fishboost is finalizing!...newsletter january 2019 view this email in y our browser in this edition:...

11
Newsletter January 2019 View this email in your browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research- oriented European education process Breeding programmes prove their worth The importance of ensuring genetic variability when establishing aquaculture breeding programmes Use of DNA pooling of the training set to reduce genotyping costs for genomic selection Two well-visited FISHBOOST sessions at European Aquaculture Society meeting In the spotlight: Andrea Doeschl- Wilson and Santiago Cabaleiro Martinez This newsletter updates you on recent developments in aquaculture breeding and the FISHBOOST project. This is FISHBOOST: 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. www.fishboost.eu FISHBOOST is finalizing! FISHBOOST had its final meeting in Brussels with an open session to policymakers and other stakeholders on January Subscribe Past Issues RSS Translate

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Page 1: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

Newsletter January 2019 View this email in your browser

In this edition

FISHBOOST is finalizingFISHBOOST announcementsThe role of FISHBOOST in research-oriented European education processBreeding programmes prove theirworthThe importance of ensuring geneticvariability when establishingaquaculture breeding programmesUse of DNA pooling of the trainingset to reduce genotyping costs forgenomic selectionTwo well-visited FISHBOOSTsessions at European AquacultureSociety meetingIn the spotlight Andrea Doeschl-Wilson and Santiago CabaleiroMartinez

This newsletter updates you on recent

developments in aquaculture breeding

and the FISHBOOST project This is FISHBOOST

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

wwwfishboosteu

FISHBOOST is finalizing

FISHBOOST had its final meeting in Brussels with an open session to policymakers and other stakeholders on January

Subscribe Past Issues RSSTranslate

22-23 2019 While the first day focused on the progress since last Annual Meeting second day focused on the impact FISHBOOSTcreated in the European aquaculture breeding and production sector Following the introduction of the main activitiesand research in FISHBOOST the industry stakeholders in FISHBOOSTSYSAAF Salmobreed and Klatryb were giventhe floor to explain their role in FISHBOOST and FISHBOOST impact in their companies The audience also had the chance to view the FISHBOOST Impact movie produced by NOFIMA during the meetingResults of the survey and round table discussions during Farmers Day event and Advanced Breeding Training werepresented by Anna Sonesson the FISHBOOST Coordinator The meeting was closed with the Horizon 2020presentation of Marta Iglesias from the European Commission and the demonstration of the Aquaculture App byFrancois Allal from Ifremer

FISHBOOST announcements Following the last General Assembly where Labogena have introduced you to their idea to create new tools toimplement the results of the FISHBOOST project They are enthusiastic to inform you that they plan to create a newldquoFishboost DNA SNP-CHIPrdquo with the following species Sea Bream 76 SNPs Carp 219 SNPs Rainbow Trout 1048 SNPs This chip will be used for the Fishboost project purposes and Labogena will be glad to discuss with you if you haveany interest for any other use eg add Sea-Bass SNPs or other species if there is any interest For furtherdiscussion please contact Julien Pradelles

The role of FISHBOOST in research-oriented European education processMartin Prchal (USB) FISHBOOST is a European research project that benefits from collaborations between top research Europeaninstitutions focused on animal breeding Within the various research groups PhD students work on their dissertationtopics Kasper Janssen PhD candidate at Wageningen University department of Animal Breeding and Genetics workson the economic evaluation of breeding programs and Cleacutemence Fraslin PhD candidate at INRA (Jouy-en-JosasFrance) in collaboration with the SYSAAF (French Poultry and Aquaculture Breeders Association) aims to investigatethe genetic architecture of rainbow trout response to Flavobacterium psychrophilum the causative agent of BacterialCold Water Disease Cleacutemence will defend her work on December 20th in Paris Recently FISHBOOSTrsquos first PhDcandidate Martin Prchal defended his thesis Martin was a PhD student at the University of South Bohemia in Českeacute Budějovice (USB) Czech Republic His workfocussed on common carp breeding Martin contributed to four research papers within the FISHBOOST project eitheras first author or co-author Martin is the first PhD student from FISHBOOST that defended his PhD thesis and isentitled ldquoEstimation of genetic variation of performance traits in common carp to predict potential of selectivebreeding under pond management conditionsrdquo The defence was on 20th September 2018 and can be viewed onlinehttpalphafrovjcuczeduartfrov2018phd_def03_prchal During the study Martin had the opportunity to collaborate with FISHBOOST partners to mutually share theirknowledge skills and infrastructure Martin also trained his presentation skills when informing and discussing aboutplans and results on the annual general assemblies of the FISHBOOST project Moreover he stayed one monthabroad for collaboration with the Natural Resources Institute (LUKE) Jokioinen in Finland one of the FISHBOOST

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partners Under supervision of Dr Antti Kause he learnt more about the quantitative genetics of fish and especiallyabout estimation of genetic parameters and possibilities to set up the selective breeding program in common carpDue to this close collaboration with experts from various fields solid results could be published in highly valuedjournals Common carp is a highly important fish species in European aquaculture Yet genetic improvement via selectivebreeding has not been developed The thesis of Martin investigated the use of modern selection methods in geneticimprovement of eg growth or slaughter yields and showed there is great potential Base populations of commoncarp have recently been established in cooperation with the Klatovy fish farm another FISHBOOST partner Moreoverthe first selection challenge for faster growth was applied Hence FISHBOOST has significantly contributed toknowledge that supports the importance of selective breeding in common carp and also fulfilled the main aim relatedto the shifting of selective breeding in this species to the first level

Breeding programmes prove their worth Rob Fletcher (orginally published at The Fish Site) The benefits that salmon farmers obtain by sourcing their stocks from cutting-edge breeding programmes arechronically undervalued according to a new study The study lsquoCost-benefit analysis of a breeding program forAtlantic salmonrsquo estimated the economic impacts of genetic improvement focusing on traits such as improvedgrowth rates lower FCRs better fillet yields and improved resistance to sea lice Results were obtained by simulationof a breeding programme that was based on the breeding programme used by SalmoBreed prior to 2016 The results of the project were presented to delegates at Aqua2018 in Montpellier by Kasper Janssen ldquoThe aim is toquantify the benefits that farmers gain from genetic improvement every generation ndash both by traditional familybreeding programmes and by the use of genomic selection ndash as the economic benefits that producers get from thebreeding companies hasnrsquot been effectively calculated beforerdquo explained Kasper Janssen from WageningenUniversity who presented the research at Aqua2018 in Montpellier last week

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The first part of the study which calculated the economic impacts of a generation produced by family selection wherethe emphasis on breeding goal traits is at its economic optimum found that the combined effect of improving growthand FCR would increase profit by euro245 per tonne of salmon produced per generation and a saving in terms of licetreatments of euro8 per tonne of salmon produced by reducing the average treatments per cycle from 37 to 36Overall according to the study using a strain produced by family selection led to a small increase in productionvolumes as well as cost savings resulting in a profit increase of euro275tonne per generation The study forecasts that the annual genetic gain should equate to euro50-80 per tonne of salmon produced per yearThe second part of the study looked at the economic impact of a generation produced by genomic selection and theresults suggest an even higher increase in profit for the producers with growth rate up an additional 4 percent FCRdown 8 percent more sea lice resistance up an extra 9 percent and fillet yield up 4 percent ndash leading to aeuro291tonne benefit for the farmer per generation (every 37 years) Moreover the study forecasts that the annual genetic gain should equate to euro50-80 per tonne per year And giventhat each egg leads to an average yield of 38 kg the genetic potential of an egg would thereby increase by euro020-030 per year despite the sales price of each egg being less than euro020 and typically increasing by only ~euro001 peryear Whether the rate of economic improvement per generation will be linear remains to be seen As Janssen reflects ldquoI expect that such results can be sustained over generations although they become moreuncertain towards the future As long as genetic diversity is maintained by controlling the rate of inbreeding (whichall breeding companies should) trait levels will be improved by selection Their effect on farm profit may however benon-linear such that future economic gains may change On the other hand gains may even increase withimprovements in genomic techniquesrdquo He also adds the caveat that his study was not able to take all variables into account Despite this however he feelsthat the underlying conclusions of the research are both striking and sound

Subscribe Past Issues RSSTranslate

ldquoItrsquos important to note that actual economic gain may have been different from the results of the study because inreality the emphasis on breeding goal traits differs genetic parameters may be different and more traits areincluded in the breeding goal ndash for example resistance to IPN PD AGD However the results suggest a significantundervaluation of genetic improvement by salmon producers Moreover consumers should also benefit from lowerprices caused by the improvements in production efficiencies while the environmental impact of production will alsobe reducedrdquo Janssen concludes

httpsthefishsitecomarticlesbreeding-programmes-prove-their-worth

The importance of ensuring genetic variability when establishing aquaculturebreeding programmes Mariacutea Saura (INIA Spain)

Designing base populations with appropriate levels of genetic variability is fundamental to ensure the viability of aquaculture breeding

programmes Using genomic data obtained within FISHBOOST INIA has determined the genetic status of commercial populations of

turbot gilthead seabream European seabass and common carp and shown the need of broadening the genetic composition of base

populations from which selection programmes start and the application of strategies for maintaining genetic diversity once the

programmes are in operation Importance of optimising the creation of base populations The success of any breeding programme critically depends on the way in which the base population of breeders isbuilt as the genetic variability initially available will determine the genetic progress achieved This is particularlyimportant in aquaculture since given the high fecundity of fish base populations can be created from very fewindividuals leading to large losses in genetic variability and increased risk of inbreeding depression (ie reduction ofperformance due to inbreeding) that can compromise the viability of the programmes Genetic variability and effective population size The rate of loss of genetic variability is directly related to the rate at which inbreeding increases and inversely relatedwith the effective population size a population parameter that can be estimated from genomic information Usingdata obtained within FISHBOOST INIA has estimated current and ancestral effective population size in populations ofturbot gilthead seabream European seabass and common carp Data used came from different challenge testscarried out in the project and corresponded to the broodstock used for creating the families challenged Thesebroodstock were sampled from different commercial European breeding programmes Turbot data were obtainedfrom the broodstock maintained at CETGA (Aquaculture Cluster of Galicia Spain) a population that is representativeof the main European breeding programmes that have the same Atlantic origin Seabream data came from twodifferent breeding programmes carried out at Ferme Marine du Douhet (FMD France) and the Andromeda Group(Greece) Carp data came from the broodstock of the Amur Mirror Carp strain recently created at the University ofSouth Bohemia (Czech Republic) from crosses between two different strains Fish were genotyped for thousands ofSingle Nucleotide Polymorphisms (SNPs) obtained using genotyping-by-sequencing (RAD-sequencing) and estimatesof current and ancestral effective population size from linkage disequilibrium measures were obtained Genetic status of turbot seabream seabass and carp commercial populations Results obtained from the analysis of genomic information revealed that current effective population size for allpopulations analysed was lower than the critical value of 50 individuals that is recommended to avoid inbreedingdepression and retain fitness in the short-term Specifically estimates for turbot seabream Andromeda seabreamFMD seabass and carp were 28 40 41 38 and 22 fish respectively These low estimates could be due to the way inwhich base populations were established (low number of breeding individuals andor strong relationships betweenthem) orand to a suboptimal inbreeding control Estimates of effective population size across time evidencedbottlenecks 4 - 11 generations ago This point in time coincides with the number of generations for which turbotseabream and seabass have been domesticated or for which selection programmes have been practised The recent

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creation of the carp strain analysed also coincides with the observed bottleneck

Estimates of effective population size (Ne) across the last 20 generations for the different populations analysed

Implications Our results highlight the need of broadening the genetic composition of base populations from which selectionprogrammes start These results also suggest that methods designed to increase the effective population size withinall farm populations analysed need to be implemented in order to ensure the sustainability of the breedingprogrammes Performing artificial fertilization and single-pair matings as well as implementing Optimal ContributionSelection and factorial mating designs would be recommendable practices This study was performed by M Saura A Fernaacutendez J Fernaacutendez and B Villanueva (INIA) Software for estimating effective population

size was facilitated by A Caballero (Universidad de Vigo Spain) and E Santiago (Universidad de Oviedo Spain) Data analysed was

provided by CETGA (S Cabaleiro) GENEAQUA (P Martiacutenez A Millaacuten) USB (M Kocour M Prchal) UEDIN (C Palaiokostas Ross Houston)

