strategic research agenda - fabre tp

StrategicResearchAgenda

2011

fabre technology platform

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strategic research agenda 2011

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ContentsIntroduction 6

Animalbreedingandreproduction:Aknowledgeintensivesector 7

FarmAnimalBreedingOrganisationStructures 9

Opportunity1:GlobalResponsibilityandCompetitiveness 11

A.Goal:Toassureglobalfoodsecurityandsustainabilityofproductionsystems

B.Goal:Toreducetheenvironmentalfootprintandwaste

C.Goal:Toaddressconsumerdemands

D.Goal:StrengthenEuropeancompetitiveness

E.Goal:Developresponsibleownershipandprotectionofnewinnovations

Opportunity2:SocialResponsibility 13

A.Goal:Producesafeanimalproducts

B.Goal:Enhanceproductqualityandconsistency

C.Goal:Maintainandenhanceanimalwelfareandhealth

D.Goal:Achieveabalancedandtransparentregulatoryframework

E.Goal:Maintaininggeneticdiversitywhilerespectingdifferentculturalandregionalneeds

F.Goal:Improveconsumerunderstandingoftheapplicationandpotentialbenefitsfromnewapproachesandtechnologies

ResearchPriorities 15

RelevantLiterature 17

Stakeholders 19

Annex:ExpertGroupReports 21


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ExpertcoregroupsparticipantsGeneticsDonaghBerry,DidierBoichard,HenkBovenhuis,PieterKnap,BjarneNielsenGenomicsAlanArchibald,SörenBorchersen,MiguelPerezEnciso,IngelaVelander,AlainVignalReproductionAndrasDinnyes,HannekeFeitsma,MargaretaHåård,PatriceHumblotFoodsafetyandqualityRolandAumüller,Marie-HélènePinardvanderLaan,EileenWallDiversityanddistinctivenessGustavoGandini,Sipke-JoostHiemstra,SabineReist,AndreaRosatiRobustnessJoelBidanel,PoulBækbo,NicolasGengler,ChristinaLigdaAquaculturePierreBoudry,PierrickHaffray,HansKomen,AshieNorris,AnnaSonesson,ArneStorset,MarcVandeputteCattleAlessandroBagnato,DonaghBerry,LaurentJournaux,BrianWickhamHorsesBartDucro,StevenJanssensHoneybees,fur-andcompanionanimalsKasparBienefeld,CristianoBoiti,HenriHeuven,ViviHunnickeNielsenPigsJean-PierreBidanel,BjarneHolm,MiguelHiguera,EgbertKnolPoultryGerardAlbers,DaveBurt,YvesJego,IliasKyriazakisSheepandgoatsJean-MichelAstruc,LoysBodin,AntonelloCarta,JoanneConington,ClaudinoMatos

WritingGroupStrategicResearchAgenda2011DonaghBerry,JoelBidanel,PierrickHaffray,HuwJones,EgbertKnol,ClaudinoMatos,BastiaanMeerburg,Anne-MarieNeeteson,MarjoleinNeuteboom,Marie-HélènePinardvanderLaan,AnnaSonesson,FennaZeilmaker.

Coordinator:FennaZeilmakerArtwork:Factor-AAmsterdam

Annex:ExpertGroupReportsGenetics,Genomics,Reproduction,FoodQualityandSafety,DiversityandDistinctiveness,Robustness,Aquaculture,Cattle,Horses,Honeybees,fur-andcompanionanimals,Pigs,Poultry,SheepandGoatsPhotoAcknowledgementsAviagenCarolinevandenHamCobbVantressGertNieuwhofHendrixGeneticsJacquesNeetesonKVLMiriamvanStraatenNAGREFNorsvinTOPIGSVeeteeltVidarVassvikVikingGeneticsWUR


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IntroductionAnimal farming plays an important role in European society. Optimised animal production systems 1) contribute to a safe, healthy and diverse diet, 2) help to maintain sustainable human communities in more marginal regions of Europe and, 3) offer opportunities to reduce the environmental footprint. A vibrant and effective animal breeding and reproduction industry is essential if Europe is to meet the future challenges of animal farming in a rapidly changing ecological, economic and social environment. Farm animal breeding and reproduc-tion is a global, highly competitive and knowledge intensive sector. Currently, European breeding organisations are major players in the global market and therefore have a major influence on the genetic makeup of future animals and hence on the whole of animal production.

Researchprogrammesonbreedingandreproductionmustfocusonthesupportofbreedingschemeswhichenablesecureandsustain-ablefoodproductionandfoodsafety;availabilityofhighquality,healthy,affordable,diversefoodproductstoconsumersinandbeyondEuropeasrealoptionsforimprovingtheirqualityoflifeisvital.ThecompetitivenessofEuropeanagricultureandaqua-cultureanditsorganisationsshouldbeenhancedbyenablingefficientbreedingofanimalsforsustainableandsecurefoodproduction.Amoresustainableagricultureandaquaculture

shouldbesupported,includingemphasisonnon-foodfunctionsofanimalssuchasforpleasure,leisure,ormedicaluse.

