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




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Project no.: 044424
Project acronym: AquaBreeding
Project title: “Towards enhanced and sustainable use of genetics

and breeding in the European aquaculture industry”
Instrument: Specific Support Action
Thematic Priority: Modernisation and sustainability of fisheries,

including aquaculture-based production systems
Final Technical Report

Period covered: from 01/12/2006 to 30/11/2008

Date of preparation: December 2008

Start date of project: 1st December 2006

Duration: 24 months

Project coordinator name: Hervé Chavanne

Project Coordinator organisation name: Istituto Sperimentale Italiano “Lazzaro Spallanzani”

TABLE OF CONTENTS



Publishable final activity report 3

1. Project execution 3

1.1. Summary of project objectives 3

1.2. Contractors involved 3

1.3. Work performed and end results 3

1.3.1. Meetings 3

1.3.2. Description of the state-of-the art in aquaculture breeding 3

1.3.3. Industrial survey 4

1.3.4. Development of a Vision document 4

1.3.5. Definition of the industrial research priorities 4

1.3.6. Proposal for a Breeding and Reproduction Aquaculture Network 4

1.4. Reference information about the project 5

1.4.1. Project logo 5

1.4.2. Project website 5

1.4.3. Reference table 5

2. Dissemination and use 6

2.1. Species reviews in breeding and reproduction 6

2.2. Industrial survey: a status of current aquaculture breeding trends to prepare the future 6

2.3. Development of a Vision for the aquaculture breeding sector 7

2.4. Industrial Research priorities 7

2.5. Breeding and reproduction aquaculture Network 7

Final plan for using and disseminating the knowledge 9

1. Section 1 - Exploitable knowledge and its Use 9

1.1. Species Reviews 9

Rainbow trout (Oncorhynchus mykiss) 11

Atlantic salmon (Salmo salar) 18

Gilthead seabream (Sparus aurata L.) 28

European seabass (Dicentrarchus labrax L.) 37

Atlantic Cod (Gadus morhua) 50

Turbot (Scophthalmus maximus) 58

Pacific oyster (Crassostrea gigas) 67

Brown trout (Salmo trutta) 77

Common carp (Cyprinus Carpio L.) 84

Charrs (Salvelinus alpinus and Salvelinus fontinalis) 95

1.2. Industrial Survey 104

1.3. Development of a Vision for the aquaculture breeding sector 138

AQUABREEDING VISION 140

1.4. Definition of the industrial research priorities 146

PRIORITIZATION TABLE 148

1.5. Proposal for a Breeding and Reproduction Aquaculture Network 154

1.6. Overview table 160

2. Section 2 – Dissemination of knowledge 161

2.1. Overview table 161

2.2. Brief description of dissemination activities 161

3. Section 3 - Publishable results 163

3.1. Species reviews in breeding and reproduction 163

3.2. Industrial survey: a status of current aquaculture breeding trends to prepare the future 163

3.3. Development of a Vision for the aquaculture breeding sector 163

3.4. Industrial Research priorities 164

3.5. Breeding and reproduction aquaculture Network 164

Final science and society reporting questionnaire 165

Final reporting questionnaire on workforce statistics 173

Final socio-economic reporting questionnaire 174



Publishable final activity report


  1. Project execution

    1. Summary of project objectives

The AquaBreeding main objective is to promote a decisive involvement of the European aquaculture industry in breeding. The current state-of-the-art drawing up the scientific context and technological advances in breeding and reproduction for the main European aquaculture species has been described first. Contemporarily, an industrial survey conducted at the European level has permitted to identify the main players of the breeding sector and the species on which selection was performed. Successively, a vision document describing the future of the aquaculture breeding sector has been written and the research priorities have been listed and ranked. Finally, in continuation to the dissemination of the project’s results, a proposal for a Breeding and Reproduction Aquaculture Network was made in order to link the European Technology Platforms (ETPs) FABRETP and EATP (now EATIP) in the above fields.


    1. Contractors involved

Istituto Sperimentale Italiano Lazzaro Spallanzani (Italy)

Akvaforsk (now NOFIMA, Norway)

Marine Harvest Ireland (Ireland)

Syndicat des Sélectionneurs Avicoles et Aquacoles Français (France)

Institut National de la Recherche Agronomique (France)


    1. Work performed and end results

      1. Meetings

Five meetings have been organized during the whole duration of the project:

- at month 1: two days starting meeting (coordination meeting, Rivolta d’Adda, Italy) permitted to detail the main project actions according to the project workplan.