ANDROMEDA (T Kostas) NOFIMA (ML Aslam) UNIPD (L Bargelloni) SYSAAF (P Haffray) and FMD (JS Bruant)

Use of DNA pooling of the training set to reduce genotyping costs for genomicselection Anna Kristina Sonesson (NOFIMA) DNA pooling of the training population for genomic selection is a method that reduces genotyping costs while maintaininghigh selection accuracy for large populations Here we present results from experiments of both real and lsquoin silicorsquo DNApooling in Atlantic salmon In aquaculture breeding genomic selection is mainly used for traits that are not measured on the selection candidatesbecause they are invasive but instead they are measured on sibs of the selection candidates Examples of these aredisease resistance and fillet quality and they often constitute a large group of the traits in the breeding goals of well-developed breeding programs Phenotypic and genomic information must be obtained from the training set of individualsie the sibs of the candidates The effects of the SNPs estimated in this dataset are thereafter used to predict genomicbreeding values of the selection candidates With large numbers of traits and individuals per trait (15-50 per family) the totalnumber of individuals to genotype becomes large Methods that reduce genotyping costs for genomic selection aretherefore important for genomic selection to be widely implemented in aquaculture breeding schemes Equal amounts of DNA from individuals can be pooled and thereafter genotyped resulting in genotyping of much fewer

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samples than individual genotyping In a large data set of~7000 Atlantic salmon that had been challenge tested forPancreas Disease (PD) and genotyped individually with a55 kSNP chip the accuracy of genomic selection was0718 We did lsquoin silicorsquo DNA pooling of the phenotypicextremes into 200 pools of SURVIVORS (that survived thewhole challenge test) and 200 pools of MORTALITIES (thatdied earliest in the test) which thus would result in 400genotypes in total This dataset resulted in an accuracy ofselection of 0693 In a smaller dataset also on PD thereduction in accuracy of selection was larger Hence thedataset must be designed to get enough phenotypicvariation for the DNA pooling to work well Here we studied

a trait where we could get large phenotypic differences (a binary trait with heritability of ~03) which has probablyinfluenced the positive results In a smaller dataset of Atlantic salmon also tested for PDand individually genotyped with a SNP chip the selectionaccuracy was 0737 DNA from these same individualswere in vivo pooled into two replicates of SURVIVORS andMORTALITIES pools each with ~200 individuals from ~30families When these pools were sequenced 40x selectionaccuracy was 0716 When these pools were genotypedwith a SNP chip and relative light intensities were used toestimate SNP alleles frequencies in the pools the accuracyof selection was 0690 In conclusion genotyping costs of genomic selection canbe dramatically reduced when performing DNA pooling of extreme phenotypes of the training population Selectionaccuracies were slightly reduced compared to individual genotyping but this reduction became smaller when the number ofpools increased The methodology worked best in large populations This work was done in collaboration between SalmoBreed AS Marine Harvest Nofima Norwegian University of Life Sciences Please contact

annasonessonnofimano if you have questions Photo credits to Frank Gregersen and Nofima

Two well-visited FISHBOOST sessions at European Aquaculture Society meeting This yearsrsquo European Aquaculture Society meeting was co-organised with the World Aquaculture Society and was heldin Montpellier France in the end of August FISHBOOSThad two very well-visited sessions at this conference One session was part of the Industry Forum where industryrelevance is in focus Overviews of the FISHBOOST resultsso far were presented The covered topics wereimprovement of disease and production efficiency traitsgenetic gains and profitability of breeding programsmanagement of inbreeding and genomic selection At theend of that session Dr Nikos Zampoukas from the

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European Commission was invited to present the new Framework Program Horizon Europe

This was followed up by a round table discussion on the future research needs within the aquaculturebreeding field The results from that discussion will be summarized and sent as input for future calls tothe European Commission via the Farm Animal Breeding and Reproduction Technology Platform

(FABRE TP) You can read more about the FABRE TP here httpwwwfabretpeu The second session was a technical session with eight presentations on the latest results from the project

The importance of ensuring genetic variability when establishing selection programmes in aquaculture B VillanuevaM Saura A Caballero E Santiago E Morales A Fernaacutendez J Fernaacutendez S Cabaleiro P Martiacutenez A Millaacuten CPalaiokostas M Kocour R Houston M Prchal L Bargelloni KTzokasGenomic selection analyses results on common carp European seabass gilthead beabream and turbot AKSonesson C Palaiokostas RD Houston B Dagnachew ML Aslam THE MeuwissenMapping sequencing and functional annotation of a QTL region affecting resistance to koi herpesvirus in commoncarp RD Houston C Palaiokostas D Robledo T Vesely M Prchal D Pokorova V Piackova L Pojezdal MKocourA closer look at turbot genome reveals a genetic component of parasite resistance new tools for selection PMartiacutenez F Maroso M Saura A Fernaacutendez A Blanco M Hermida S Cabaleiro A Doeschl-Wilson O AnacletoR Houston A Millaacuten J Fernaacutendez L Bargelloni G dalla Rovere MA Toro MJ Carabantildeo C Bouza BVillanuevaUse of DNA pooling in genomic selection for a disease trait in Atlantic salmon B Dagnachew A K SonessonTHE MeuwissenSuccessful realized selection response for fillet yield in rainbow trout (Oncorhynchus mykiss) M Vandeputte JBugeon A Bestin A Desgranges S Courant J-M Allamellou AS Tyran F Allal M Dupont-Nivet P HaffrayPotential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictorsM Prchal J Bugeon M Vandeputte A Kause A Vergnet J Zhao D Gela L Genestout A Bestin P Haffray MKocourOptimal schemes for advancing selective breeding to the next level for the main species of European aquaculture BVillanueva S Garciacutea-Ballesteros J FernaacutendezCost-benefit analysis of a breeding program for Atlantic salmon K Janssen H Saatkamp H Komen

A summary of this session can be found at of wwwaquaeaseu Thanks to everybody that has visited the FISHBOOST sessions at this and previous EAS meetings for stimulatingdiscussions

In the spotlight Andrea Doeschl-Wilson (The Roslin Institute) Irsquom contributing to the disease resistance workpackage (WP1) Specifically we are looking at how the genetics of individualsaffects disease spread and survival in fish populations In addition to the conventional trait lsquodisease resistancersquo we considernew traits (disease phenotypes) such as tolerance and infectivity We know from theory that all of these traits also have astrong influence on disease spread and resulting mortality rates However at present very little is known about the genetic regulation of these traits and whether it is possible to breed fishthat are not only genetically less prone to becoming infected but also less likely to transmit infection once infected andpossibly also more likely to survive or recover from infections If this was possible genetic selection would be a powerful toolto prevent disease outbreaks ndash potentially much more powerful than selection on survival which is the current practice In

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FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

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experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

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technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

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Page 2: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

22-23 2019 While the first day focused on the progress since last Annual Meeting second day focused on the impact FISHBOOSTcreated in the European aquaculture breeding and production sector Following the introduction of the main activitiesand research in FISHBOOST the industry stakeholders in FISHBOOSTSYSAAF Salmobreed and Klatryb were giventhe floor to explain their role in FISHBOOST and FISHBOOST impact in their companies The audience also had the chance to view the FISHBOOST Impact movie produced by NOFIMA during the meetingResults of the survey and round table discussions during Farmers Day event and Advanced Breeding Training werepresented by Anna Sonesson the FISHBOOST Coordinator The meeting was closed with the Horizon 2020presentation of Marta Iglesias from the European Commission and the demonstration of the Aquaculture App byFrancois Allal from Ifremer

FISHBOOST announcements Following the last General Assembly where Labogena have introduced you to their idea to create new tools toimplement the results of the FISHBOOST project They are enthusiastic to inform you that they plan to create a newldquoFishboost DNA SNP-CHIPrdquo with the following species Sea Bream 76 SNPs Carp 219 SNPs Rainbow Trout 1048 SNPs This chip will be used for the Fishboost project purposes and Labogena will be glad to discuss with you if you haveany interest for any other use eg add Sea-Bass SNPs or other species if there is any interest For furtherdiscussion please contact Julien Pradelles

The role of FISHBOOST in research-oriented European education processMartin Prchal (USB) FISHBOOST is a European research project that benefits from collaborations between top research Europeaninstitutions focused on animal breeding Within the various research groups PhD students work on their dissertationtopics Kasper Janssen PhD candidate at Wageningen University department of Animal Breeding and Genetics workson the economic evaluation of breeding programs and Cleacutemence Fraslin PhD candidate at INRA (Jouy-en-JosasFrance) in collaboration with the SYSAAF (French Poultry and Aquaculture Breeders Association) aims to investigatethe genetic architecture of rainbow trout response to Flavobacterium psychrophilum the causative agent of BacterialCold Water Disease Cleacutemence will defend her work on December 20th in Paris Recently FISHBOOSTrsquos first PhDcandidate Martin Prchal defended his thesis Martin was a PhD student at the University of South Bohemia in Českeacute Budějovice (USB) Czech Republic His workfocussed on common carp breeding Martin contributed to four research papers within the FISHBOOST project eitheras first author or co-author Martin is the first PhD student from FISHBOOST that defended his PhD thesis and isentitled ldquoEstimation of genetic variation of performance traits in common carp to predict potential of selectivebreeding under pond management conditionsrdquo The defence was on 20th September 2018 and can be viewed onlinehttpalphafrovjcuczeduartfrov2018phd_def03_prchal During the study Martin had the opportunity to collaborate with FISHBOOST partners to mutually share theirknowledge skills and infrastructure Martin also trained his presentation skills when informing and discussing aboutplans and results on the annual general assemblies of the FISHBOOST project Moreover he stayed one monthabroad for collaboration with the Natural Resources Institute (LUKE) Jokioinen in Finland one of the FISHBOOST

Subscribe Past Issues RSSTranslate

partners Under supervision of Dr Antti Kause he learnt more about the quantitative genetics of fish and especiallyabout estimation of genetic parameters and possibilities to set up the selective breeding program in common carpDue to this close collaboration with experts from various fields solid results could be published in highly valuedjournals Common carp is a highly important fish species in European aquaculture Yet genetic improvement via selectivebreeding has not been developed The thesis of Martin investigated the use of modern selection methods in geneticimprovement of eg growth or slaughter yields and showed there is great potential Base populations of commoncarp have recently been established in cooperation with the Klatovy fish farm another FISHBOOST partner Moreoverthe first selection challenge for faster growth was applied Hence FISHBOOST has significantly contributed toknowledge that supports the importance of selective breeding in common carp and also fulfilled the main aim relatedto the shifting of selective breeding in this species to the first level

Breeding programmes prove their worth Rob Fletcher (orginally published at The Fish Site) The benefits that salmon farmers obtain by sourcing their stocks from cutting-edge breeding programmes arechronically undervalued according to a new study The study lsquoCost-benefit analysis of a breeding program forAtlantic salmonrsquo estimated the economic impacts of genetic improvement focusing on traits such as improvedgrowth rates lower FCRs better fillet yields and improved resistance to sea lice Results were obtained by simulationof a breeding programme that was based on the breeding programme used by SalmoBreed prior to 2016 The results of the project were presented to delegates at Aqua2018 in Montpellier by Kasper Janssen ldquoThe aim is toquantify the benefits that farmers gain from genetic improvement every generation ndash both by traditional familybreeding programmes and by the use of genomic selection ndash as the economic benefits that producers get from thebreeding companies hasnrsquot been effectively calculated beforerdquo explained Kasper Janssen from WageningenUniversity who presented the research at Aqua2018 in Montpellier last week