TheSustainableFarmAnimalBreedingandReproductionTechnologyPlatform(FABRE-TP)worksasacontactpointfortheFarmAnimalBreedingandReproductionsectorinEuropefororganisingupdatesonresearchandimplementationandinitiatingEuropeaneffortsandactivities.FABRE-TPissupportedby116organisationsacrossEuropetoenhancethesustainabilityofanimalbreedingandreproduction

in(andoutside)Europe.Afteritsstartasanindependentinitiativein2005,thedevelopmentofaStrategicResearchAgendaandImplementationPlanwasfundedbytheEuropeanCommission(FOOD-CT-2006-044228).Since2009,FABRE-TPhasbeenfundedasajointinitiativeoftheEuropeanForumofFarmAnimalBreeders(EFFAB),FrenchNationalInstituteforAgriculturalresearch(INRA),BiosciencesKnowledgeTransferNetwork(BKTN),NOFIMA,andWageningenUniversityandResearchCentre(WUR).

FABRE-TPispresentingitsupdatedStrategicResearchAgenda,highlightingthechallengesandopportunitiesofanimalbreedingandreproductiontoanswerthegreatchallenges.Morespecificinformationperspecie,techniqueorthemearepresentedintheannex.

Allextendedversionsoftheexpertgroupreports,countryreports,theSRAfrom2007,aswellasaleafletandposterareavailablefromthewebsite:http://www.fabretp.info


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Animal breeding and reproduction: A knowledge intensive sector

FABRE-TP stands for Sustainable Farm Animal Breeding & Reproduction Technology Platform. The concept of sustainabi-lity is highly elastic and therefore different for each type of organisation. In farm animal breeding, the concerns gathered under the umbrella of “sustainability” include animal welfare and health, animal integrity, biodiversity, environmental pro-tection, consumer safety, food quality, profitability and gene-ral commercial viability. Obviously, each of these concerns is a topic in its own right. The key challenge set by sustainability is that of clarifying and balancing these concerns.

AddedValueAnimalBreedinginEurope(SRA2007)

Economicgain(cumulative,permanent) €1,89billion/yofwhichDairycattle €430million/yBeefcattle € 70million/yPigs(Europe) €520million/ySheep/goats(Europe) €156million/yBroilers(Europe) €610million/yLayers(Europe) €125million/ySalmon/rainbowtrout/seabass/seabream/turbot € 80million/y

AnimalProductionintheEU(EuroStat2010)

Value(EU27,2010) €141billion/yOftotalagriculturalproduction 40%

AgriFoodintheEU(EuroStat2010)

Numberoffarms(EU27,2007) 14millionNumberofjobs(EU27,2007) 12millionfteAnnualturnoverAgriFoodindustry €600billionNumberofjobs 2,6millionfte

Theexpectedrateofgeneticgainfromeffectivebreedingprogramsgenerallyliesaround1%peryear(e.g.Humeetal.,2011).Geneticgainsarepermanentandcumulativesothatthegainmadeinoneyearwillgivebenefitsoverallsubsequentyearswithoutfurtherinter-vention.Observedchangesinproductivityasreflectedbyannualstatisticsresultfromthecombinedeffectofgene-ticimprovementandimpro-vementsinhousing,nutritionanddiseasecontrol.Inthepasthalfcentury,importantincreaseshavebeenrealized

AsimpleconceptAnimalBreedingisbasedonthesimpleconceptofselectingthemostsuitableanimalsasparentsofthenextgeneration.Thepro-cessofdeterminingsuitabilityfocusesontwomainparts,name-lydevelopingassessmentsasaccuratelyaspossibleof:

i) Theenvironmentinwhichtheanimalsproduces,andthedemandsofthemarketintowhichtheanimalproductsaretobesold.

ii)Theanimal’sgeneticpotentialinrelationtotheseneeds.

Theprocessworksbyharnessingthenaturallyoccurringgeneticvariationthatexistsbetweenindividualanimals.Asthebenefitsofselectionarecumulative,conti-nuedselectionforthesamegoalsoverseveralgenerationsallowssubstantialgeneticimprovementstobemade.Theonlyconditionisthatthetraitthathastobeimproved,hastobeheritable.Throughhighreproductiverates(especiallyinmalesformostspecies)andtheavailabilityofadvancedreproductivetechniques,theimprovementsmadecanbedisseminatedwidely,allowingveryhigheconomicimpactstobeachievedatacompany(breedingorganisation)orindustry(farm)level.

inproductivityofpig,poultryanddairycattle.Theincreaseinpro-ductivityinthesespeciesinWesterncountriesoverthelast50yearsliesaround1%peryear(VanderSteen,2005).Atleasthalfoftheincreaseinproductivity(efficiency)resultsfromanimalbreedingactivities.

Withinanimalbreedingandreproduction,theaimistoinfluencefutureanimals-byselectingani-malsthatareoptimallyequippedtoproducemeat,milk,eggs,piglets,etctoproducethenextgeneration.Althoughanimalbreedinghasalonghistory,developmentoftheindustryasrecognisedtodaystartedwiththewidespreaduseofnewrepro-ductivetechniquesandselectionmethodsinthemid1900’s.Sincethattime,thesectorhasbecomeaknowledgeintensive,highlycompetitivesectorwithhighratesofinnovation(oftenoriginatingfromtheEU)playinganimportantroleinallowingthesectortodeveloprapidly(e.g.new


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Figure 1. Increase in meat demand, by region between 2008/2010 and 2020 (carcass weight equivalent or ready to cook) Consumption growth of 60 Mt is projected by 2020; predominantly in Asia

Source: OECD-FAO Agricultural Outlook 2011-2020

http://dx.doi.org/10.1787/888932427094

Figure 2. World fish utilisation and consumption projectionsDevelopment of utilisation of world fish production and per capita fish consumption between 2000-2020

Note: Non-food uses of fish include utilisation of aquatic products for reduction to meal and oil, for feed and bait, for ornamental purposes, withdrawals from markets and any other non-food uses of fish production (e.g. fertilisers, medical uses, etc.).

