Inside this issue:

• Coordinator’s Introduction • Report on awarded

mobility grants • New call open for mobility

and resource grants • Sign up details to receive

Aquagenome announcements

• Report on Applied Training Workshop

• Inventory of Available Genomic Resources

• Results from Mini Symposium - Bergen

• Aquagenome website

Coordinator’s Introduction

March 2008 NEWSLETTER Edition 4

To contact the Co-ordinator of Aquagenome please email Patrick Prunet at the follow-ing address: Patrick.Prunet@rennes.inra.fr The Aquagenome website http://genomics.aquaculture-europe.org

After more than a year of activity and the launch of several major activities, the Aquagenome project is now tackling another impor-tant aim of this Co-ordination Action. This aim is to determine the steps required to allow the application of genomic tools and knowl-edge in an effective and sustainable manner in aquaculture, by in-teracting with producers and stakeholders.

This task will be addressed using a workshop that will gather to-gether experts in genomics and representatives from the large community of stakeholders. The workshop will be unique in terms of the processes involved and the subject examined, and we will gather input from all attendees throughout the sessions. By inter-acting with these representatives from aquaculture, we will identify the main constraints that prevent them from adopting the new ge-nomic technologies coming from research. This work will be carried out using road-mapping and Brain-pooling techniques during a 2 day meeting near Heathrow, London on the 19th and 20th June.

This road mapping exercise will identify priority research and knowledge transfer issues in the short, medium and long term that will need to be addresses at a national and/or European level. The success of such a workshop relies on the presence at the June meeting of a large variety of aquaculture stakeholders. Therefore, all persons interested in participating in this exercise should contact Carol Didcock (carol.didcock@genesis-faraday.org) as soon possi-ble for registration. There are still a few places available.

In advance, we thank you for your participation in the collective construction of an effective roadmap for genetics and genomics in aquaculture!

Patrick Prunet

Aquagenome – Mobility grants and Resource Ex-change Grants- Snuttan Sundell and Deborah Power, WP 3 leaders.

Two rounds of applications for the Aquagenome Mobility grant and Resource exchange grant have been concluded within the Aquagenome project. At the first cut off date; 1st of August, two applications were submitted of which one of them has been successfully concluded and reported. PhD student Christopher Sauvage from IFREMER, La Tremblade, visited Prof. Chris Haley at the Roslin Institute, UK, for four weeks during October and November of 2007. The main aim of the four week stay was to learn and ap-ply the linkage mapping software, Crimap, as well as approaches to QTL mapping using the software QTL express. Christoph Sauvage took his own data to the Roslin Institute, in order to start to build a con-sensus linkage map for a large data set he had collected from the Pacific oyster. The scientific question of Christoph Sauvage’s PhD project is related to summer mortalities in this aquacultured species. The teaching and training in the use of the above mentioned tools were very successful and the QTL detec-tion started at the Roslin Institute will now be continued at IFREMER. The second application funded was a request from Dr. Antonio Ibarz, University of Barcelona to visit Profs. Deborah Power and Adelino Canario at CCMAR, University of Algarve, Portugal. This visit is planned for February and March 2008 and will aim at using genomic and proteomic approaches to study changes in the sea bream pituitary in response to estradiol treatment.

The second round of applications closed November 1st, 2007 and five applications were submitted. All five were of high quality and within the scope of Aquagenome and met all the criteria set up for the Aqua-genome grants. Therefore all five applications were granted and most visits will take place at the begin-ning of 2008 – with the exception of the trip of PhD student Lars Niklasson, Göteborg University, Swe-den, who visited Dr. Bertrand Collet, FRS Marine Lab, UK, to learn qPCR and set up protocols for sev-eral newly characterised immune related genes. Lars Niklasson stay in Aberdeen was reported to be very successful and Lars is now transferring his new knowledge to Göteborg University and setting up the qPCR protocols in his home lab. The other four applications granted were: Dr. Ingunn Stubbhaug, NIFES, Bergen who will visit Dr Douglas Tocher at Univeristy of Stirling, UK, in order to run the microar-ray TRAITS/SGP developed at University of Stirling, to investigate the effect of dietary omega-3 fatty ac-ids on Atlantic salmon hepatocytes. Dr. Isabell Morgado, CCMAR, Portugal, has been granted support to visit Dr. Mirjam Czjzek, at Station Biologique de Roscoff, France, to undergo training in the field of pro-teomics. The work will include clone construction, recombinant protein production and crystallography. Next application to be granted was PhD student Dimitrios Loukovitis, ATEI, Thessaloniki, Greece, who will visit Prof Georgios Kotoulas at IMBG-HCMR, Greece, in order to carry out parts of his PhD-project there. With the aid of the genomic resources and know how of the host institute, Dimitrios Loukovitis’ work will aim to characterise and asses level of genetic diversity in samples from selected broodstock of the gilthead seabream from Selonda Aquaculture S.A. and do partial QTL mapping. Finally, the fifth ap-plication to be granted support was PhD student Bruno Louro from CCMAR, Faro, Portugal who will visit Prof Filip Volckaert at KU in Leuven, Belgium. The purpose of Bruno Luoros visit is to perform genomic screening and detailed analysis of the distal region of linkage group1 using microsatellite markers for sea bass. This will allow an increased resolution and narrow down the location of a growth QTL which was previously identified in the EU funded Bassmap project. With this short summary of the seven exciting projects granted so far within WP 3.1, Exchange program; Training activities, of the Aquagenome project we would like to wish all applicants good luck with their visits and encourage other researchers, both young and senior to take advantage of this scheme.