Subscribe Past Issues RSSTranslate

The first part of the study which calculated the economic impacts of a generation produced by family selection wherethe emphasis on breeding goal traits is at its economic optimum found that the combined effect of improving growthand FCR would increase profit by euro245 per tonne of salmon produced per generation and a saving in terms of licetreatments of euro8 per tonne of salmon produced by reducing the average treatments per cycle from 37 to 36Overall according to the study using a strain produced by family selection led to a small increase in productionvolumes as well as cost savings resulting in a profit increase of euro275tonne per generation The study forecasts that the annual genetic gain should equate to euro50-80 per tonne of salmon produced per yearThe second part of the study looked at the economic impact of a generation produced by genomic selection and theresults suggest an even higher increase in profit for the producers with growth rate up an additional 4 percent FCRdown 8 percent more sea lice resistance up an extra 9 percent and fillet yield up 4 percent ndash leading to aeuro291tonne benefit for the farmer per generation (every 37 years) Moreover the study forecasts that the annual genetic gain should equate to euro50-80 per tonne per year And giventhat each egg leads to an average yield of 38 kg the genetic potential of an egg would thereby increase by euro020-030 per year despite the sales price of each egg being less than euro020 and typically increasing by only ~euro001 peryear Whether the rate of economic improvement per generation will be linear remains to be seen As Janssen reflects ldquoI expect that such results can be sustained over generations although they become moreuncertain towards the future As long as genetic diversity is maintained by controlling the rate of inbreeding (whichall breeding companies should) trait levels will be improved by selection Their effect on farm profit may however benon-linear such that future economic gains may change On the other hand gains may even increase withimprovements in genomic techniquesrdquo He also adds the caveat that his study was not able to take all variables into account Despite this however he feelsthat the underlying conclusions of the research are both striking and sound

Subscribe Past Issues RSSTranslate

ldquoItrsquos important to note that actual economic gain may have been different from the results of the study because inreality the emphasis on breeding goal traits differs genetic parameters may be different and more traits areincluded in the breeding goal ndash for example resistance to IPN PD AGD However the results suggest a significantundervaluation of genetic improvement by salmon producers Moreover consumers should also benefit from lowerprices caused by the improvements in production efficiencies while the environmental impact of production will alsobe reducedrdquo Janssen concludes

httpsthefishsitecomarticlesbreeding-programmes-prove-their-worth

The importance of ensuring genetic variability when establishing aquaculturebreeding programmes Mariacutea Saura (INIA Spain)

Designing base populations with appropriate levels of genetic variability is fundamental to ensure the viability of aquaculture breeding

programmes Using genomic data obtained within FISHBOOST INIA has determined the genetic status of commercial populations of

turbot gilthead seabream European seabass and common carp and shown the need of broadening the genetic composition of base

populations from which selection programmes start and the application of strategies for maintaining genetic diversity once the

programmes are in operation Importance of optimising the creation of base populations The success of any breeding programme critically depends on the way in which the base population of breeders isbuilt as the genetic variability initially available will determine the genetic progress achieved This is particularlyimportant in aquaculture since given the high fecundity of fish base populations can be created from very fewindividuals leading to large losses in genetic variability and increased risk of inbreeding depression (ie reduction ofperformance due to inbreeding) that can compromise the viability of the programmes Genetic variability and effective population size The rate of loss of genetic variability is directly related to the rate at which inbreeding increases and inversely relatedwith the effective population size a population parameter that can be estimated from genomic information Usingdata obtained within FISHBOOST INIA has estimated current and ancestral effective population size in populations ofturbot gilthead seabream European seabass and common carp Data used came from different challenge testscarried out in the project and corresponded to the broodstock used for creating the families challenged Thesebroodstock were sampled from different commercial European breeding programmes Turbot data were obtainedfrom the broodstock maintained at CETGA (Aquaculture Cluster of Galicia Spain) a population that is representativeof the main European breeding programmes that have the same Atlantic origin Seabream data came from twodifferent breeding programmes carried out at Ferme Marine du Douhet (FMD France) and the Andromeda Group(Greece) Carp data came from the broodstock of the Amur Mirror Carp strain recently created at the University ofSouth Bohemia (Czech Republic) from crosses between two different strains Fish were genotyped for thousands ofSingle Nucleotide Polymorphisms (SNPs) obtained using genotyping-by-sequencing (RAD-sequencing) and estimatesof current and ancestral effective population size from linkage disequilibrium measures were obtained Genetic status of turbot seabream seabass and carp commercial populations Results obtained from the analysis of genomic information revealed that current effective population size for allpopulations analysed was lower than the critical value of 50 individuals that is recommended to avoid inbreedingdepression and retain fitness in the short-term Specifically estimates for turbot seabream Andromeda seabreamFMD seabass and carp were 28 40 41 38 and 22 fish respectively These low estimates could be due to the way inwhich base populations were established (low number of breeding individuals andor strong relationships betweenthem) orand to a suboptimal inbreeding control Estimates of effective population size across time evidencedbottlenecks 4 - 11 generations ago This point in time coincides with the number of generations for which turbotseabream and seabass have been domesticated or for which selection programmes have been practised The recent

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creation of the carp strain analysed also coincides with the observed bottleneck

Estimates of effective population size (Ne) across the last 20 generations for the different populations analysed

Implications Our results highlight the need of broadening the genetic composition of base populations from which selectionprogrammes start These results also suggest that methods designed to increase the effective population size withinall farm populations analysed need to be implemented in order to ensure the sustainability of the breedingprogrammes Performing artificial fertilization and single-pair matings as well as implementing Optimal ContributionSelection and factorial mating designs would be recommendable practices This study was performed by M Saura A Fernaacutendez J Fernaacutendez and B Villanueva (INIA) Software for estimating effective population

size was facilitated by A Caballero (Universidad de Vigo Spain) and E Santiago (Universidad de Oviedo Spain) Data analysed was

provided by CETGA (S Cabaleiro) GENEAQUA (P Martiacutenez A Millaacuten) USB (M Kocour M Prchal) UEDIN (C Palaiokostas Ross Houston)

ANDROMEDA (T Kostas) NOFIMA (ML Aslam) UNIPD (L Bargelloni) SYSAAF (P Haffray) and FMD (JS Bruant)

Use of DNA pooling of the training set to reduce genotyping costs for genomicselection Anna Kristina Sonesson (NOFIMA) DNA pooling of the training population for genomic selection is a method that reduces genotyping costs while maintaininghigh selection accuracy for large populations Here we present results from experiments of both real and lsquoin silicorsquo DNApooling in Atlantic salmon In aquaculture breeding genomic selection is mainly used for traits that are not measured on the selection candidatesbecause they are invasive but instead they are measured on sibs of the selection candidates Examples of these aredisease resistance and fillet quality and they often constitute a large group of the traits in the breeding goals of well-developed breeding programs Phenotypic and genomic information must be obtained from the training set of individualsie the sibs of the candidates The effects of the SNPs estimated in this dataset are thereafter used to predict genomicbreeding values of the selection candidates With large numbers of traits and individuals per trait (15-50 per family) the totalnumber of individuals to genotype becomes large Methods that reduce genotyping costs for genomic selection aretherefore important for genomic selection to be widely implemented in aquaculture breeding schemes Equal amounts of DNA from individuals can be pooled and thereafter genotyped resulting in genotyping of much fewer

Subscribe Past Issues RSSTranslate

samples than individual genotyping In a large data set of~7000 Atlantic salmon that had been challenge tested forPancreas Disease (PD) and genotyped individually with a55 kSNP chip the accuracy of genomic selection was0718 We did lsquoin silicorsquo DNA pooling of the phenotypicextremes into 200 pools of SURVIVORS (that survived thewhole challenge test) and 200 pools of MORTALITIES (thatdied earliest in the test) which thus would result in 400genotypes in total This dataset resulted in an accuracy ofselection of 0693 In a smaller dataset also on PD thereduction in accuracy of selection was larger Hence thedataset must be designed to get enough phenotypicvariation for the DNA pooling to work well Here we studied

a trait where we could get large phenotypic differences (a binary trait with heritability of ~03) which has probablyinfluenced the positive results In a smaller dataset of Atlantic salmon also tested for PDand individually genotyped with a SNP chip the selectionaccuracy was 0737 DNA from these same individualswere in vivo pooled into two replicates of SURVIVORS andMORTALITIES pools each with ~200 individuals from ~30families When these pools were sequenced 40x selectionaccuracy was 0716 When these pools were genotypedwith a SNP chip and relative light intensities were used toestimate SNP alleles frequencies in the pools the accuracyof selection was 0690 In conclusion genotyping costs of genomic selection canbe dramatically reduced when performing DNA pooling of extreme phenotypes of the training population Selectionaccuracies were slightly reduced compared to individual genotyping but this reduction became smaller when the number ofpools increased The methodology worked best in large populations This work was done in collaboration between SalmoBreed AS Marine Harvest Nofima Norwegian University of Life Sciences Please contact

annasonessonnofimano if you have questions Photo credits to Frank Gregersen and Nofima

Two well-visited FISHBOOST sessions at European Aquaculture Society meeting This yearsrsquo European Aquaculture Society meeting was co-organised with the World Aquaculture Society and was heldin Montpellier France in the end of August FISHBOOSThad two very well-visited sessions at this conference One session was part of the Industry Forum where industryrelevance is in focus Overviews of the FISHBOOST resultsso far were presented The covered topics wereimprovement of disease and production efficiency traitsgenetic gains and profitability of breeding programsmanagement of inbreeding and genomic selection At theend of that session Dr Nikos Zampoukas from the

Subscribe Past Issues RSSTranslate

European Commission was invited to present the new Framework Program Horizon Europe

This was followed up by a round table discussion on the future research needs within the aquaculturebreeding field The results from that discussion will be summarized and sent as input for future calls tothe European Commission via the Farm Animal Breeding and Reproduction Technology Platform

(FABRE TP) You can read more about the FABRE TP here httpwwwfabretpeu The second session was a technical session with eight presentations on the latest results from the project

The importance of ensuring genetic variability when establishing selection programmes in aquaculture B VillanuevaM Saura A Caballero E Santiago E Morales A Fernaacutendez J Fernaacutendez S Cabaleiro P Martiacutenez A Millaacuten CPalaiokostas M Kocour R Houston M Prchal L Bargelloni KTzokasGenomic selection analyses results on common carp European seabass gilthead beabream and turbot AKSonesson C Palaiokostas RD Houston B Dagnachew ML Aslam THE MeuwissenMapping sequencing and functional annotation of a QTL region affecting resistance to koi herpesvirus in commoncarp RD Houston C Palaiokostas D Robledo T Vesely M Prchal D Pokorova V Piackova L Pojezdal MKocourA closer look at turbot genome reveals a genetic component of parasite resistance new tools for selection PMartiacutenez F Maroso M Saura A Fernaacutendez A Blanco M Hermida S Cabaleiro A Doeschl-Wilson O AnacletoR Houston A Millaacuten J Fernaacutendez L Bargelloni G dalla Rovere MA Toro MJ Carabantildeo C Bouza BVillanuevaUse of DNA pooling in genomic selection for a disease trait in Atlantic salmon B Dagnachew A K SonessonTHE MeuwissenSuccessful realized selection response for fillet yield in rainbow trout (Oncorhynchus mykiss) M Vandeputte JBugeon A Bestin A Desgranges S Courant J-M Allamellou AS Tyran F Allal M Dupont-Nivet P HaffrayPotential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictorsM Prchal J Bugeon M Vandeputte A Kause A Vergnet J Zhao D Gela L Genestout A Bestin P Haffray MKocourOptimal schemes for advancing selective breeding to the next level for the main species of European aquaculture BVillanueva S Garciacutea-Ballesteros J FernaacutendezCost-benefit analysis of a breeding program for Atlantic salmon K Janssen H Saatkamp H Komen

A summary of this session can be found at of wwwaquaeaseu Thanks to everybody that has visited the FISHBOOST sessions at this and previous EAS meetings for stimulatingdiscussions

In the spotlight Andrea Doeschl-Wilson (The Roslin Institute) Irsquom contributing to the disease resistance workpackage (WP1) Specifically we are looking at how the genetics of individualsaffects disease spread and survival in fish populations In addition to the conventional trait lsquodisease resistancersquo we considernew traits (disease phenotypes) such as tolerance and infectivity We know from theory that all of these traits also have astrong influence on disease spread and resulting mortality rates However at present very little is known about the genetic regulation of these traits and whether it is possible to breed fishthat are not only genetically less prone to becoming infected but also less likely to transmit infection once infected andpossibly also more likely to survive or recover from infections If this was possible genetic selection would be a powerful toolto prevent disease outbreaks ndash potentially much more powerful than selection on survival which is the current practice In