Source: OECD-FAO Agricultural Outlook 2011-2020 http://dx.doi.org/10.1787/888932427189

computingmethods,genetics,genomics,measuringtechniques).Theuseofsometechnologies(e.g.cloningorgeneticmodificati-on)raisesethicalconsiderationsregardingbalancinge.g.environ-ment,health,welfare,feasibility,choiceandanimalintegrity.Recentadvanceshaveallowedhigherratesofgeneticchangestobepossible,andalsohaveallo-wedagreaterrangeofanimalcharacteristicstobeincludedin

breedingprogrammes,especiallyinrelationtoanimalhealth,wel-fareandproductquality.

Inthefuturetheglobalconsump-tionofanimalproductssuchasfishandmeatwillincreaseevenfurther,especiallyinAsiaandthePacific,asisrepresentedinFigures1and2.Althoughanimalproductionisspreadallovertheworld,thegeneticmaterialfortheseanimalsismostlyprovided

byEuropeanbasedorganisations.Forexampleinthepoultrysectorboththebreedingorganisationsforlayersandturkeyshaveaworldwidemarketshareof>90%andareEuropeanbased.ThereforeitisimportantthatresearchinEuropeonallaspectsofsustainableanimalbreedingandreproductioncontinues.


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Farm Animal Breeding Organisation StructuresUntilthe1950s,mostbreedsofruminants—i.e.mostcattle,sheepandgoats—weremulti-purpose.Asinglebreedofcattle,forexample,wouldbekeptforbothbeefandmilk.Thatsamebreedmightevenbekeptfordraughtpurposes,aswell.Overthelastfiftyyears,specialisationhastakenplace.Ingeneral,cattlearenowbredeitherformeatortoproducemilk,andsheepbredfortheirmilkaregenerallydistinctfromthosebredfortheirmeat(woolismainlyaco-productinEurope).

Incattleasmallnumberofmajorbreedsareusedextensivelyaroundtheworld.Globallytherearemanybreeds,someofwhichareatriskorendangered.Manyofthesearegeographicallyspecialisedandthereforealsoatriskfromdiseaseoutbreaks.MostEuropeanbeefcattlebree-dersareindividualfarmerswhoaremembersoffarmercoopera-tivesorbreedsocieties.Dairyfarmercooperativesoftenprovidetheirmemberswithsemenofseveralbreedsofbulls.Bothbreedsocietiesandcoopera-tivesmaysupportresearchonartificialinsemination(AI)andembryotechnologies(ET),andundertakedataregistrationfortheirmembers.AIiswidelyusedindairybreeds.Forbeefbreeds,naturalmatingstillisimportant.Indairycattlebreeding,nexttoproduction,functionaltraitssuchasdiseaseresistance,fertility,calvingeaseandlongevityaretakenintoaccount.Newdevelop-mentsofincorporatinggeneticmarkerinformationwillassistprogressfurther,especiallyfortraitswhicharenotdirectlymeasuredorwhichhavelowheri-tability.

Theorganisationofsheepandgoatfarmersinregionalandnationalfarmercooperativesorsocietiesisoftensimilartothatincattlebutwithagreaternumberofbreederswithfewanimalsandalowerfrequencyofdatarecor-dingandperformancetesting.Thisisinpartaresultoflowermarginsfromtheirsalesofmilk,meatandespeciallyforwool.Naturalmatingwithramsisthewidelyusedpracticeforreproduc-tion.Nexttoproductionandreproductiontraits,sheepandgoatbreedingprogrammeshavestartedincludingtraitsforresistancetodiseases/endopara-sites.

Horsesareprimarilybredforsportandleisurepurposes.BreedingformeatistakingplaceinafewmemberstatesandhorsemilkhasbecomemorepopularinEuropewithsomeconsumers.Breedinghorsestoworkonthefarmisofminorimportance.Therearemanysmallandprivatebreedingunits(farmsandhobbybreeders),organisedinregionalornationalstudbookorganisationsespeciallyinsporthorses.Breedingofhor-sesischaracterisedformanybreedsbyaconstantprocessofintroductionofgenesfromtho-roughbredbreedstoimproveregionalbreeds.Breedinggoalsfocusonperfor-mance,conformation,andfuncti-onaltraitssuchasfertility,beha-viour,andanimalhealth.Performancetestingschemesneedtoovercomeproblemsrela-tedtosubjectiveanddifficulttomeasuretraits,smallgroupsfordataanalysis(e.g.raceonatrack),andselectionbias.Europehasaleadingglobalpositioninsporthorses.

