Newsletter September 2016
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In this edition:
- FISHBOOST Results:
 - Genotyping by sequencing efforts
- Genetic resistance to VNN in sea bass
   - Winter survival in common carp

- Researcher Exchange
- FISHBOOST at EU Open Doors
- In the Spotlight: Wendy Rauw, INIA
- Publications
- General Assembly 2016


This newsletter updates you about recent developments on aquaculture breeding and the FISHBOOST project.

FISHBOOST is an FP7 EU resesarch project that works on improving the main components of breeding programmes for the main six fish species produced in Europe:

Atlantic salmon, common carp, European seabass, gilthead seabream, rainbow trout and turbot.

FISHBOOST at EAS 2016 in Edinburgh!
From 20 -23 September, the European Aquaculture Society (EAS) holds its annual Aquaculture Europe event in Edinburgh, Scotland. This year, FISHBOOST has a dedicated session on Friday 23 September (10.30 – 12.50), chaired by our project coordinator Anna Sonesson. During the session, many results from FISHBOOST will be presented by our project partners.

In addition, FISHBOOST will also be presented at the EU Session on Wednesday 21 September by Anna Sonesson as an example of Research and Innovation support for the European Aquaculture sector by the EU.

Don't miss it! 

Programme FISHBOOST Session

FISHBOOST Results: one of the largest co-ordinated genotyping by sequencing efforts

FISHBOOST has successfully performed one of the largest co-ordinated genotyping by sequencing efforts in the world to date. 

Large-scale experiments
In work package 1 (WP1) of the project, large-scale disease challenge experiments were performed for several species and diseases (Table 1), and samples were collected for sequencing. For each disease challenge experiment, between 800 and 1600 individual fish samples were genotyped using various Restriction-site Associated DNA (RAD) sequencing approaches (RAD-Seq, ddRAD-Seq, 2bRAD-Seq).
The different RAD techniques were chosen according to the skills and experience of the laboratories involved and the characteristics of the experimental design and the genomes of the species. 

Table 1: Sequencing efforts

RAD-Seq techniques
RAD-Seq techniques combine the use of genome complexity reduction with restriction enzymes, and the high sequencing output of Next Generation Sequencing (NGS) technologies. Individual samples are given a nucleotide barcode, and m
any individuals are then sequenced in a single lane. This results in high coverage of sequence reads at specific sites in the genome, from which single nucleotide polymorphisms (SNPs) can be identified. These SNPs are concurrently genotyped, resulting in genome-wide genotypes for all animals in the sampled population. 

Application of Results
The results from the large genotyping by sequencing effort have highlighted the utility of RAD techniques for cost-effective genotyping in aquaculture species. Analyses are now ongoing to map genes for disease resistance traits and calculate genomic breeding values. A comparison of the merits of each of the different RAD techniques will also be performed to guide future work in this area. 

Read more
FISHBOOST Results: New insights into genetic resistance to viral nervous necrosis (VNN) in European sea bass

Viral nervous necrosis in sea bass
Improving genetic resistance of farmed fish to infectious disease is one of the major goals of the FISHBOOST project. Viral nervous necrosis (VNN) is a disease that has a large negative impact on aquaculture of sea bass in several European countries. It causes major economic losses mainly in larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance has potential to control the disease. 

FISHBOOST research to understand the genetic background of VNN resistance
In a collaborative FISHBOOST experiment, a team comprising The Roslin Institute at the University of Edinburgh, and French partners Ferme Marine Du Douhet, SYSAAF, ANSES, Ifremer and INRA, made a significant breakthrough in the use of genetic markers to understand and improve resistance to VNN in sea bass.

Based on the results of a large experimental challenge study including approximately 1,500 juvenile sea bass, a genomic prediction approach was taken to assess the accuracy of prediction breeding values for VNN resistance using all the SNPs simultaneously. This analysis demonstrated that breeding values can be estimated with high accuracy, significantly improving the state-of-the-art method which relies on pedigree information for breeding value prediction.

Implications for sea bass farming
The practical outcome of this research is likely to be improved selective breeding of sea bass stock to have higher resistance to VNN, potentially leading to reduction in the frequency and severity of outbreaks of this problematic disease.

More results at EAS 2016
Christos Palaiokostas (University of Edinburgh) will present these results at the FISHBOOST session of the European Aquaculture Society meeting in Edinburgh on 23rd September.