Subscribe Past Issues RSSTranslate

FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

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experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

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The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

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technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

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Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

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Page 3: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

partners Under supervision of Dr Antti Kause he learnt more about the quantitative genetics of fish and especiallyabout estimation of genetic parameters and possibilities to set up the selective breeding program in common carpDue to this close collaboration with experts from various fields solid results could be published in highly valuedjournals Common carp is a highly important fish species in European aquaculture Yet genetic improvement via selectivebreeding has not been developed The thesis of Martin investigated the use of modern selection methods in geneticimprovement of eg growth or slaughter yields and showed there is great potential Base populations of commoncarp have recently been established in cooperation with the Klatovy fish farm another FISHBOOST partner Moreoverthe first selection challenge for faster growth was applied Hence FISHBOOST has significantly contributed toknowledge that supports the importance of selective breeding in common carp and also fulfilled the main aim relatedto the shifting of selective breeding in this species to the first level

Breeding programmes prove their worth Rob Fletcher (orginally published at The Fish Site) The benefits that salmon farmers obtain by sourcing their stocks from cutting-edge breeding programmes arechronically undervalued according to a new study The study lsquoCost-benefit analysis of a breeding program forAtlantic salmonrsquo estimated the economic impacts of genetic improvement focusing on traits such as improvedgrowth rates lower FCRs better fillet yields and improved resistance to sea lice Results were obtained by simulationof a breeding programme that was based on the breeding programme used by SalmoBreed prior to 2016 The results of the project were presented to delegates at Aqua2018 in Montpellier by Kasper Janssen ldquoThe aim is toquantify the benefits that farmers gain from genetic improvement every generation ndash both by traditional familybreeding programmes and by the use of genomic selection ndash as the economic benefits that producers get from thebreeding companies hasnrsquot been effectively calculated beforerdquo explained Kasper Janssen from WageningenUniversity who presented the research at Aqua2018 in Montpellier last week

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The first part of the study which calculated the economic impacts of a generation produced by family selection wherethe emphasis on breeding goal traits is at its economic optimum found that the combined effect of improving growthand FCR would increase profit by euro245 per tonne of salmon produced per generation and a saving in terms of licetreatments of euro8 per tonne of salmon produced by reducing the average treatments per cycle from 37 to 36Overall according to the study using a strain produced by family selection led to a small increase in productionvolumes as well as cost savings resulting in a profit increase of euro275tonne per generation The study forecasts that the annual genetic gain should equate to euro50-80 per tonne of salmon produced per yearThe second part of the study looked at the economic impact of a generation produced by genomic selection and theresults suggest an even higher increase in profit for the producers with growth rate up an additional 4 percent FCRdown 8 percent more sea lice resistance up an extra 9 percent and fillet yield up 4 percent ndash leading to aeuro291tonne benefit for the farmer per generation (every 37 years) Moreover the study forecasts that the annual genetic gain should equate to euro50-80 per tonne per year And giventhat each egg leads to an average yield of 38 kg the genetic potential of an egg would thereby increase by euro020-030 per year despite the sales price of each egg being less than euro020 and typically increasing by only ~euro001 peryear Whether the rate of economic improvement per generation will be linear remains to be seen As Janssen reflects ldquoI expect that such results can be sustained over generations although they become moreuncertain towards the future As long as genetic diversity is maintained by controlling the rate of inbreeding (whichall breeding companies should) trait levels will be improved by selection Their effect on farm profit may however benon-linear such that future economic gains may change On the other hand gains may even increase withimprovements in genomic techniquesrdquo He also adds the caveat that his study was not able to take all variables into account Despite this however he feelsthat the underlying conclusions of the research are both striking and sound

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ldquoItrsquos important to note that actual economic gain may have been different from the results of the study because inreality the emphasis on breeding goal traits differs genetic parameters may be different and more traits areincluded in the breeding goal ndash for example resistance to IPN PD AGD However the results suggest a significantundervaluation of genetic improvement by salmon producers Moreover consumers should also benefit from lowerprices caused by the improvements in production efficiencies while the environmental impact of production will alsobe reducedrdquo Janssen concludes

httpsthefishsitecomarticlesbreeding-programmes-prove-their-worth

The importance of ensuring genetic variability when establishing aquaculturebreeding programmes Mariacutea Saura (INIA Spain)

Designing base populations with appropriate levels of genetic variability is fundamental to ensure the viability of aquaculture breeding

programmes Using genomic data obtained within FISHBOOST INIA has determined the genetic status of commercial populations of

turbot gilthead seabream European seabass and common carp and shown the need of broadening the genetic composition of base

populations from which selection programmes start and the application of strategies for maintaining genetic diversity once the

programmes are in operation Importance of optimising the creation of base populations The success of any breeding programme critically depends on the way in which the base population of breeders isbuilt as the genetic variability initially available will determine the genetic progress achieved This is particularlyimportant in aquaculture since given the high fecundity of fish base populations can be created from very fewindividuals leading to large losses in genetic variability and increased risk of inbreeding depression (ie reduction ofperformance due to inbreeding) that can compromise the viability of the programmes Genetic variability and effective population size The rate of loss of genetic variability is directly related to the rate at which inbreeding increases and inversely relatedwith the effective population size a population parameter that can be estimated from genomic information Usingdata obtained within FISHBOOST INIA has estimated current and ancestral effective population size in populations ofturbot gilthead seabream European seabass and common carp Data used came from different challenge testscarried out in the project and corresponded to the broodstock used for creating the families challenged Thesebroodstock were sampled from different commercial European breeding programmes Turbot data were obtainedfrom the broodstock maintained at CETGA (Aquaculture Cluster of Galicia Spain) a population that is representativeof the main European breeding programmes that have the same Atlantic origin Seabream data came from twodifferent breeding programmes carried out at Ferme Marine du Douhet (FMD France) and the Andromeda Group(Greece) Carp data came from the broodstock of the Amur Mirror Carp strain recently created at the University ofSouth Bohemia (Czech Republic) from crosses between two different strains Fish were genotyped for thousands ofSingle Nucleotide Polymorphisms (SNPs) obtained using genotyping-by-sequencing (RAD-sequencing) and estimatesof current and ancestral effective population size from linkage disequilibrium measures were obtained Genetic status of turbot seabream seabass and carp commercial populations Results obtained from the analysis of genomic information revealed that current effective population size for allpopulations analysed was lower than the critical value of 50 individuals that is recommended to avoid inbreedingdepression and retain fitness in the short-term Specifically estimates for turbot seabream Andromeda seabreamFMD seabass and carp were 28 40 41 38 and 22 fish respectively These low estimates could be due to the way inwhich base populations were established (low number of breeding individuals andor strong relationships betweenthem) orand to a suboptimal inbreeding control Estimates of effective population size across time evidencedbottlenecks 4 - 11 generations ago This point in time coincides with the number of generations for which turbotseabream and seabass have been domesticated or for which selection programmes have been practised The recent

Subscribe Past Issues RSSTranslate

creation of the carp strain analysed also coincides with the observed bottleneck

Estimates of effective population size (Ne) across the last 20 generations for the different populations analysed

Implications Our results highlight the need of broadening the genetic composition of base populations from which selectionprogrammes start These results also suggest that methods designed to increase the effective population size withinall farm populations analysed need to be implemented in order to ensure the sustainability of the breedingprogrammes Performing artificial fertilization and single-pair matings as well as implementing Optimal ContributionSelection and factorial mating designs would be recommendable practices This study was performed by M Saura A Fernaacutendez J Fernaacutendez and B Villanueva (INIA) Software for estimating effective population

size was facilitated by A Caballero (Universidad de Vigo Spain) and E Santiago (Universidad de Oviedo Spain) Data analysed was

provided by CETGA (S Cabaleiro) GENEAQUA (P Martiacutenez A Millaacuten) USB (M Kocour M Prchal) UEDIN (C Palaiokostas Ross Houston)

ANDROMEDA (T Kostas) NOFIMA (ML Aslam) UNIPD (L Bargelloni) SYSAAF (P Haffray) and FMD (JS Bruant)

Use of DNA pooling of the training set to reduce genotyping costs for genomicselection Anna Kristina Sonesson (NOFIMA) DNA pooling of the training population for genomic selection is a method that reduces genotyping costs while maintaininghigh selection accuracy for large populations Here we present results from experiments of both real and lsquoin silicorsquo DNApooling in Atlantic salmon In aquaculture breeding genomic selection is mainly used for traits that are not measured on the selection candidatesbecause they are invasive but instead they are measured on sibs of the selection candidates Examples of these aredisease resistance and fillet quality and they often constitute a large group of the traits in the breeding goals of well-developed breeding programs Phenotypic and genomic information must be obtained from the training set of individualsie the sibs of the candidates The effects of the SNPs estimated in this dataset are thereafter used to predict genomicbreeding values of the selection candidates With large numbers of traits and individuals per trait (15-50 per family) the totalnumber of individuals to genotype becomes large Methods that reduce genotyping costs for genomic selection aretherefore important for genomic selection to be widely implemented in aquaculture breeding schemes Equal amounts of DNA from individuals can be pooled and thereafter genotyped resulting in genotyping of much fewer

Subscribe Past Issues RSSTranslate

samples than individual genotyping In a large data set of~7000 Atlantic salmon that had been challenge tested forPancreas Disease (PD) and genotyped individually with a55 kSNP chip the accuracy of genomic selection was0718 We did lsquoin silicorsquo DNA pooling of the phenotypicextremes into 200 pools of SURVIVORS (that survived thewhole challenge test) and 200 pools of MORTALITIES (thatdied earliest in the test) which thus would result in 400genotypes in total This dataset resulted in an accuracy ofselection of 0693 In a smaller dataset also on PD thereduction in accuracy of selection was larger Hence thedataset must be designed to get enough phenotypicvariation for the DNA pooling to work well Here we studied

a trait where we could get large phenotypic differences (a binary trait with heritability of ~03) which has probablyinfluenced the positive results In a smaller dataset of Atlantic salmon also tested for PDand individually genotyped with a SNP chip the selectionaccuracy was 0737 DNA from these same individualswere in vivo pooled into two replicates of SURVIVORS andMORTALITIES pools each with ~200 individuals from ~30families When these pools were sequenced 40x selectionaccuracy was 0716 When these pools were genotypedwith a SNP chip and relative light intensities were used toestimate SNP alleles frequencies in the pools the accuracyof selection was 0690 In conclusion genotyping costs of genomic selection canbe dramatically reduced when performing DNA pooling of extreme phenotypes of the training population Selectionaccuracies were slightly reduced compared to individual genotyping but this reduction became smaller when the number ofpools increased The methodology worked best in large populations This work was done in collaboration between SalmoBreed AS Marine Harvest Nofima Norwegian University of Life Sciences Please contact

annasonessonnofimano if you have questions Photo credits to Frank Gregersen and Nofima

Two well-visited FISHBOOST sessions at European Aquaculture Society meeting This yearsrsquo European Aquaculture Society meeting was co-organised with the World Aquaculture Society and was heldin Montpellier France in the end of August FISHBOOSThad two very well-visited sessions at this conference One session was part of the Industry Forum where industryrelevance is in focus Overviews of the FISHBOOST resultsso far were presented The covered topics wereimprovement of disease and production efficiency traitsgenetic gains and profitability of breeding programsmanagement of inbreeding and genomic selection At theend of that session Dr Nikos Zampoukas from the

Subscribe Past Issues RSSTranslate

European Commission was invited to present the new Framework Program Horizon Europe

This was followed up by a round table discussion on the future research needs within the aquaculturebreeding field The results from that discussion will be summarized and sent as input for future calls tothe European Commission via the Farm Animal Breeding and Reproduction Technology Platform

(FABRE TP) You can read more about the FABRE TP here httpwwwfabretpeu The second session was a technical session with eight presentations on the latest results from the project