Europeanpigbreedingorganisa-tionsareorganisedincooperativesandprivatelyownedcompanies.Theyhavebeen,andstillare,worldleadersintheirsector.Atrendtowardsamalgamationexists.Purebredanimalsofseveralspecialisedsireanddamlinesinnucleusherdsformthetopofthebreedingpyramid,areprovidingtheanimalsusedforcrossbree-dingfortheproductionlevel.Thebreedinggoalshaveevolvedfromhighlyheritabletraitssuchasgrowth,feedefficiencyandcarcasscompositiontonowinclu-desustainabilityrelatedtraitssuchaslittersize,pigletvitality,sowlongevityandmeatquality.

Inpoultry,afewlarge-scale(about€500–700mlnannualturnover)privatecompaniessupplybreedingstocks.Mosteggstodaycomefromspecialistcrossbredlayinghens.Broilersarealsocrossbredfortheirmeat.Themainselectioncriteriainpoultrybreedingareproductivity,productquality,reproductionandfitness,healthandwelfareaswellastraitsenhancingtheprocessingandmarketability,suchasbreastmeatyieldanduniformityofproducts.Crossbreedingfarmanimalsbringsnaturalbenefits.Forexample,productionbirdsbredformeat(broilerchickens,turkeysandducks)combinemaleandfemalelinesselectedtoensureabalancebetweengrowth,uniformityandreproductiveperformance.Inthecross,hybridvigourisalsosecured,andsotheoffspringhaveaddedvitalityandproductivity.

Breedinginaquacultureisarecentdevelopment.Theoldestbreedingprogrammesinaquacul-turehavebeenrunningfortenor


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lessgenerations.Todateithastargetedalimitednumberofspeciesoffreshwaterfish(trout,carpandsalmon)andmarinespecies(bass,bream,codandhalibut)andnoneinmolluscs.Thedegreeofdevelopmentofbreedingprogramsfordifferentspeciesdiffersgreatlyasdoesthedegreeofbusinessspecialisationofcompanies.Geneticimprove-mentisbasedonthedevelopmentoflargeselectivebreedingpro-grammesusinggenealogicperfor-mances(mostlybymultinationalsorbigcompanies)andonthedevelopmentofsmallerscaleselectivebreedingprogrammes,moreadaptedtoSmallandMediumEnterprises,usingindivi-dualselectionandinsomecasesfingerprintingtoallowgenealogicalreproduction.Thetraitscurrentlyofinterestrelatetogrowthandprocessingyieldsincludingfatcontent,diseaseresistance,spawningseason,ageatmatura-tionandbodyshape.

Europeisinternationallyleadingwithinfuranimal,honeybee,andrabbitresearch,breedingandproduction,andplaysanimpor-tantrolegloballyintrainingofworkingdogssuchasforpolice/army/customs.Inrabbits,cross-breedingisthecommonbreedingpolicywithspecialiseddamandsirelinessimilartopigs.Selectiontraitsarelittersizeandmilkpro-ductionindamlinesandmeat%forsirelines.Farmedrabbitsaregeneticallynotfarremovedfromrabbitsinthewild-theirneedsandtheirsusceptibilitytodiseaseareverysimilar.Furanimalbreedingfocusesonminkandfoxes,concentratingtoNorthernEurope(highqualityfur)innationallyorganizedschemesandinnon-Europeancountries(e.g.China)withmuchlowerproductioncosts.

Inhoneybeesthereis,nexttotheproductionofhoney,abenefitfromthepollinationofplants.The25geographicalhoneybeeracesarosefromnaturalselection.Naturalhoneybeepopulationsarestronglyaffectedbythetransportofnon-nativeraces.Breedinghoneybeesforresistancetoparasitesisbecomingmoreandmoreimportant.

Dogsareusedbothascompanionanimalsandworkingdogs.Companionanimalbreedingisinthehandsofprivatepeopleandislargelynon-commercial.Workingdogs(e.g.herdingandguarding,guiding,dogsforpolice,customs,andarmy,assistancedogs)aremainlyarelativelynewfieldofbreeding.


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Opportunity 1: Global Responsibility and Competitiveness

Scope: European farm animal breeding and reproduction organisations are market leaders in a competitive global environment. Opportunities originate from the global demand for food that is produced transparently and with respect for the environment. For this, a favourable competi-tive business and regulatory climate is a necessity.

A.Goal:ToassureglobalfoodsecurityandsustainabilityofproductionsystemsTheglobalpopulationisexpectedtogrowto9,2billionpeoplein2050(UnitedNations,WorldPopulationProspects,2010).Evenwithoutanychangeinpercapitaconsumptionoffoodproductsfromanimalorigin,thedemandwillgrowenormously.Moreover,urbanpopulationsinalldevelopingcountriesareexpectedtogrowatanaverageof2.9%peryear(Delgadoetal.,1999).Percapitaincomewillalsoincreaseandthiswillsignificantlycontributetotheincreasingdemandforanimalfoodproducts.Forinstance,theexpecteddemandforpoultrymeatwillgrowfrom80millionmetrictonnesperyear(2005)to132millionmetrictonnesperyearin2022.Thiswillmeanthatthereneedstobealargergrand-parentsstockinthebroilerindustry:46%moreby2019.Theneedforbalancedbreedingprogrammesmaybedemonstratedbythefactthatsuchanincreaseinfooddemandscanbemetwith33%extrafeedinsteadof46%.TheEuropeananimalbreedingandreproductionsectorwillcontributetoEuropeanandglobalfoodsecurityandaffordabilityofanimalproductsbyincreasingthepotentialofanimalstoproduceefficiently.Thisisdonebytrans-ferringknowledgeandsharingtechnologiesanddataacrosstheEuropeanUnion.