Sign Up to Receive Aquagenome News If you would like to receive further news regarding Aqua-genome, please email carol.didcock@genesis-faraday.org. By signing up to the distribution list you will automatically receive all further newsletters, announce-ments of funding opportunities, details regarding work-shops and other opportunities.

Please also invite your colleagues to sign up to the distri-bution list. We would like to reach as many interested stakeholders as possible, therefore, please pass this on to any contacts you feel may be interested in the Aqua-genome project.

New Call Open: Mobility Grants and Research Exchange Grants

4th call for Aquagenome – Mobility grants and Resource exchange grants

The EU project Aquagenome – Genomics in fish and shellfish: From research to aquaculture - funds mobility of scientists and genomic resources between European laboratories active in the field of genomics in fish and shellfish aquaculture.

The Mobility grants will cover travel and subsistence costs up to a maximum of 2500 € for a pe-riod of one to six weeks, and the Resource exchange grant will cover costs for labour and con-sumables needed for handling and if appropriate shipping of genomic resources within Europe up to a maximum of 1000 €.

Detailed information on the calls, guidelines for proposers, electronic application forms and condi-tions for reporting along with forms for reporting and reimbursement can be found on the Aquage-nome webpage: http://genomics.aquaculture-europe.org/

Preference will be given to applications from junior scientists from research or the aquaculture industry.

Women are encouraged to apply.

The deadline for applications is May 1st, 2008. 

Report on the Applied Training Workshop: Towards applications of genomics in European tem-perate and Mediterranean aquaculture The first AQUAGENOME (http://www.aquaculture-europe.org/) training workshop for the Euro-pean aquaculture industry: “From genomics to applications in European temperate and Mediter-ranean Aquaculture: Basis and prospects” was held on the 7th and 8th of February in the Central Office of IFREMER at Issy-les-Moulineaux (close to Paris). This workshop was co-organised by SYSAAF, INRA, IFREMER, as part of the AQUAGENOME EU project work package on dissemi-nation of knowledge and training in genomics in aquaculture. The workshop focused on the appli-cation of genomic technologies in temperate and Mediterranean aquaculture species (trout, bass, bream, turbot, oyster, carp, etc.), a second workshop is also being organised in Scotland (Stirling) in March to focus on Northern European species (Atlantic salmon, cod, halibut) by GENESIS FARADAY. The development of fish and shellfish farming is facing several challenges linked to the infancy of the industry: i.e. domestication, genetic improvement of disease resistance, genetic improvement of feed efficiency to fish meal and fish oil substitution by vegetal products, development of adapted vaccines, supply of fry or spat at high quality and high robustness, adaptation to environ-mental change, production of healthy, high quality consumer products and limitation of environ-mental impact of the activity and escapees. Over recent years, the EU and individual countries have supported the development of genomic tools for some aquaculture species (e.g. rainbow trout, sea bass, sea bream, turbot pacific oyster, Atlantic salmon). New perspectives arise with the development of genome sequencing, genetic and physical maps and genetic markers. Also, new high-throughput technologies will reduce the cost of genotyping and give access to large amounts of genetic information, useful in several ap-plications: •reproduction, •breeding programs and new traits (disease resistance, quality, etc…), •development of new vaccines or new drugs or prophylaxy practices to improve broodstock sani-tary status and animal health, feed formulations and substitutions and feeding practices, etc… The objectives of the training session were to : • Provide adapted information and technology definitions used in genomic research • Give a clear view of the steps from research to potential application in aquaculture • Present the state-of-the-art in the use of genomics for selective breeding • Visit infrastructures involved in the development and use of genomic tools (spotting unit, bio-resource centre, genotyping private lab) in livestock and aquaculture breeding Scientists from different EU countries gave 21 short presentations (20-25 min) each, followed 10 min of discussion. After an introduction of the biological basis of reproduction and genetics, sev-eral examples of genome sequencing and genetic maps were presented and discussed (blue mussel, flat oyster, Pacific oyster, rainbow trout, sea bass, sea bream). ). The first application of functional genomics (i.e. how genes are expressed differently between individuals and treat-ments) using micro-array were illustrated in reproduction, nutrition, stress and welfare, summer survival and pathology. After an introduction of selective breeding theory and application, the fu-ture use of genomic tools in breeding was illustrated to trace family relationships (DNA finger-