The importance of ensuring genetic variability when establishing selection programmes in aquaculture B VillanuevaM Saura A Caballero E Santiago E Morales A Fernaacutendez J Fernaacutendez S Cabaleiro P Martiacutenez A Millaacuten CPalaiokostas M Kocour R Houston M Prchal L Bargelloni KTzokasGenomic selection analyses results on common carp European seabass gilthead beabream and turbot AKSonesson C Palaiokostas RD Houston B Dagnachew ML Aslam THE MeuwissenMapping sequencing and functional annotation of a QTL region affecting resistance to koi herpesvirus in commoncarp RD Houston C Palaiokostas D Robledo T Vesely M Prchal D Pokorova V Piackova L Pojezdal MKocourA closer look at turbot genome reveals a genetic component of parasite resistance new tools for selection PMartiacutenez F Maroso M Saura A Fernaacutendez A Blanco M Hermida S Cabaleiro A Doeschl-Wilson O AnacletoR Houston A Millaacuten J Fernaacutendez L Bargelloni G dalla Rovere MA Toro MJ Carabantildeo C Bouza BVillanuevaUse of DNA pooling in genomic selection for a disease trait in Atlantic salmon B Dagnachew A K SonessonTHE MeuwissenSuccessful realized selection response for fillet yield in rainbow trout (Oncorhynchus mykiss) M Vandeputte JBugeon A Bestin A Desgranges S Courant J-M Allamellou AS Tyran F Allal M Dupont-Nivet P HaffrayPotential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictorsM Prchal J Bugeon M Vandeputte A Kause A Vergnet J Zhao D Gela L Genestout A Bestin P Haffray MKocourOptimal schemes for advancing selective breeding to the next level for the main species of European aquaculture BVillanueva S Garciacutea-Ballesteros J FernaacutendezCost-benefit analysis of a breeding program for Atlantic salmon K Janssen H Saatkamp H Komen

A summary of this session can be found at of wwwaquaeaseu Thanks to everybody that has visited the FISHBOOST sessions at this and previous EAS meetings for stimulatingdiscussions

In the spotlight Andrea Doeschl-Wilson (The Roslin Institute) Irsquom contributing to the disease resistance workpackage (WP1) Specifically we are looking at how the genetics of individualsaffects disease spread and survival in fish populations In addition to the conventional trait lsquodisease resistancersquo we considernew traits (disease phenotypes) such as tolerance and infectivity We know from theory that all of these traits also have astrong influence on disease spread and resulting mortality rates However at present very little is known about the genetic regulation of these traits and whether it is possible to breed fishthat are not only genetically less prone to becoming infected but also less likely to transmit infection once infected andpossibly also more likely to survive or recover from infections If this was possible genetic selection would be a powerful toolto prevent disease outbreaks ndash potentially much more powerful than selection on survival which is the current practice In

Subscribe Past Issues RSSTranslate

FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

Subscribe Past Issues RSSTranslate

experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

Subscribe Past Issues RSSTranslate

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate

Page 4: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

The first part of the study which calculated the economic impacts of a generation produced by family selection wherethe emphasis on breeding goal traits is at its economic optimum found that the combined effect of improving growthand FCR would increase profit by euro245 per tonne of salmon produced per generation and a saving in terms of licetreatments of euro8 per tonne of salmon produced by reducing the average treatments per cycle from 37 to 36Overall according to the study using a strain produced by family selection led to a small increase in productionvolumes as well as cost savings resulting in a profit increase of euro275tonne per generation The study forecasts that the annual genetic gain should equate to euro50-80 per tonne of salmon produced per yearThe second part of the study looked at the economic impact of a generation produced by genomic selection and theresults suggest an even higher increase in profit for the producers with growth rate up an additional 4 percent FCRdown 8 percent more sea lice resistance up an extra 9 percent and fillet yield up 4 percent ndash leading to aeuro291tonne benefit for the farmer per generation (every 37 years) Moreover the study forecasts that the annual genetic gain should equate to euro50-80 per tonne per year And giventhat each egg leads to an average yield of 38 kg the genetic potential of an egg would thereby increase by euro020-030 per year despite the sales price of each egg being less than euro020 and typically increasing by only ~euro001 peryear Whether the rate of economic improvement per generation will be linear remains to be seen As Janssen reflects ldquoI expect that such results can be sustained over generations although they become moreuncertain towards the future As long as genetic diversity is maintained by controlling the rate of inbreeding (whichall breeding companies should) trait levels will be improved by selection Their effect on farm profit may however benon-linear such that future economic gains may change On the other hand gains may even increase withimprovements in genomic techniquesrdquo He also adds the caveat that his study was not able to take all variables into account Despite this however he feelsthat the underlying conclusions of the research are both striking and sound

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ldquoItrsquos important to note that actual economic gain may have been different from the results of the study because inreality the emphasis on breeding goal traits differs genetic parameters may be different and more traits areincluded in the breeding goal ndash for example resistance to IPN PD AGD However the results suggest a significantundervaluation of genetic improvement by salmon producers Moreover consumers should also benefit from lowerprices caused by the improvements in production efficiencies while the environmental impact of production will alsobe reducedrdquo Janssen concludes

httpsthefishsitecomarticlesbreeding-programmes-prove-their-worth

The importance of ensuring genetic variability when establishing aquaculturebreeding programmes Mariacutea Saura (INIA Spain)

Designing base populations with appropriate levels of genetic variability is fundamental to ensure the viability of aquaculture breeding

programmes Using genomic data obtained within FISHBOOST INIA has determined the genetic status of commercial populations of

turbot gilthead seabream European seabass and common carp and shown the need of broadening the genetic composition of base

populations from which selection programmes start and the application of strategies for maintaining genetic diversity once the

programmes are in operation Importance of optimising the creation of base populations The success of any breeding programme critically depends on the way in which the base population of breeders isbuilt as the genetic variability initially available will determine the genetic progress achieved This is particularlyimportant in aquaculture since given the high fecundity of fish base populations can be created from very fewindividuals leading to large losses in genetic variability and increased risk of inbreeding depression (ie reduction ofperformance due to inbreeding) that can compromise the viability of the programmes Genetic variability and effective population size The rate of loss of genetic variability is directly related to the rate at which inbreeding increases and inversely relatedwith the effective population size a population parameter that can be estimated from genomic information Usingdata obtained within FISHBOOST INIA has estimated current and ancestral effective population size in populations ofturbot gilthead seabream European seabass and common carp Data used came from different challenge testscarried out in the project and corresponded to the broodstock used for creating the families challenged Thesebroodstock were sampled from different commercial European breeding programmes Turbot data were obtainedfrom the broodstock maintained at CETGA (Aquaculture Cluster of Galicia Spain) a population that is representativeof the main European breeding programmes that have the same Atlantic origin Seabream data came from twodifferent breeding programmes carried out at Ferme Marine du Douhet (FMD France) and the Andromeda Group(Greece) Carp data came from the broodstock of the Amur Mirror Carp strain recently created at the University ofSouth Bohemia (Czech Republic) from crosses between two different strains Fish were genotyped for thousands ofSingle Nucleotide Polymorphisms (SNPs) obtained using genotyping-by-sequencing (RAD-sequencing) and estimatesof current and ancestral effective population size from linkage disequilibrium measures were obtained Genetic status of turbot seabream seabass and carp commercial populations Results obtained from the analysis of genomic information revealed that current effective population size for allpopulations analysed was lower than the critical value of 50 individuals that is recommended to avoid inbreedingdepression and retain fitness in the short-term Specifically estimates for turbot seabream Andromeda seabreamFMD seabass and carp were 28 40 41 38 and 22 fish respectively These low estimates could be due to the way inwhich base populations were established (low number of breeding individuals andor strong relationships betweenthem) orand to a suboptimal inbreeding control Estimates of effective population size across time evidencedbottlenecks 4 - 11 generations ago This point in time coincides with the number of generations for which turbotseabream and seabass have been domesticated or for which selection programmes have been practised The recent

Subscribe Past Issues RSSTranslate

creation of the carp strain analysed also coincides with the observed bottleneck

Estimates of effective population size (Ne) across the last 20 generations for the different populations analysed

Implications Our results highlight the need of broadening the genetic composition of base populations from which selectionprogrammes start These results also suggest that methods designed to increase the effective population size withinall farm populations analysed need to be implemented in order to ensure the sustainability of the breedingprogrammes Performing artificial fertilization and single-pair matings as well as implementing Optimal ContributionSelection and factorial mating designs would be recommendable practices This study was performed by M Saura A Fernaacutendez J Fernaacutendez and B Villanueva (INIA) Software for estimating effective population

size was facilitated by A Caballero (Universidad de Vigo Spain) and E Santiago (Universidad de Oviedo Spain) Data analysed was

provided by CETGA (S Cabaleiro) GENEAQUA (P Martiacutenez A Millaacuten) USB (M Kocour M Prchal) UEDIN (C Palaiokostas Ross Houston)

ANDROMEDA (T Kostas) NOFIMA (ML Aslam) UNIPD (L Bargelloni) SYSAAF (P Haffray) and FMD (JS Bruant)

Use of DNA pooling of the training set to reduce genotyping costs for genomicselection Anna Kristina Sonesson (NOFIMA) DNA pooling of the training population for genomic selection is a method that reduces genotyping costs while maintaininghigh selection accuracy for large populations Here we present results from experiments of both real and lsquoin silicorsquo DNApooling in Atlantic salmon In aquaculture breeding genomic selection is mainly used for traits that are not measured on the selection candidatesbecause they are invasive but instead they are measured on sibs of the selection candidates Examples of these aredisease resistance and fillet quality and they often constitute a large group of the traits in the breeding goals of well-developed breeding programs Phenotypic and genomic information must be obtained from the training set of individualsie the sibs of the candidates The effects of the SNPs estimated in this dataset are thereafter used to predict genomicbreeding values of the selection candidates With large numbers of traits and individuals per trait (15-50 per family) the totalnumber of individuals to genotype becomes large Methods that reduce genotyping costs for genomic selection aretherefore important for genomic selection to be widely implemented in aquaculture breeding schemes Equal amounts of DNA from individuals can be pooled and thereafter genotyped resulting in genotyping of much fewer

Subscribe Past Issues RSSTranslate

samples than individual genotyping In a large data set of~7000 Atlantic salmon that had been challenge tested forPancreas Disease (PD) and genotyped individually with a55 kSNP chip the accuracy of genomic selection was0718 We did lsquoin silicorsquo DNA pooling of the phenotypicextremes into 200 pools of SURVIVORS (that survived thewhole challenge test) and 200 pools of MORTALITIES (thatdied earliest in the test) which thus would result in 400genotypes in total This dataset resulted in an accuracy ofselection of 0693 In a smaller dataset also on PD thereduction in accuracy of selection was larger Hence thedataset must be designed to get enough phenotypicvariation for the DNA pooling to work well Here we studied

a trait where we could get large phenotypic differences (a binary trait with heritability of ~03) which has probablyinfluenced the positive results In a smaller dataset of Atlantic salmon also tested for PDand individually genotyped with a SNP chip the selectionaccuracy was 0737 DNA from these same individualswere in vivo pooled into two replicates of SURVIVORS andMORTALITIES pools each with ~200 individuals from ~30families When these pools were sequenced 40x selectionaccuracy was 0716 When these pools were genotypedwith a SNP chip and relative light intensities were used toestimate SNP alleles frequencies in the pools the accuracyof selection was 0690 In conclusion genotyping costs of genomic selection canbe dramatically reduced when performing DNA pooling of extreme phenotypes of the training population Selectionaccuracies were slightly reduced compared to individual genotyping but this reduction became smaller when the number ofpools increased The methodology worked best in large populations This work was done in collaboration between SalmoBreed AS Marine Harvest Nofima Norwegian University of Life Sciences Please contact

annasonessonnofimano if you have questions Photo credits to Frank Gregersen and Nofima

Two well-visited FISHBOOST sessions at European Aquaculture Society meeting This yearsrsquo European Aquaculture Society meeting was co-organised with the World Aquaculture Society and was heldin Montpellier France in the end of August FISHBOOSThad two very well-visited sessions at this conference One session was part of the Industry Forum where industryrelevance is in focus Overviews of the FISHBOOST resultsso far were presented The covered topics wereimprovement of disease and production efficiency traitsgenetic gains and profitability of breeding programsmanagement of inbreeding and genomic selection At theend of that session Dr Nikos Zampoukas from the

Subscribe Past Issues RSSTranslate

European Commission was invited to present the new Framework Program Horizon Europe