Challengesandopportunities:• Developmentofmoreeffectiveanimalbreedingandreproductivetechnologies

• Improvementofknowledgeandtechnologytransfer(betterexchangeofknowledge,technologiesandskills)

• Developmentofmoreefficientandsustainableanimalproductionsystems

• Increasethevalueofdatacollected,throughstandardisa-tionofrecordingmethodsandcollationofdatasets

B.Goal:ToreducetheenvironmentalfootprintandwasteIncreasedemphasisontheenvironmentwillhaveasignifi-cantimpactontheviabilityofanimalproductionandthelevelofproductionintheEU.Improvedbiologicalefficiencyandmorespecificallyareducedamountofwasteperunitoutputwillbeimportantfuturebreedinggoals.Anotheropportunityistoreducelabourinput,whilstmaintainingorimprovinganimalhealthandwelfare,andproductquality.SelectionforimprovedFoodConversionRatio(FCR)andadap-tabilitytoutilisealternativefeedsourcesislikelytohaveanimportanteffectandthereispotentialforthistobeachievedinseveralmorespecies.Possiblythereisgeneticvariationinotherimportanttraitsthathavenotyetbeendiscovered.

Globalecologicalandgeo-politicalfactorswillhaveanimpact,particularlyinthelongerterm.Therisingcostsofenergyandtransportmaystimulateproductionclosetoconsumption.Competitionforlandusebetweensubsidisedenergyproduction(e.g.bioethanol)andanimalfeedhasalreadyincreasedfeedprices.

Climatechangewillresultintheneedtomoreefficientlyuseavailableresources,toreduceemissionsofgreenhousegases,tomodifysystemsofanimalhusbandry,todevelopcropsthatcanbegrownasanimalfeedunderthenewclimaticconditions,andtocopewithemergingpatho-gensandpests.Theproductionofgreenhousegases(GHG)willimposestrongsocialandpoliticalpressuresonall(European)industriestoreducetheiremissions.Thelivestocksector(globally)iscurrentlyresponsiblefor18%oftotalhuman-relatedGHGpro-duction(CO2equivalents).Inthefutureanincreaseddemandforanimalproductionmayincreasethislevelevenfurther,thereforetheneedforbalancedbreedingandefficientanimalsisessential.

Challengesandopportunities:• Definitionanddevelopmentofpertinenttraitsreflectingenvi-ronmentalfootprintforinclusioninbreedingprogrammes

• Quantificationofthereallifebenefitsandadditionalopportu-nitiesforanimalbreedingtoreduceemissionsperunitofanimalproduct

C.Goal:ToaddressconsumerdemandsConsumerdemands,includingbothproductqualityandsafety


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aswellasthewelfareoftheanimalsproducingtheproductandtheenvironmentfootprintoftheproductionsystemsareincreasinglyintensifying.Suchdemands,butmoreimportantly,futureexpecteddemands,mustbeconsideredwhendevelopingbreedingprogrammesaswellasensuringtheconsumerthatresourcesarebeingexpendedingeneratinganimalssuitableforfutureproductionsystemswithoutcompromisingtheresul-tingproduct.Suchinitiativescanonlysucceedthroughmulti-disci-plinarycollaborationincludingani-malbreedingandreproduction.

Challengesandopportunities:• Improvedtranslationofconsumerandpurchaserdemandsinbreedingprogrammedevelop-ment

D.Goal:StrengthenEuropeancompetitivenessEuropehasalwaysplayedanimportantroleinimprovingtheworld’smajorlivestockandaquaculturespecies.Europeanbreedsareusedacrosstheworld,andEuropeanfarmersandbreedingorganisationsaremajorplayersontheglobalmarket.TheEuropeanfarmanimalbreedingandreproductionsectorwillthushaveagreatinfluenceon,andthereforeresponsibilityfor,thefuturegeneticmakeupandcharacteristicsoffarmanimalpopulationsworldwide.

ThefuturesuccessoftheEuropeanfarmanimalbreedingandreproductionsectordependsonitsabilitytoremaincompetitiveandacceptedbysociety.Farmanimalbreedingandrepro-ductionisaknowledge-intensivesector.Thismeansnotonlythatitexploitsknowledgetoprovidetheworldwithbreedingstock,butalsothattheknowledgedevelopedisorcanbeusedtomeetlocal,niche,orculturaldemandsinsideoroutsideEurope.Thepast

successofEuropeanbreedingowesmuchtoitslongstandingclosetieswithuniversitiesandresearchinstitutes,fosteringthedisseminationofknowledgetothefarmandindividualbreederlevel.

Breedingfarmanimalsthatperformoptimallyineconomicallyviableproductionenvironmentsisakeychallenge.Thiswillrequireavibrantbasicresearchandedu-cationbase,linkedwitheffective,industriallyandgovernmentallysupportedappliedresearchandtechnologytransfer.ItisvitaltoenableEuropetohavearealchoiceregardingnewtechnologiesandasolidbasisfordiscussionoftheirpossibilities,desirabilityanduncertainties.