- at month 7: the second meeting (Alesund, Norway) focussed on the preparation of the species reviews and the industrial survey. This meeting was held on the sidelines of the Fish Breeder’s Round Table organized by Akvaforsk.

- at month 17: the third meeting (Brunel, UK) allowed to highlight the current and future needs of the industry in the field of breeding and reproduction. In the same breath, the fourth meeting was held in conjunction with the AquaGenome roadmapping workshop, in part dedicated to future developments of breeding strategies based on present findings on aquaculture genomics.

- at month 23: the final meeting (Paris, France) was organised in collaboration with the ReproFish project as an open workshop. It has allowed a large dissemination of both projects’ results and has opened the way to the networking of the sector.

In parallel, cross participations of AquaBreeding partners to FABRETP and EATIP meetings has maintained constant links between both platforms in view of possible future interactions.





      1. Description of the state-of-the art in aquaculture breeding

Reviews on updated research findings and technological applications in aquaculture breeding and reproduction have been prepared for 10 targeted species: the Atlantic salmon, the rainbow and brown trouts, the Atlantic cod, the common carp, the European seabass, the gilthead seabream, the Pacific oyster, the charrs (alpinus and fontinalis) and the turbot. Each review contains an exhaustive list of scientific references and follows the same general layout: (1) General information on production and breeding, (2) Genetic variability of the species, (3) Reproduction, (4) Selection, (5) Polyploidisation and monosexing and hybrids, (6) Genomics.

The reviews represent updated and exhaustive references of the state-of-the-art and the knowledge gaps in breeding and reproduction for the major European aquaculture species. They have been published on the project website (http://www.aquabreeding.eu/) and printed in 100 copies for dissemination during the AquaBreeding-ReproFish final workshop.

Further description of the breeding sector have been illustrated during the final workshop, centred on the changing breeding experience according to the countries and the challenges they represent for the whole production sector (presentations available at http://www.aquabreeding.eu/Documents/tabid/98/Default.aspx).


      1. Industrial survey

A questionnaire focusing on aquaculture breeding practices was prepared and sent in 28 countries through national contacts. The answers received from single breeding organisations were aggregated into a final report. An updated document has been prepared lately to include breeding programs set up in Central and East European countries. The results give an extended view, even if not exhaustive, of current commercial breeding activities in Europe (37 selective breeding programmes listed, 14 selected species) with a description of practices split by strategy, country and species.

This survey brings a clearer view of the European aquaculture breeding sector, today still small and fragmented, showing a trend of development across species and countries. It highlights the diversity of strategies implemented and brings to light specificities linked to the species biology and markets structure. It also shows strong disparities among countries, suggesting measures of readjustment where few or nothing is done.




      1. Development of a Vision document

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 analyses 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.




      1. Definition of the industrial research priorities

Based on the knowledge gaps, the industrial research priorities have been defined from an extended list (50 topics) built on the following pillars: (1) market-value traits, (2) health and welfare traits, (3) reproduction, (4) breeding schemes efficiency, (5) sex control, (6) genetic resources and banking, (7) social and knowledge transfer issues.

The resulting prioritization table, distributed among the project partners and on the occasion of the final workshop, has been ranked from the poll of 48 responses received, half of which were from the industry. The 4 top priorities have been written as call text to be submitted to EC services and ETPs working groups.

The extended list will serve as memorandum for future research prioritization works.


      1. Proposal for a Breeding and Reproduction Aquaculture Network

The evidence of fruitful development perspectives deriving from a strong collaboration between the breeding and reproduction sectors, already implemented at the ETPs level, conduced to the launch of a network gathering the aquaculture industry and academics active in these areas.

A call of interest has been sent to the AquaBreeding-ReproFish-AquaGenome projects’ mailing list (220 e-mail addresses) on the first of January 2009. Within the end of that month, the consortium will take stock of the registrations received and decide how to move for the future. End-January, 43 industry representatives and 67 academics had registered.