This was followed up by a round table discussion on the future research needs within the aquaculturebreeding field The results from that discussion will be summarized and sent as input for future calls tothe European Commission via the Farm Animal Breeding and Reproduction Technology Platform

(FABRE TP) You can read more about the FABRE TP here httpwwwfabretpeu The second session was a technical session with eight presentations on the latest results from the project

The importance of ensuring genetic variability when establishing selection programmes in aquaculture B VillanuevaM Saura A Caballero E Santiago E Morales A Fernaacutendez J Fernaacutendez S Cabaleiro P Martiacutenez A Millaacuten CPalaiokostas M Kocour R Houston M Prchal L Bargelloni KTzokasGenomic selection analyses results on common carp European seabass gilthead beabream and turbot AKSonesson C Palaiokostas RD Houston B Dagnachew ML Aslam THE MeuwissenMapping sequencing and functional annotation of a QTL region affecting resistance to koi herpesvirus in commoncarp RD Houston C Palaiokostas D Robledo T Vesely M Prchal D Pokorova V Piackova L Pojezdal MKocourA closer look at turbot genome reveals a genetic component of parasite resistance new tools for selection PMartiacutenez F Maroso M Saura A Fernaacutendez A Blanco M Hermida S Cabaleiro A Doeschl-Wilson O AnacletoR Houston A Millaacuten J Fernaacutendez L Bargelloni G dalla Rovere MA Toro MJ Carabantildeo C Bouza BVillanuevaUse of DNA pooling in genomic selection for a disease trait in Atlantic salmon B Dagnachew A K SonessonTHE MeuwissenSuccessful realized selection response for fillet yield in rainbow trout (Oncorhynchus mykiss) M Vandeputte JBugeon A Bestin A Desgranges S Courant J-M Allamellou AS Tyran F Allal M Dupont-Nivet P HaffrayPotential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictorsM Prchal J Bugeon M Vandeputte A Kause A Vergnet J Zhao D Gela L Genestout A Bestin P Haffray MKocourOptimal schemes for advancing selective breeding to the next level for the main species of European aquaculture BVillanueva S Garciacutea-Ballesteros J FernaacutendezCost-benefit analysis of a breeding program for Atlantic salmon K Janssen H Saatkamp H Komen

A summary of this session can be found at of wwwaquaeaseu Thanks to everybody that has visited the FISHBOOST sessions at this and previous EAS meetings for stimulatingdiscussions

In the spotlight Andrea Doeschl-Wilson (The Roslin Institute) Irsquom contributing to the disease resistance workpackage (WP1) Specifically we are looking at how the genetics of individualsaffects disease spread and survival in fish populations In addition to the conventional trait lsquodisease resistancersquo we considernew traits (disease phenotypes) such as tolerance and infectivity We know from theory that all of these traits also have astrong influence on disease spread and resulting mortality rates However at present very little is known about the genetic regulation of these traits and whether it is possible to breed fishthat are not only genetically less prone to becoming infected but also less likely to transmit infection once infected andpossibly also more likely to survive or recover from infections If this was possible genetic selection would be a powerful toolto prevent disease outbreaks ndash potentially much more powerful than selection on survival which is the current practice In

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FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

Subscribe Past Issues RSSTranslate

experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

Subscribe Past Issues RSSTranslate

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate

Page 5: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

ldquoItrsquos important to note that actual economic gain may have been different from the results of the study because inreality the emphasis on breeding goal traits differs genetic parameters may be different and more traits areincluded in the breeding goal ndash for example resistance to IPN PD AGD However the results suggest a significantundervaluation of genetic improvement by salmon producers Moreover consumers should also benefit from lowerprices caused by the improvements in production efficiencies while the environmental impact of production will alsobe reducedrdquo Janssen concludes

httpsthefishsitecomarticlesbreeding-programmes-prove-their-worth

The importance of ensuring genetic variability when establishing aquaculturebreeding programmes Mariacutea Saura (INIA Spain)

Designing base populations with appropriate levels of genetic variability is fundamental to ensure the viability of aquaculture breeding

programmes Using genomic data obtained within FISHBOOST INIA has determined the genetic status of commercial populations of

turbot gilthead seabream European seabass and common carp and shown the need of broadening the genetic composition of base

populations from which selection programmes start and the application of strategies for maintaining genetic diversity once the

programmes are in operation Importance of optimising the creation of base populations The success of any breeding programme critically depends on the way in which the base population of breeders isbuilt as the genetic variability initially available will determine the genetic progress achieved This is particularlyimportant in aquaculture since given the high fecundity of fish base populations can be created from very fewindividuals leading to large losses in genetic variability and increased risk of inbreeding depression (ie reduction ofperformance due to inbreeding) that can compromise the viability of the programmes Genetic variability and effective population size The rate of loss of genetic variability is directly related to the rate at which inbreeding increases and inversely relatedwith the effective population size a population parameter that can be estimated from genomic information Usingdata obtained within FISHBOOST INIA has estimated current and ancestral effective population size in populations ofturbot gilthead seabream European seabass and common carp Data used came from different challenge testscarried out in the project and corresponded to the broodstock used for creating the families challenged Thesebroodstock were sampled from different commercial European breeding programmes Turbot data were obtainedfrom the broodstock maintained at CETGA (Aquaculture Cluster of Galicia Spain) a population that is representativeof the main European breeding programmes that have the same Atlantic origin Seabream data came from twodifferent breeding programmes carried out at Ferme Marine du Douhet (FMD France) and the Andromeda Group(Greece) Carp data came from the broodstock of the Amur Mirror Carp strain recently created at the University ofSouth Bohemia (Czech Republic) from crosses between two different strains Fish were genotyped for thousands ofSingle Nucleotide Polymorphisms (SNPs) obtained using genotyping-by-sequencing (RAD-sequencing) and estimatesof current and ancestral effective population size from linkage disequilibrium measures were obtained Genetic status of turbot seabream seabass and carp commercial populations Results obtained from the analysis of genomic information revealed that current effective population size for allpopulations analysed was lower than the critical value of 50 individuals that is recommended to avoid inbreedingdepression and retain fitness in the short-term Specifically estimates for turbot seabream Andromeda seabreamFMD seabass and carp were 28 40 41 38 and 22 fish respectively These low estimates could be due to the way inwhich base populations were established (low number of breeding individuals andor strong relationships betweenthem) orand to a suboptimal inbreeding control Estimates of effective population size across time evidencedbottlenecks 4 - 11 generations ago This point in time coincides with the number of generations for which turbotseabream and seabass have been domesticated or for which selection programmes have been practised The recent

Subscribe Past Issues RSSTranslate

creation of the carp strain analysed also coincides with the observed bottleneck

Estimates of effective population size (Ne) across the last 20 generations for the different populations analysed

Implications Our results highlight the need of broadening the genetic composition of base populations from which selectionprogrammes start These results also suggest that methods designed to increase the effective population size withinall farm populations analysed need to be implemented in order to ensure the sustainability of the breedingprogrammes Performing artificial fertilization and single-pair matings as well as implementing Optimal ContributionSelection and factorial mating designs would be recommendable practices This study was performed by M Saura A Fernaacutendez J Fernaacutendez and B Villanueva (INIA) Software for estimating effective population

size was facilitated by A Caballero (Universidad de Vigo Spain) and E Santiago (Universidad de Oviedo Spain) Data analysed was

provided by CETGA (S Cabaleiro) GENEAQUA (P Martiacutenez A Millaacuten) USB (M Kocour M Prchal) UEDIN (C Palaiokostas Ross Houston)

ANDROMEDA (T Kostas) NOFIMA (ML Aslam) UNIPD (L Bargelloni) SYSAAF (P Haffray) and FMD (JS Bruant)

Use of DNA pooling of the training set to reduce genotyping costs for genomicselection Anna Kristina Sonesson (NOFIMA) DNA pooling of the training population for genomic selection is a method that reduces genotyping costs while maintaininghigh selection accuracy for large populations Here we present results from experiments of both real and lsquoin silicorsquo DNApooling in Atlantic salmon In aquaculture breeding genomic selection is mainly used for traits that are not measured on the selection candidatesbecause they are invasive but instead they are measured on sibs of the selection candidates Examples of these aredisease resistance and fillet quality and they often constitute a large group of the traits in the breeding goals of well-developed breeding programs Phenotypic and genomic information must be obtained from the training set of individualsie the sibs of the candidates The effects of the SNPs estimated in this dataset are thereafter used to predict genomicbreeding values of the selection candidates With large numbers of traits and individuals per trait (15-50 per family) the totalnumber of individuals to genotype becomes large Methods that reduce genotyping costs for genomic selection aretherefore important for genomic selection to be widely implemented in aquaculture breeding schemes Equal amounts of DNA from individuals can be pooled and thereafter genotyped resulting in genotyping of much fewer

Subscribe Past Issues RSSTranslate

samples than individual genotyping In a large data set of~7000 Atlantic salmon that had been challenge tested forPancreas Disease (PD) and genotyped individually with a55 kSNP chip the accuracy of genomic selection was0718 We did lsquoin silicorsquo DNA pooling of the phenotypicextremes into 200 pools of SURVIVORS (that survived thewhole challenge test) and 200 pools of MORTALITIES (thatdied earliest in the test) which thus would result in 400genotypes in total This dataset resulted in an accuracy ofselection of 0693 In a smaller dataset also on PD thereduction in accuracy of selection was larger Hence thedataset must be designed to get enough phenotypicvariation for the DNA pooling to work well Here we studied

a trait where we could get large phenotypic differences (a binary trait with heritability of ~03) which has probablyinfluenced the positive results In a smaller dataset of Atlantic salmon also tested for PDand individually genotyped with a SNP chip the selectionaccuracy was 0737 DNA from these same individualswere in vivo pooled into two replicates of SURVIVORS andMORTALITIES pools each with ~200 individuals from ~30families When these pools were sequenced 40x selectionaccuracy was 0716 When these pools were genotypedwith a SNP chip and relative light intensities were used toestimate SNP alleles frequencies in the pools the accuracyof selection was 0690 In conclusion genotyping costs of genomic selection canbe dramatically reduced when performing DNA pooling of extreme phenotypes of the training population Selectionaccuracies were slightly reduced compared to individual genotyping but this reduction became smaller when the number ofpools increased The methodology worked best in large populations This work was done in collaboration between SalmoBreed AS Marine Harvest Nofima Norwegian University of Life Sciences Please contact

annasonessonnofimano if you have questions Photo credits to Frank Gregersen and Nofima

Two well-visited FISHBOOST sessions at European Aquaculture Society meeting This yearsrsquo European Aquaculture Society meeting was co-organised with the World Aquaculture Society and was heldin Montpellier France in the end of August FISHBOOSThad two very well-visited sessions at this conference One session was part of the Industry Forum where industryrelevance is in focus Overviews of the FISHBOOST resultsso far were presented The covered topics wereimprovement of disease and production efficiency traitsgenetic gains and profitability of breeding programsmanagement of inbreeding and genomic selection At theend of that session Dr Nikos Zampoukas from the

Subscribe Past Issues RSSTranslate

European Commission was invited to present the new Framework Program Horizon Europe

This was followed up by a round table discussion on the future research needs within the aquaculturebreeding field The results from that discussion will be summarized and sent as input for future calls tothe European Commission via the Farm Animal Breeding and Reproduction Technology Platform

(FABRE TP) You can read more about the FABRE TP here httpwwwfabretpeu The second session was a technical session with eight presentations on the latest results from the project