Challengesandopportunities:• Continuousdevelopmentandinvestmentinimproved(breeding)technologiesandprogrammesthatexploitstateofthearttechnologiesandmethodologies

• Developmentofeffectivestructuresandmethodsfordisseminationofresultsthroughrelevantindustries

• Ensuringanimalbreedingprogrammestakeaccountofchangingregulatoryframe-worksandmarketneeds

E.Goal:DevelopresponsibleownershipandprotectionofnewinnovationsAstheopportunitiesthatarisefrombiotechnologicaldevelop-mentsincreaseandlargerinvest-mentsinresearcharemade,theinterestinandquestionsaboutintellectualpropertygrow.Inanimalbreeding,thereareno“AnimalBreeder’sRights”equi-valenttoPlantBreeder’sRights.Arrangementsforthetransferofownershipofimprovedgeneticmaterialaretypicallygovernedbycontractualarrangements.Breedinganimalsareexpensive–youpayfortheanimalandfortherighttouseitforbreeding.

InordertoencourageinvestmentinR&D,breedersarekeenthattheregulatoryframeworkshouldprovideaperiodofprotectionforthosethatinvestinnewtech-nologies.

Patentsarefrequentlywrittenwithanumberofclaims,whichmaycovergenesorgenesequen-ces.Suchproductsarepatentable,eveniftheirstructureisidenticaltothatofnaturalelementspre-sentintheanimalbody.Aslongasthegenehasbeenisolatedfromtheanimalbodyandtheinventorhasdiscloseditsconcre-teuse,itisnolongerconsideredasadiscoverybutasaninventi-on.Insuchcasesasdevelopingaselectiontestbasedonthesequenceinformation,utilisingthegenetoproduceatransgenicanimalorasamarkergeneetc.,thegeneitselfmaybepatenta-ble.Suchpatentshavenoeffectontraditionalbreeders:patentholdersarenotabletoclaimrightsonfarmanimalsnaturallycarryingthisgene;theymayonlyclaimrightsontheusetheypro-posedofthisgene(Noiville,inFarmAnimalBreedingandSociety,1999).

Whereexcessivelybroadpatentclaimsarebeingmade,orpatentsareappliedthatcoveralreadyrunningbusinesses,companiescanaskforre-examinationwiththerespectivepatentoffices.Inpractice,breedersexercisepatentwatchesjointly,soastoassurethatpatentsaregrantedon‘newinventionscoveringreasonablebreadthsofapplication’.

Challengesandopportunities:• EnsuringabalancebetweenprotectionandopennessofintellectualpropertywithoutsuppressingindustrialR&Dinvestments


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Opportunity 2: Social Responsibility

Scope: Animal breeding and reproduction has an enormous potential to improve our lifestyle and prosperity. Opportunities arise from the possibilities to simultaneously improve efficiency, animal welfare, health and product quality that ensure safe animal products. However, the links with the society are important: therefore accessible information, full transparency and constructive dialogue are necessary.

A.Goal:ProducesafeanimalproductsFood-borneinfectionisasignificantcauseofhumanmorbidityandevenmortality.Often,infectionoriginatesfromanimalsortheirproducts(zoonosis).Farmanimalsmaydisplaydifferentresponsestomanyzoonoticpathogens(e.g.Salmonella,Campylobacter)becauseoftheirsusceptibility.However,therelationshipsbetweenhostsandtheirmanypathogensarecomplex-diseaseresistanceofthehostislikelytobeonlyonecomponentofeffectivehealthcontrolstrategies.Moreover,newzoonoticinfectionscanemerge,suchasinfluenza.Opportunitiesmayarisethroughgenetics/genomicsresearchtoreducetheriskofrecombinationofnon-humanwithhumaninfluenzavirustypes.Suchoppor-tunitiesmightincludegeneticallymodified(GM)animalsresistanttospecificdiseases.However,selectionforresistancetoonediseasemayhaveunwantedeffectsonotherdiseases.Thus,morescientificworkneedstobedoneinthisareaofexpertise.

Foranimalbreedingorganisations,theproductionofbreedingstockthatisdisease-freeisanecessity.

Challengesandopportunities:• Exploitgeneticvariationtoredu-cesusceptibilityoffarmanimalstozoonoticandotherdiseases

• BasicGMresearchonzoonosesandfarmanimals

B.Goal:EnhanceproductqualityandconsistencyTastier,aswellashealthier,foodisbecominganincreasinglyimportantdemandfromconsu-mers.Someattributesinanimalfoodproducts(e.g.tenderness,colour,textureofmeatoralbu-menqualityofeggs)areheritable.Thismeansthattheseaspectscanbeimprovedthroughanimalbreeding.Thefarmanimalbreedingandreproductionsectorneedstotakesuchaspectsintoaccountintheirselectiondecisions.Newopportunitiesarisefromthepotentialdiscoveryofvaluablebioactivecompoundsinanimalfoodstuffs.Thesecompoundsmayprovevaluable,especiallyintheformofdietarysupplementsforimmune-suppressedindividuals.However,atthesametime,harmfuloranti-nutritivecompo-nentsmayalsobediscoveredinfoodsofanimalorigin.

Challengesandopportunities:• Exploitgeneticvariationtoimprovethequalityandconsi-stencyofproductsofanimalorigin,nexttoselectionforenvironmentalefficiency,productionleveletc.