When it will come, the network will operate on a voluntary basis and will be managed by a core-group linking the respective FABRETP and EATIP working groups.

To proposed activities will concentrate on 4 pillars: (1) Define the industrial research priorities, (2) Organise applied training courses, (3) Perform a periodic industrial survey on aquaculture breeding practices, (4) Disseminate information and enhance interactions through a dedicated website.



This network is expected to give continuity to the collaboration initiated between the AquaBreeding, ReproFish and AquaGenome projects’ stakeholders. Making the link between the FABRETP and EATIP platforms, it will reinforce the awareness of ETPs’ opportunities and highlight industrial challenges throughout Europe in the fields of aquaculture breeding, reproduction and genomics. In particular, it will contribute to the definition and implementation of the FABRETP and EATIP Strategic Research Agenda in the above fields. Gathering users and suppliers of knowledge, it will also enhance innovation transfer and projects build-up opportunities.


    1. Reference information about the project

      1. Project logo





      1. Project website


http://www.aquabreeding.eu

      1. Reference table

European aquaculture breeding 2008: countries and species




  1. Dissemination and use

This section provides a publishable summary of each exploitable result the project has generated.

    1. Species reviews in breeding and reproduction

Description: The species reviews have been elaborated with the objective to provide updated information on the state-of-the-art of breeding and reproduction for aquaculture species having a relevant economic weight or presenting a development potential at the European level. Each review contains an exhaustive list of scientific references and follows the same general layout: (1) General information on production and breeding, (2) Genetic variability of the species, (3) Reproduction, (4) Selection, (5) Polyploidisation and monosexing and hybrids, (6) Genomics. The reviews have been prepared for the 10 following species: the Atlantic salmon, the rainbow and brown trouts, the Atlantic cod, the common carp, the European seabass, the gilthead seabream, the Pacific oyster, the charrs (alpinus and fontinalis) and the turbot.

Use in further research: The reviews are directly useable as updated references in the fields of breeding and reproduction for the targeted species.

Stage of development: Reviews completed

Collaboration sought or offered: Without object

Collaborator details: Without object

Intellectual property rights granted or published: Without object

Contact details: See main author of each single review or send a mail to the project coordinator: herve.chavanne@istitutospallanzani.it


    1. Industrial survey: a status of current aquaculture breeding trends to prepare the future

Description: An industrial survey has been conducted from European private companies, research organisations and professional associations managing closed aquaculture broodstocks of freshwater and marine aquaculture species. The objective of this study is to get an overview of the breeding strategies and assess the extent of their implementation in the European aquaculture industry. The document, elaborated from questionnaires compiled by 33 breeding organisations, gives an extended view of current commercial breeding activities in Europe (37 selective breeding programmes listed, 14 selected species) with a detailed description of practices split by strategy, country and species.

Possible market applications: The survey brings a clearer view of the aquaculture breeding sector, still small and fragmented, and shows a trend of development across species and countries

Stage of development: Industrial survey completed

Collaboration sought or offered: Information exchange

Collaborator details: Commercial aquaculture breeding companies active in Europe providing, in a confidential basis, updated information on the breeding strategies implemented and the company profile.

Intellectual property rights granted or published: Without object

Contact details: AquaBreeding project coordinator: herve.chavanne@istitutospallanzani.it


    1. Development of a Vision for the aquaculture breeding sector

Description:

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 analyses the world and European aquaculture production context, details the challenges for the European aquaculture breeding sector and lists the fundamentals to face such challenges.



Stage of development: Vision document completed

Collaboration sought or offered: Information exchange

Collaborator details: EATIP Vision Paper under completion for the pillar “Managing the biological life cycle”, working group “Breeding and Reproduction.

Intellectual property rights granted or published: Without object

Contact details: AquaBreeding project coordinator: herve.chavanne@istitutospallanzani.it


    1. Industrial Research priorities

Description:

Based on the knowledge gaps, the industrial research priorities have been defined and ranked from an extended list built on the following pillars: (1) market-value traits, (2) health and welfare traits, (3) reproduction, (4) breeding schemes efficiency, (5) sex control, (6) genetic resources and banking, (7) social and knowledge transfer issues.

The 4 top priorities, resulting from the poll of 48 stakeholders responses (half of which were from the industry), were written as call text (presented hereafter) for a submission to the EC services and ETPs working groups. The extended list will serve as memorandum for future research prioritization works.