The importance of ensuring genetic variability when establishing selection programmes in aquaculture B VillanuevaM Saura A Caballero E Santiago E Morales A Fernaacutendez J Fernaacutendez S Cabaleiro P Martiacutenez A Millaacuten CPalaiokostas M Kocour R Houston M Prchal L Bargelloni KTzokasGenomic selection analyses results on common carp European seabass gilthead beabream and turbot AKSonesson C Palaiokostas RD Houston B Dagnachew ML Aslam THE MeuwissenMapping sequencing and functional annotation of a QTL region affecting resistance to koi herpesvirus in commoncarp RD Houston C Palaiokostas D Robledo T Vesely M Prchal D Pokorova V Piackova L Pojezdal MKocourA closer look at turbot genome reveals a genetic component of parasite resistance new tools for selection PMartiacutenez F Maroso M Saura A Fernaacutendez A Blanco M Hermida S Cabaleiro A Doeschl-Wilson O AnacletoR Houston A Millaacuten J Fernaacutendez L Bargelloni G dalla Rovere MA Toro MJ Carabantildeo C Bouza BVillanuevaUse of DNA pooling in genomic selection for a disease trait in Atlantic salmon B Dagnachew A K SonessonTHE MeuwissenSuccessful realized selection response for fillet yield in rainbow trout (Oncorhynchus mykiss) M Vandeputte JBugeon A Bestin A Desgranges S Courant J-M Allamellou AS Tyran F Allal M Dupont-Nivet P HaffrayPotential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictorsM Prchal J Bugeon M Vandeputte A Kause A Vergnet J Zhao D Gela L Genestout A Bestin P Haffray MKocourOptimal schemes for advancing selective breeding to the next level for the main species of European aquaculture BVillanueva S Garciacutea-Ballesteros J FernaacutendezCost-benefit analysis of a breeding program for Atlantic salmon K Janssen H Saatkamp H Komen

A summary of this session can be found at of wwwaquaeaseu Thanks to everybody that has visited the FISHBOOST sessions at this and previous EAS meetings for stimulatingdiscussions

In the spotlight Andrea Doeschl-Wilson (The Roslin Institute) Irsquom contributing to the disease resistance workpackage (WP1) Specifically we are looking at how the genetics of individualsaffects disease spread and survival in fish populations In addition to the conventional trait lsquodisease resistancersquo we considernew traits (disease phenotypes) such as tolerance and infectivity We know from theory that all of these traits also have astrong influence on disease spread and resulting mortality rates However at present very little is known about the genetic regulation of these traits and whether it is possible to breed fishthat are not only genetically less prone to becoming infected but also less likely to transmit infection once infected andpossibly also more likely to survive or recover from infections If this was possible genetic selection would be a powerful toolto prevent disease outbreaks ndash potentially much more powerful than selection on survival which is the current practice In

Subscribe Past Issues RSSTranslate

FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

Subscribe Past Issues RSSTranslate

experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

Subscribe Past Issues RSSTranslate

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate

Page 6: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

creation of the carp strain analysed also coincides with the observed bottleneck

Estimates of effective population size (Ne) across the last 20 generations for the different populations analysed

Implications Our results highlight the need of broadening the genetic composition of base populations from which selectionprogrammes start These results also suggest that methods designed to increase the effective population size withinall farm populations analysed need to be implemented in order to ensure the sustainability of the breedingprogrammes Performing artificial fertilization and single-pair matings as well as implementing Optimal ContributionSelection and factorial mating designs would be recommendable practices This study was performed by M Saura A Fernaacutendez J Fernaacutendez and B Villanueva (INIA) Software for estimating effective population

size was facilitated by A Caballero (Universidad de Vigo Spain) and E Santiago (Universidad de Oviedo Spain) Data analysed was

provided by CETGA (S Cabaleiro) GENEAQUA (P Martiacutenez A Millaacuten) USB (M Kocour M Prchal) UEDIN (C Palaiokostas Ross Houston)

ANDROMEDA (T Kostas) NOFIMA (ML Aslam) UNIPD (L Bargelloni) SYSAAF (P Haffray) and FMD (JS Bruant)

Use of DNA pooling of the training set to reduce genotyping costs for genomicselection Anna Kristina Sonesson (NOFIMA) DNA pooling of the training population for genomic selection is a method that reduces genotyping costs while maintaininghigh selection accuracy for large populations Here we present results from experiments of both real and lsquoin silicorsquo DNApooling in Atlantic salmon In aquaculture breeding genomic selection is mainly used for traits that are not measured on the selection candidatesbecause they are invasive but instead they are measured on sibs of the selection candidates Examples of these aredisease resistance and fillet quality and they often constitute a large group of the traits in the breeding goals of well-developed breeding programs Phenotypic and genomic information must be obtained from the training set of individualsie the sibs of the candidates The effects of the SNPs estimated in this dataset are thereafter used to predict genomicbreeding values of the selection candidates With large numbers of traits and individuals per trait (15-50 per family) the totalnumber of individuals to genotype becomes large Methods that reduce genotyping costs for genomic selection aretherefore important for genomic selection to be widely implemented in aquaculture breeding schemes Equal amounts of DNA from individuals can be pooled and thereafter genotyped resulting in genotyping of much fewer

Subscribe Past Issues RSSTranslate

samples than individual genotyping In a large data set of~7000 Atlantic salmon that had been challenge tested forPancreas Disease (PD) and genotyped individually with a55 kSNP chip the accuracy of genomic selection was0718 We did lsquoin silicorsquo DNA pooling of the phenotypicextremes into 200 pools of SURVIVORS (that survived thewhole challenge test) and 200 pools of MORTALITIES (thatdied earliest in the test) which thus would result in 400genotypes in total This dataset resulted in an accuracy ofselection of 0693 In a smaller dataset also on PD thereduction in accuracy of selection was larger Hence thedataset must be designed to get enough phenotypicvariation for the DNA pooling to work well Here we studied

a trait where we could get large phenotypic differences (a binary trait with heritability of ~03) which has probablyinfluenced the positive results In a smaller dataset of Atlantic salmon also tested for PDand individually genotyped with a SNP chip the selectionaccuracy was 0737 DNA from these same individualswere in vivo pooled into two replicates of SURVIVORS andMORTALITIES pools each with ~200 individuals from ~30families When these pools were sequenced 40x selectionaccuracy was 0716 When these pools were genotypedwith a SNP chip and relative light intensities were used toestimate SNP alleles frequencies in the pools the accuracyof selection was 0690 In conclusion genotyping costs of genomic selection canbe dramatically reduced when performing DNA pooling of extreme phenotypes of the training population Selectionaccuracies were slightly reduced compared to individual genotyping but this reduction became smaller when the number ofpools increased The methodology worked best in large populations This work was done in collaboration between SalmoBreed AS Marine Harvest Nofima Norwegian University of Life Sciences Please contact

annasonessonnofimano if you have questions Photo credits to Frank Gregersen and Nofima

Two well-visited FISHBOOST sessions at European Aquaculture Society meeting This yearsrsquo European Aquaculture Society meeting was co-organised with the World Aquaculture Society and was heldin Montpellier France in the end of August FISHBOOSThad two very well-visited sessions at this conference One session was part of the Industry Forum where industryrelevance is in focus Overviews of the FISHBOOST resultsso far were presented The covered topics wereimprovement of disease and production efficiency traitsgenetic gains and profitability of breeding programsmanagement of inbreeding and genomic selection At theend of that session Dr Nikos Zampoukas from the

Subscribe Past Issues RSSTranslate

European Commission was invited to present the new Framework Program Horizon Europe

This was followed up by a round table discussion on the future research needs within the aquaculturebreeding field The results from that discussion will be summarized and sent as input for future calls tothe European Commission via the Farm Animal Breeding and Reproduction Technology Platform

(FABRE TP) You can read more about the FABRE TP here httpwwwfabretpeu The second session was a technical session with eight presentations on the latest results from the project

The importance of ensuring genetic variability when establishing selection programmes in aquaculture B VillanuevaM Saura A Caballero E Santiago E Morales A Fernaacutendez J Fernaacutendez S Cabaleiro P Martiacutenez A Millaacuten CPalaiokostas M Kocour R Houston M Prchal L Bargelloni KTzokasGenomic selection analyses results on common carp European seabass gilthead beabream and turbot AKSonesson C Palaiokostas RD Houston B Dagnachew ML Aslam THE MeuwissenMapping sequencing and functional annotation of a QTL region affecting resistance to koi herpesvirus in commoncarp RD Houston C Palaiokostas D Robledo T Vesely M Prchal D Pokorova V Piackova L Pojezdal MKocourA closer look at turbot genome reveals a genetic component of parasite resistance new tools for selection PMartiacutenez F Maroso M Saura A Fernaacutendez A Blanco M Hermida S Cabaleiro A Doeschl-Wilson O AnacletoR Houston A Millaacuten J Fernaacutendez L Bargelloni G dalla Rovere MA Toro MJ Carabantildeo C Bouza BVillanuevaUse of DNA pooling in genomic selection for a disease trait in Atlantic salmon B Dagnachew A K SonessonTHE MeuwissenSuccessful realized selection response for fillet yield in rainbow trout (Oncorhynchus mykiss) M Vandeputte JBugeon A Bestin A Desgranges S Courant J-M Allamellou AS Tyran F Allal M Dupont-Nivet P HaffrayPotential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictorsM Prchal J Bugeon M Vandeputte A Kause A Vergnet J Zhao D Gela L Genestout A Bestin P Haffray MKocourOptimal schemes for advancing selective breeding to the next level for the main species of European aquaculture BVillanueva S Garciacutea-Ballesteros J FernaacutendezCost-benefit analysis of a breeding program for Atlantic salmon K Janssen H Saatkamp H Komen

A summary of this session can be found at of wwwaquaeaseu Thanks to everybody that has visited the FISHBOOST sessions at this and previous EAS meetings for stimulatingdiscussions

In the spotlight Andrea Doeschl-Wilson (The Roslin Institute) Irsquom contributing to the disease resistance workpackage (WP1) Specifically we are looking at how the genetics of individualsaffects disease spread and survival in fish populations In addition to the conventional trait lsquodisease resistancersquo we considernew traits (disease phenotypes) such as tolerance and infectivity We know from theory that all of these traits also have astrong influence on disease spread and resulting mortality rates However at present very little is known about the genetic regulation of these traits and whether it is possible to breed fishthat are not only genetically less prone to becoming infected but also less likely to transmit infection once infected andpossibly also more likely to survive or recover from infections If this was possible genetic selection would be a powerful toolto prevent disease outbreaks ndash potentially much more powerful than selection on survival which is the current practice In

Subscribe Past Issues RSSTranslate

FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

Subscribe Past Issues RSSTranslate

experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

Subscribe Past Issues RSSTranslate

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate

Page 7: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

samples than individual genotyping In a large data set of~7000 Atlantic salmon that had been challenge tested forPancreas Disease (PD) and genotyped individually with a55 kSNP chip the accuracy of genomic selection was0718 We did lsquoin silicorsquo DNA pooling of the phenotypicextremes into 200 pools of SURVIVORS (that survived thewhole challenge test) and 200 pools of MORTALITIES (thatdied earliest in the test) which thus would result in 400genotypes in total This dataset resulted in an accuracy ofselection of 0693 In a smaller dataset also on PD thereduction in accuracy of selection was larger Hence thedataset must be designed to get enough phenotypicvariation for the DNA pooling to work well Here we studied

a trait where we could get large phenotypic differences (a binary trait with heritability of ~03) which has probablyinfluenced the positive results In a smaller dataset of Atlantic salmon also tested for PDand individually genotyped with a SNP chip the selectionaccuracy was 0737 DNA from these same individualswere in vivo pooled into two replicates of SURVIVORS andMORTALITIES pools each with ~200 individuals from ~30families When these pools were sequenced 40x selectionaccuracy was 0716 When these pools were genotypedwith a SNP chip and relative light intensities were used toestimate SNP alleles frequencies in the pools the accuracyof selection was 0690 In conclusion genotyping costs of genomic selection canbe dramatically reduced when performing DNA pooling of extreme phenotypes of the training population Selectionaccuracies were slightly reduced compared to individual genotyping but this reduction became smaller when the number ofpools increased The methodology worked best in large populations This work was done in collaboration between SalmoBreed AS Marine Harvest Nofima Norwegian University of Life Sciences Please contact

annasonessonnofimano if you have questions Photo credits to Frank Gregersen and Nofima

Two well-visited FISHBOOST sessions at European Aquaculture Society meeting This yearsrsquo European Aquaculture Society meeting was co-organised with the World Aquaculture Society and was heldin Montpellier France in the end of August FISHBOOSThad two very well-visited sessions at this conference One session was part of the Industry Forum where industryrelevance is in focus Overviews of the FISHBOOST resultsso far were presented The covered topics wereimprovement of disease and production efficiency traitsgenetic gains and profitability of breeding programsmanagement of inbreeding and genomic selection At theend of that session Dr Nikos Zampoukas from the