• Exploitthegeneticvariationintheamountofbioactiveandanti-nutritivefoodcomponentsindifferentgenotypesoffarmanimals

• Developmentofqualityassuranceschemes

C.Goal:MaintainandenhanceanimalwelfareandhealthItisimportantthatanimalwelfareisidentifiedthroughtheuseofobjectivecriteria.Forbreedingpurposes,onlythosecriteriathatareheritableandthatcanberoutinelymeasuredwithahighlevelofrepeatabilityareuseful.Theshifttoselectionforimprovedproductqualityandhealthiscon-sideredamajoropportunityinallfarmedanimalspecies.Breedingprogrammescontainevermoretraits,thusbalancingproduction,environmentalefficiency,health-welfareandfitnesstraits.Thereisacontinuoussearchforreliablehealthandwelfaretraitsthatcanbeincludedinbreedingpro-grammes.Currently,thesearchforrobustanimalsthatcancopewithvariableenvironments,andanimalsthatareresistanttospecificdiseasesisahottopicingeneticsresearch.

Thereisconsiderablescientificopportunitytodevelopabetterunderstandingofthemoleculargeneticsofhost/pathogeninteractions,butthereismuchweneedtoknowbeforethisopportunityisconvertedintorealimpactsonanimalhealth.Theimpactofimprovedhealthacrosspopulationsisnotknown(herdimmunity).

Commercialproducers,especiallyofextensivelyfarmedspecies,wantbreedingstockthatcontinue


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toproduceprofitablyinarangeofdifferentproductionenviron-ments.If,forexample,supplyofanimalfeedislimited,themorerobustanimaldivertsresourcestomaintainingfitnessattheexpenseofproductivity,butwillremainproductiveatalowerlevel.

Challengesandopportunities:• Quantificationandexploitationofgeneticvariationunderlyingsustainableanimalwelfareandhealthindifferentproductionsystems

• Definitionanddevelopmentofpertinenttraitsdescribinganimalrobustness

• Developunderstandingofgeneticvariationinresponsivenesstodrugsandtherapeutics

• Developeffectivesystemsforcollectinganimalhealthandwelfaredata

D.Goal:AchieveabalancedandtransparentregulatoryframeworkFuturepolicydecisionsandregu-latoryframeworkswillhaveastronginfluenceonthedevelop-mentofasustainableanimalbreedingandreproductionsectorinEurope.Itisessentialthatdecisionsaremadeasinclusiveandtransparentaspossible.Duetotheglobalenvironmentinwhichanimalbreedingandreproductionorganisationsoperate,itisessentialthatthereisaneffectiveregulatoryframeworkwhichencouragesbusinessandinnovationontheonehand,andwhichprovidesproperconsumerinformationontheother.Apolicyenvironmentthatfacilitatesbusinessandinnovation,i.e.aworkable,practicalregulatoryandlegalframeworkandglobaltraderulesareimportantforthefurtherdevelopmentofthefarmanimalbreedingandreproductionsectorinEurope.AnexampleofpastsuccessisthedevelopmentofavoluntaryCodeofGoodPractice,Code-EFABAR®forfarmanimalbreedingandreproductionasa

resultofanEUfundedproject.Code-EFABAR®isusefulbothasaguidelinewithintheprofessionalorganisationsandasaninstru-mentfordialoguewithsociety.

Challengesandopportunities:• FurtherimplementationofCodeofGoodPracticeforfarmanimalbreedingandreproduction:Code-EFABAR®

• Ensuringanopenandtranspa-rentdialoguebetweendifferentstakeholderswhilstdevelopingnewregulationsandindustrydrivenresearchpolicies

E.Goal:MaintaininggeneticdiversitywhilerespectingdifferentculturalandregionalneedsInrecentyears,thebreedingandreproductionsectorhassignifi-cantlyconsolidateditsenterprises.Althoughcooperativeandnationalbreedingprogrammesarelikelytobemoreresistanttothistrend,wemayseeincreasedglobalisationofbusinessthereaswell.Attheotherend,therearesmallandlocalbreedingandreproductionenterprises.Bothgroupsofenter-prisescontributetomaintaingeneticvariationwithintheirspe-cies,andareimportantforthegeneticdiversityofthespecies.Geneticdiversitywithinaspeciesisimportanttobeabletoprovideanimalsthatareoptimallysuitedtomarginalareasorextensiveproductionsystems,thusincrea-singtheeconomicefficiencyoffarminginlessfavourableareas.Oftenhighermarketpricesofrecognisedlocalfoodtypesistheonlyreasonthatproductioninsomemarginalareascanbeeco-nomicallysustainable.Thereareconsiderablenationalandregionaldifferencesinbreedingpracticesandinpublicattitudestowardsthem.Eachcountrytriestoidentifyequilibriumbetweenlocalneedsandglobaluniformitydemands.Geneticdiversityisalso

importanttoaddressfutureunknownchangesinmarkets,climate,politicsetc.