-print) or to improve breeding programs using genetic markers (QTL, major genes, SNPs, ge-nome-wide selection) as exemplified in the French dairy cattle breeding program. The workshop concluded with visits to facilities involved with genomic research (robot, PCR, sequencing) in the INRA Jouy en Josas research center (Bioressource Center CRB GADIE, Bioinformatic Re-source Center SIGENAE) and the private LABOGENA laboratory involved in the use of genomic tools (DNA parentage assignement, QTL, genetic mutations, …) for livestock and aquaculture species in France; such as rainbow trout, sea bass, sea beam or turbot. The targeted audience was aquaculture professionals from Southern and Eastern European and Mediterranean countries involved in rainbow trout, sea bass, sea bream and oyster produc-tion who may fall into the category of : • hatchery managers, • R&D feed manufacturer, • R&D pharmaceutical industry professionals and veterinarians, • professional body representatives, • national authority representatives. Trained aquaculture professionals were invited to participate to the meeting planned the 19th and 20th of June in London to elaborate a “road map” that will be presented to the EU to define priorities of research in genomics for the EU aquaculture industry. To download presentations or to get information about the “road map” meeting (London, 19th and 20th of June), visit the AQUAGE-NOME web site : http://www.aquaculture-europe.org/

Automatic pipeting by robots to produce rainbow trout micro-array (Courtesy of Yann Guiguen, INRA and Karine Hugot, CRB GADIE).

Inventory of Genomic Resources Available on Aquagenome Website

The Aquagenome website now has an in-ventory of the available genomic resources for aquaculture species. This includes both a list of the ESTs available in public data-bases and also a list of the genomics re-sources for the fish and shellfish species including markers and maps. To access these lists you must register via the website, but this is a simple and easy p r o c e s s . P l e a s e r e g i s t e r a t h t t p : / / g e n o m i c s . a q u a c u l t u r e -europe.org/index.php?id=41

This publication represents the views of the Authors, not the EC.

The EC is not liable for any use that may be made of the information.

Whilst all reasonable effort is made to ensure the accuracy of information contained in this newsletter, this newsletter is provided without warranty and we accept no responsi-bility for any use to which it may be put.

Images sourced from Wikipedia, Microsoft Clip Art 2006 and Genesis Faraday’s personal collections.

Aquagenome Website

The Aqaugenome website has now been upgraded with various details and further information for all interested partners. The site, www.aquaculture-europe.org, gives a full overview of the project and the partners that are involved as well as advertising any current workshops and available grants. In addition, you can register on the website to access lists of the genomic resources for the main fish and shellfish aquaculture species as well as the number of ESTs in publicly available databases or these species. Registering for access to the area is a simple and easy process, allowing access to valuable information. All editions of the newsletter can also be downloaded from the website for your information.

Results from the Mini Symposium 'State-of-the-art and future of genomics in aquaculture research', Ber-gen 20th to 21st September 2007

The mini symposium on ‘state-of-the-art and future of genomics in aquaculture research; was held in Bergen last year. As a result of this workshop a series of reports have been produced on subject areas relevant to the topic. These reports are available for viewing on the Aquagenome website and can be viewed at http://genomics.aquaculture-europe.org/index.php?id=82. In addition, these reports will also form the basis of a white paper to be submitted to the EC regarding the current state of genomic research in aquaculture and some recommendations for future areas of work. This paper is under construction at the moment and once complete, will also become available to interested parties.