 2009).

The survey reports 37 selective breeding programs performed in Europe on 14 different species. Half of the programs are implemented on only three species: Oncorhynchus mykiss, Salmo salar and Sparus aurata. These species are also those reaching the major production volume in the three European countries having the highest number of programs implemented (respectively, France, Norway and Greece). On the other side, the implementation of a selective breeding program does not depend on the turnover of the company (from 50.000 € to 500 Million €), the number of “seeds” commercialised (from 100.000 to 65 million fry) or the aquaculture volume produced within a country (The Netherlands versus Italy).

Most of the breeding organisations (83%) rely on consultancy services to run their program. Organisations having their own experts are either research organisations, or have their core business centred on breeding, or have reached a critical size (turnover above 30 million €).

The combined selection strategy is preponderant among the listed breeding programs (21 out of 37). It is followed by the individual based strategy reported on 13 breeding programs.

Breeding programs of Atlantic salmon and rainbow trout count the highest number of selected traits in their breeding goal. Only one program includes all 8 groups of traits analysed, while 5 others include 6 of them. Most marine fish species are selected on no more than 3 out of the 8 groups of traits.

Artificial fertilisation is systematically used on salmonids breeding programs, while mass spawning dominates for species characterised by difficulties in fully mastering the artificial fertilization (Atlantic cod, seabass, gilthead seabream and common sole).

Only two salmonid programs have implemented a marker assisted selection. Molecular fingerprinting for parentage assignment is implemented by 15 out of 16 breeding organisations making use of molecular tools in their breeding program. When such a technique is implemented, about half of them use that information for genetic traceability as protection strategy.

Potential of breeding for EU aquaculture:

The species that are cultured in EU have all wild counterparts and are still in an early domestication process, which gives breeders the possibility to speed up and control the domestication process. Any important trait can be selected for, e.g. growth, shape, fat% and resistance to specific diseases. The genetic gain is cumulative, such that what is gained is gained. In general, a breeding objective changes over time, such that more traits are continuously being evaluated.

Some documentation on the effects of aquaculture breeding:

  • A reduction in production time until slaughter Norwegian Atlantic salmon from 23 to 14 months in 5 generations. (Gjerde, pers. comm.)

  • After one generation of selection of European seabass, weight was increased by 23% at commercial size. (Vandeputte et al., 2009)

  • After two generations of divergent selection for fat fillet content, the fillet fat content of rainbow trout was 4.1% in the low line vs. 6.0% in the high line (Quillet et al., 2007)

  • After 1 generation of divergent selection for resistance against IPN resistance of Atlantic salmon, the cumulative mortality after an IPN challenge in sea water was 32% in the low line vs. 79% in the high line (Storset et al., 2007).

Hence, the effects of breeding has been documented for different traits in all major species of EU.

Breeding pillars:

The successful development of the EU aquaculture industry in the medium to long term depends on the implementation of breeding programs in the industry which are economically viable, environmentally friendly and socially acceptable.

  • Economically viable

At present, only a part of European aquaculture production relies on genetically improved stocks. An extension of breeding programs across countries and among species is therefore desirable.

In the context of strong international competition and reduction of profit margins, securing high quality eggs and juveniles is crucial to ensure the cost-effectiveness of the industry. The target industry is characterised by disparities of the species biology, the enterprises size and the production systems, all factors that impact on the profitability of a program. As breeding programs represent a long-term investment, it is crucial to adapt breeding schemes, species and production systems to the specificities and capacities of each company and market demands.

The breeding goals, which determine the direction in which one wants to improve the fish population, must fit with the market specificities. Benchmarking across strains, rearing systems and environment is crucial to access and measure production performance and offer value to breeder and producer.

The accurate prediction of strain performances is of prime importance to manage efficiently a breeding program. It will increase the rate of genetic progress over time, allow the control of known sources of variation and ensure the best expression of performances under commercial conditions.

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