Use in further research: The listed priorities will serve as input for the EATIP Strategic Research Agenda under preparation in 2009.

Stage of development: Industrial research priorities in aquaculture breeding and reproduction completed

Collaboration sought or offered: financial support or investment, information exchange

Collaborator details: Users and providers of updated knowledge in the fields of aquaculture breeding and reproduction.

Intellectual property rights granted or published: Without object

Contact details: Network manager. In the meantime, AquaBreeding project coordinator: herve.chavanne@istitutospallanzani.it


    1. Breeding and reproduction aquaculture Network

Description: A call of interest for a pilot Network bringing together the aquaculture industry and academics active in the fields of breeding and reproduction has been launched on the first of 2009. The objective of the Network is to strengthen the capacity of innovation of the European aquaculture industry in the above areas, supporting an effective interaction between the two European technology platforms of reference, FABRETP and EATIP.

The Network will adopt a multi-stakeholder approach, gathering representatives of breeding companies, hatcheries, research organisations, genotyping and biotech reproduction companies or consultancy firms active in the above fields. As the development of genomic tools is expected to bring great benefits to the aquaculture sector, in particular opening up new possibilities in the fields of breeding and reproduction, the Network will also include research organisations active in genomics.

To start, the activities will be limited to 4 levels: (1) Define the research priorities, (2) Organise applied training courses, (3) Perform a periodic industrial survey on aquaculture breeding practices, (4) Disseminate information and enhance interactions through a dedicated website.

Possible market applications: The network will support an effective interaction between the two European technology platforms FABRETP and EATIP in the fields of breeding and reproduction.

Use in further research: The network will contribute to the definition and implementation of the FABRETP and EATIP Strategic Research Agenda in the fields of breeding and reproduction. Gathering users and suppliers of knowledge, it will also enhance innovation transfer and projects build-up opportunities.

Stage of development: Network in a preparatory phase

Collaboration sought or offered: financial support or investment, information exchange, training

Collaborator details: Any stakeholders active in the fields of aquaculture breeding and reproduction willing to develop innovative approaches in the above fields

Intellectual property rights granted or published: Without object

Contact details: Network manager. In the meantime, AquaBreeding project coordinator: herve.chavanne@istitutospallanzani.it

Final plan for using and disseminating the knowledge


  1. Section 1 - Exploitable knowledge and its Use

    1. Species Reviews

Reviews on updated research findings and technological applications in aquaculture breeding and reproduction have been prepared for 10 targeted species: the Atlantic salmon, the rainbow and brown trouts, the Atlantic cod, the common carp, the European seabass, the gilthead seabream, the Pacific oyster, the charrs (alpinus and fontinalis) and the turbot. Each review contains an exhaustive list of scientific references and follows the same general layout: (1) General information on production and breeding, (2) Genetic variability of the species, (3) Reproduction, (4) Selection, (5) Polyploidisation and monosexing and hybrids, (6) Genomics.

The reviews represent updated and exhaustive references of the state-of-the-art and the knowledge gaps in breeding and reproduction for the major European aquaculture species. They have been published on the project website (http://www.aquabreeding.eu/) and printed in 100 copies for dissemination during the AquaBreeding-ReproFish final workshop. They will be further disseminated through the Network website when it will emerge (expected mid-2009). Additional work has been provided during the final project workshop, illustrating the changing breeding experience according to the countries and the challenges they represent for the whole production sector (presentations available at http://www.aquabreeding.eu/Documents/tabid/98/Default.aspx).


The species leaflets mentioned in the interim report have not been prepared as they did not bring more information as compared to the extended reviews.
Each partner has been involved in the writing of the specific reviews, as presented in the next table.


Fish and shellfish species

Responsible of the review

Atlantic salmon

Marine Harvest

Rainbow trout

INRA

Seabream

ISILS and INRA/Ifremer

Seabass

ISILS and INRA/Ifremer

Common carp

INRA

Turbot

SYSAAF

Atlantic cod

Akvaforsk

Brown trout

INRA

Chars

SYSAAF

Pacific oyster

Ifremer

The work performed is presented in the Deliverable 1.





DELIVERABLE 1

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