Read more

FISHBOOST Results: Genetic background of winter survival in carp

FISHBOOST research on common carp
Common carp is one of the most cultured freshwater fish species worldwide and is one of the targeted fish species in FISHBOOST. Common carp use energetic reserves (fat, glycogen, protein) during winter to maintain their body functions, and thus, these reserves are essential for winter survival. Within FISHBOOST, genetic parameters of body reserves that might affect winter survival in one-year old common carp have been estimated to assess the potential for using selective breeding to enhance winter survival. Until now, common carp has not been bred using systematic selection programmes and FISHBOOST aims to change this situation. To do that, data on genetic parameter estimates in different traits (e.g. body weight, body length, muscle fat, visceral fat) that affect winter survival are essential. Amur mirror carp, a newly produced strain of carp from the Czech Republic, was used for the research experiments. This strain is suitable for crossbreeding with other carp breeds to produce commercial hybrids, because it has high performance in e.g. resistance to KHV.

Presently, first results on estimating these genetic parameters in one-year old common carp before and after wintering are obtained (WP2). Before wintering, low to medium heritabilities (0.13 – 0.35) for the examined traits were observed. In the spring period, the heritabilities for most traits were even higher (0.34 – 0.58). Energetic reserve management seems to have a complicated genetic background, but preliminary results indicate that important traits such as body weight (BW), muscle fat content (MF) and visceral fat (VSI) can be significantly changed in carp by selection. 

So, we may draw a general conclusion that carp has a similar potential for boosting its performance as shown in salmon or rainbow trout, when applying a systematic selection programme. The effectivity and applicability of a selection programme in carp culture and management conditions will be investigated.  

Read more.

FISHBOOST Researcher exchange: Diego Robledo

Besides boosting European aquaculture, the FISHBOOST project also aims to boost the exchange of knowledge between the project partners. To show the importance of this exchange, we want to share the experiences of Diego Robledo (left) and Ross Houston (right).

They worked together during one of these successful researcher exchanges which happened last year between Geneaqua and The
Roslin Institute, University of Edinburgh (UoE).  Read more.

(photo credits: The Roslin Institute)
FISHBOOST at EU Open Doors

In celebration of the anniversary of the European Union, each year on Europe Day, EU institutions open their doors to the public.

This year at this European Open Doors day on 28 May, FISHBOOST was invited by DG Research & DG Mare to have a stand in the Commision’s Berlaymont building in Brussels and show what FISHBOOST is all about.

By showing DNA and quizzing the audience, people could learn about selective breeding in aquaculture and the differences between wild and farmed fish. Several hundred visitors stopped by, making this event a success for FISHBOOST!  
Read more

(photo credits:  European Union, 2016)

In the spotlight: 

Dr. Wendy Rauw, Researcher at INIA, Spain

'Today, only a small part of the global aquaculture production is based on genetically improved stocks. In our research we expect to develop a method to record between-family variation in feed efficiency in fish that can be used to genetically improve feed efficiency in fish species. This may improve both the economic efficiency of production and sustainability of aquaculture.' 

Read more about Wendy's research on feed efficiency!
  • 'Strong effect of long-term Sparicotyle chrysophrii infection on the cellular and innate immune responses of gilthead sea bream, Sparus aurata' in Developmental & Comparative ImmunologyBy M.A. Henry, C. Nikoloudaki, C. Tsigenopoulos and G. Rigos
  • 'A comprehensive survey on selective breeding programs and seed market in the European aquaculture fish industry' in Aquaculture International. By H. Chavanne, K. Janssen, J. Hofherr, F. Contini, P. Haffray, Aquatrace Consortium, H. Komen, E. Eg Nielsen and L. Bargelloni 
  • 'Impact of selective breeding on European aquaculture' in Aquaculture. By K. Janssen, H. Chavanne, P. Berentsen and H. Komen
  • 'Effect of assortative mating on genetic gain and inbreeding in aquaculture selective breeding programs' in Aquaculture. By M. Saura, B. Villanueva, J. Fernández and M. A. Toro
FISHBOOST General Assembly 2016

FISHBOOST had its annual General Assembly in Heraklion, Crete on 26-27 April 2016. Nearly halfway through the project, almost all the experiments are carried out and a number of analyses are well underway. 

Read more

(photo credit: Nofima, 2016)
The research leading to these results has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement n° 613611 - FISHBOOST.

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