Subscribe Past Issues RSSTranslate

European Commission was invited to present the new Framework Program Horizon Europe

This was followed up by a round table discussion on the future research needs within the aquaculturebreeding field The results from that discussion will be summarized and sent as input for future calls tothe European Commission via the Farm Animal Breeding and Reproduction Technology Platform

(FABRE TP) You can read more about the FABRE TP here httpwwwfabretpeu The second session was a technical session with eight presentations on the latest results from the project

The importance of ensuring genetic variability when establishing selection programmes in aquaculture B VillanuevaM Saura A Caballero E Santiago E Morales A Fernaacutendez J Fernaacutendez S Cabaleiro P Martiacutenez A Millaacuten CPalaiokostas M Kocour R Houston M Prchal L Bargelloni KTzokasGenomic selection analyses results on common carp European seabass gilthead beabream and turbot AKSonesson C Palaiokostas RD Houston B Dagnachew ML Aslam THE MeuwissenMapping sequencing and functional annotation of a QTL region affecting resistance to koi herpesvirus in commoncarp RD Houston C Palaiokostas D Robledo T Vesely M Prchal D Pokorova V Piackova L Pojezdal MKocourA closer look at turbot genome reveals a genetic component of parasite resistance new tools for selection PMartiacutenez F Maroso M Saura A Fernaacutendez A Blanco M Hermida S Cabaleiro A Doeschl-Wilson O AnacletoR Houston A Millaacuten J Fernaacutendez L Bargelloni G dalla Rovere MA Toro MJ Carabantildeo C Bouza BVillanuevaUse of DNA pooling in genomic selection for a disease trait in Atlantic salmon B Dagnachew A K SonessonTHE MeuwissenSuccessful realized selection response for fillet yield in rainbow trout (Oncorhynchus mykiss) M Vandeputte JBugeon A Bestin A Desgranges S Courant J-M Allamellou AS Tyran F Allal M Dupont-Nivet P HaffrayPotential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictorsM Prchal J Bugeon M Vandeputte A Kause A Vergnet J Zhao D Gela L Genestout A Bestin P Haffray MKocourOptimal schemes for advancing selective breeding to the next level for the main species of European aquaculture BVillanueva S Garciacutea-Ballesteros J FernaacutendezCost-benefit analysis of a breeding program for Atlantic salmon K Janssen H Saatkamp H Komen

A summary of this session can be found at of wwwaquaeaseu Thanks to everybody that has visited the FISHBOOST sessions at this and previous EAS meetings for stimulatingdiscussions

In the spotlight Andrea Doeschl-Wilson (The Roslin Institute) Irsquom contributing to the disease resistance workpackage (WP1) Specifically we are looking at how the genetics of individualsaffects disease spread and survival in fish populations In addition to the conventional trait lsquodisease resistancersquo we considernew traits (disease phenotypes) such as tolerance and infectivity We know from theory that all of these traits also have astrong influence on disease spread and resulting mortality rates However at present very little is known about the genetic regulation of these traits and whether it is possible to breed fishthat are not only genetically less prone to becoming infected but also less likely to transmit infection once infected andpossibly also more likely to survive or recover from infections If this was possible genetic selection would be a powerful toolto prevent disease outbreaks ndash potentially much more powerful than selection on survival which is the current practice In

Subscribe Past Issues RSSTranslate

FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

Subscribe Past Issues RSSTranslate

experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

Subscribe Past Issues RSSTranslate

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate

Page 8: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

European Commission was invited to present the new Framework Program Horizon Europe

This was followed up by a round table discussion on the future research needs within the aquaculturebreeding field The results from that discussion will be summarized and sent as input for future calls tothe European Commission via the Farm Animal Breeding and Reproduction Technology Platform

(FABRE TP) You can read more about the FABRE TP here httpwwwfabretpeu The second session was a technical session with eight presentations on the latest results from the project

The importance of ensuring genetic variability when establishing selection programmes in aquaculture B VillanuevaM Saura A Caballero E Santiago E Morales A Fernaacutendez J Fernaacutendez S Cabaleiro P Martiacutenez A Millaacuten CPalaiokostas M Kocour R Houston M Prchal L Bargelloni KTzokasGenomic selection analyses results on common carp European seabass gilthead beabream and turbot AKSonesson C Palaiokostas RD Houston B Dagnachew ML Aslam THE MeuwissenMapping sequencing and functional annotation of a QTL region affecting resistance to koi herpesvirus in commoncarp RD Houston C Palaiokostas D Robledo T Vesely M Prchal D Pokorova V Piackova L Pojezdal MKocourA closer look at turbot genome reveals a genetic component of parasite resistance new tools for selection PMartiacutenez F Maroso M Saura A Fernaacutendez A Blanco M Hermida S Cabaleiro A Doeschl-Wilson O AnacletoR Houston A Millaacuten J Fernaacutendez L Bargelloni G dalla Rovere MA Toro MJ Carabantildeo C Bouza BVillanuevaUse of DNA pooling in genomic selection for a disease trait in Atlantic salmon B Dagnachew A K SonessonTHE MeuwissenSuccessful realized selection response for fillet yield in rainbow trout (Oncorhynchus mykiss) M Vandeputte JBugeon A Bestin A Desgranges S Courant J-M Allamellou AS Tyran F Allal M Dupont-Nivet P HaffrayPotential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictorsM Prchal J Bugeon M Vandeputte A Kause A Vergnet J Zhao D Gela L Genestout A Bestin P Haffray MKocourOptimal schemes for advancing selective breeding to the next level for the main species of European aquaculture BVillanueva S Garciacutea-Ballesteros J FernaacutendezCost-benefit analysis of a breeding program for Atlantic salmon K Janssen H Saatkamp H Komen

A summary of this session can be found at of wwwaquaeaseu Thanks to everybody that has visited the FISHBOOST sessions at this and previous EAS meetings for stimulatingdiscussions

In the spotlight Andrea Doeschl-Wilson (The Roslin Institute) Irsquom contributing to the disease resistance workpackage (WP1) Specifically we are looking at how the genetics of individualsaffects disease spread and survival in fish populations In addition to the conventional trait lsquodisease resistancersquo we considernew traits (disease phenotypes) such as tolerance and infectivity We know from theory that all of these traits also have astrong influence on disease spread and resulting mortality rates However at present very little is known about the genetic regulation of these traits and whether it is possible to breed fishthat are not only genetically less prone to becoming infected but also less likely to transmit infection once infected andpossibly also more likely to survive or recover from infections If this was possible genetic selection would be a powerful toolto prevent disease outbreaks ndash potentially much more powerful than selection on survival which is the current practice In

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FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

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experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

Subscribe Past Issues RSSTranslate

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate

Page 9: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

FISHBOOST we develop the methods and know-how needed toestimate genetic effects for the different disease traits

The Roslin Institute is one of the world leading research institute in livestock genomics and breeding including aquacultureTogether with CETGA and INIA we have designed a large scale disease transmission experiment for an important diseasein Turbot (Scuticociliatosis) to generate data that allow us to simultaneously estimate genetic effects for resistancetolerance in infectivity This is the first experiment in the world that dissects the black box lsquomortalityrsquo as indicator for diseaseresistance into its underlying components If you are selecting fish that are genetically more prone to survive infectionwithout knowing what underlies survival you could accidentally select fish that are more tolerant to infection and act assource of infection to others In FISHBOOST we are developing the experiment design and also the mathematical modelsand computational algorithms needed to estimate genetic effects for the new traits infectivity and tolerance in addition tosusceptibility We apply them to the experimental data generated within FISHBOOST We hope to apply these to otherdiseases in aquaculture species in the future Irsquom very impressed about the scope of this project and the immense dedication of the project leaders and partners tocollaboratively carry out relevant research that will have important practical implications to the aquaculture sector Thisproject generates a number of important technological and statistical tools and know-how to move aquaculture production inEurope a significant step forward Irsquom very grateful to be part of it

We could show that it is possible to conduct singletransmission experiments that allows detection of geneticvariation not only in mortality following a disease challengebut also in all three important underlying host traitsresistance infectivity and tolerance The data from theTurbot transmission experiments revealed that there issignificant genetic variation in all of these traits meaningthat it would be possible in principle to include all threedisease traits into a breeding programme ForScuticocciliatosis in Turbot resistance and toleranceappear to be genetically different traits (ie low genetic

correlations) but resistance seems to be highly genetically correlated with mortality Genome-wide association analysescarried out by our INIA collaborators also detected QTLs controlling tolerance and mortality Although no significantassociations were found for resistance the pattern of association was the same as for mortality The transmission

Subscribe Past Issues RSSTranslate

experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

Subscribe Past Issues RSSTranslate

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate

Page 10: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

experiment also provided the first empirical evidence that individuals not only differ genetically in their risk of becominginfected and how they cope with infection but also in their ability to transmit infection (ie their infectivity) So far we coulddemonstrate that the genetic differences in infectivity not only affect disease spread but also survival rates Analyses toestimate the relationship between infectivity and the other disease traits are currently under way The results and tools generated in FISHBOOST could help breeders to develop more effective breeding programmes thatcan exploit genetic variation in several key host traits underlying disease spread and survival Breeding for disease resistance is currently still in itrsquos infancy I believe that there are far more opportunities for geneticdisease control in particular in aquaculture by optimising experimental and field study designs by making better use ofgenomic technologies and developing better statistical models that combine genetic and epidemiological concepts I hopethat eventually these will be taken up by industry Santiago Cabaleiro Martinez (CETGA) CETGA is involved in FISHBOOST concerning culturing all thefamilies used for turbot challenges in all the Work Packages As Research Centre we developed most of the trials regardingturbot detecting genetic parameters to improve feed efficiencyperforming different disease challenges and recording mortalitiestime-to-death and growth The cooperation among all the participants allow us to obtain accurate data about the geneticbreeding selection establishing for the first time a correlation between resilience tolerance and infectivity that will allow toimprove the breeding selection process All the results obtained from this project are relevant to the stakeholders and this is what makes a project profitable SoAquaculture industry can improve growth rates minimize mortality and enhance filet taking into account the results of the

project These results establishes a closer relationship with thestakeholders we can improve their breeding selection thanks to newtechnologies and innovative procedures Moreover our cluster includes the largest aquaculture producers inSpain and South Europe which allows us to be directly in contactwith the industry what let us know about their concerns difficultiesand necessities All the data obtained in research projects aretransferred to the European industry

Share Tweet Forward

The research leading to these results has received funding from the European Unionrsquos Seventh Framework Programme for research

Subscribe Past Issues RSSTranslate

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate

Page 11: FISHBOOST is finalizing!...Newsletter January 2019 View this email in y our browser In this edition: FISHBOOST is finalizing! FISHBOOST announcements The role of FISHBOOST in research-oriented

technological development and demonstration under grant agreement ndeg 613611 - FISHBOOST

Copyright copy 2014 FISHBOOST Project All rights reserved

We take the EU General Data Protection Regulation (GDPR) seriously You receive this newsletter because you are on the FISHBOOST contact

list or on the contact list of one of our project partners and we sincerely think you might be interested in the FISHBOOST project news All

personal data that the project receives through personal contact mail email and our website are registered Personal data will not be

distributed to third parties You are entitled to view correct or erase your personal data You also have the right to withdraw your consent to

data processing or to object to the processing of your personal data Moreover you are entitled to data portability This means that you can

submit a request to us to send the personal information we have available to you or another organization You can send a request to view

correct delete or transfer your personal data or request to cancel your consent or object to the processing of your personal data by replying

to this email

Do you wish not to receive further newsletters of FISHBOOST please click the unsubscribe button

unsubscribe from this list update subscription preferences

Contact information EFFAB

EFFAB is an independent European forum representing farm animal reproduction and selection organisations Our membership includes

cattle pigs poultry and aquaculture

T +31 317412006

E effabeffabinfo

W wwweffabinfo

Office Dreijenlaan 2 6703 HA Wageningen the Netherlands

Postage PO Box 76 6700 AB Wageningen the Netherlands

This publication reflects the views only of the author and not the European Commission (EC) The EC is not liable for any use that may be

made of the information contained herein

Subscribe Past Issues RSSTranslate