Challengesandopportunities:• Achievesustainablemanage-mentoffarmanimalgeneticresources

• Adaptselectivebreedingpro-grammestospecificregional/culturalneedsandgoals

F.Goal:Improveconsumerunderstan-dingoftheapplicationandpotentialbenefitsfromnewapproachesandtechnologiesUnderstandingtheapplicationandpotentialbenefitsfromnewscien-tificapproachesandtechnologiesiskeytoacceptanceandexploita-tionofresearch.Communicationwiththeconsumerisalsokeytoensuretransparencyintheresearchmethodsandimplicationsoftheresults.However,anycom-municationmustbeinasuitableformatforeaseofunderstandingbytheconsumerandeducationofthecommunicator,whichinthemajorityofcasesarethescientists,isanecessity.Communicationmustbecontinuousandmustuseseveralmediaincludingstateofthearttoolslikesocialmedia.Potentialrepercussionsaswellasbenefitsmustbeclearlyidentifiedincludinglong-termconsequencesandrisks.

Challengesandopportunities:• Communicatewithconsumersandtheend-usersoftechnolo-giesonongoingdevelopments

• Educationofscientistsandani-malbreedingandreproductionorganisationoncommunicationwithconsumers.


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Research PrioritiesTheexpertgroupreports(seeAnnex1)generallymentionthreeimportantdriversofchange.SocietaldemandsintheEuropeanUnionarechangingrapidlyandbothcitizensandconsumershaveanopinionaboutcurrentmethodsofanimalproduction.Foodshouldbenotonlycheap(asotherwisecompetitionfromnon-EUcountrieswillarise),butalsosafeandbeproducedundergoodenviron-mentalandanimalwelfarecondi-tions.Futureresearchprioritiesshouldtaketheirconsiderationsintoaccount.Moreover,theneedtofeedagrowingworldpopulation(anestimated9,2billionpeoplein2050(UnitedNations,WorldPopulationProspects,2010))emphasizestheneedforanefficient,thoughenvironmental-

Figure 3 Main drivers of change that direct current animal breeding

Figure 4 Breeding challenges for the five domains

friendly,animalproductionindustry.Lastbutnotleast,climatechangemayhaveaninfluenceonanimalproduction:animalswillhavetoproduceunderchangingweatherandtemperatureconditions.Newhost-pathogeninteractionpatternsmayleadtoincreaseddiseasepressure;animalsofthefuturehavetobeadaptedtodealwiththesechallenges.

Intotal,fivedifferentdomainsweredefinedbytheexpertgroups,whereimprovementscanbemade(Figure4).Theseimpro-vements,whichwewillnowcallbreedingchallenges,varyfromimprovementinproductiontraitswhichwillimprovetheeconomicviabilityofthefarmerstoimprovedexchangeofknowledgebetween

differentsectors(e.g.breedingandfeedindustriesinEurope).InFigure4anoverviewofthesechallengesisprovided.Theexploitationoftherapidlydevelopingtechnologiesandunderstandinginbiologyandgeneticsprovidesanopportunitytoadapttothedriversofchange,generatingmajoropportunitiesforeffectiveanimalbreeding.


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Figure 5 Overview of the research priorities

Theseopportunitiescanonlyberealisediftools,resourcesandunderstandingthatarecurrentlymissingaredeveloped,exploitedanddisseminatedattheappropriatelevel.

FromthebreedingchallengesthatareprovidedinFigure4theresearchprioritiesmaybederived.TheseprioritiesarevisualisedinFigure5.

Thefirstresearchpriorityistheredefinitionofsomeofthebreedinggoals.Productivitywillnotbetheonlyrelevantbreedinggoalanymore,butalsoenvironmentalandwelfareaspectshavetobemoreandmoreincludedinfuturebreedinggoals,whichmayofcoursedifferbetweenthedifferentanimalproductionsectors.

Inordertokeeptrackofthebreedinggoal,itisessentialtoselecttherighttraitsforbreeding.Understandingofthebiologyofindividualtraits,howtheyinteractwitheachotherandtheenvironmentisessentialinordertobeabletoselectthe

rightsetofbreedingtraits.

Then,insomepartsoftheanimalproductionsector,animalrecordinganddatacollectionisstillsub-optimal.Performancerecordingisessentialtochoosetherightanimalsasbreedingstock.Cost-effectivemethodstocollectstandardised,comparableandappropriatedataareanecessityforoptimalfunctioningofbreedingprogrammes.

Moreover,newtoolsandtech-nologiesofferhugeopportunitieswithintheanimalbreedingsector.Newsequencingtechnologiesthatofferhighthroughputoptions,wholegenomesequencingofmostfarmedanimalspecies,thevalidationofSNPpanels,thedevelopmentofoligo-tilingpatharraysandnewbioinformaticsprogrammesarejustacoupleofthecurrentdevelopments.Thesetechnologiesofferlotsofpossibili-tiestounderstandhowbreedingworksatthemolecularlevel.

However,theneedfornewtraitsandanincreaseinthenumberofinvolvedphenotypes(themost

likelyoutcomeofthere-definitionofbreedinggoals)willimpactthebreedinggoalsbecauseoftheincreasedcomplexitythatisrequired.Theoutcomeof‘omics’informationneedstobeembeddedwithinbreedingprogrammesinordertoimprovegeneticevaluation.Moreover,specificstatisticsandalgorithmsneedtobedeveloped,whichareadaptedtothenewtraits(e.g.productquality,environmentalefficiency)andphenotypes.Amethodshouldbefoundtoaccountforenviron-mentalvariationandsensitivity,andspecifictechniquesshouldbeappliedinordertoassesslowheritabilitytraitsandtraitsasso-ciatedwithhealth,welfare,animalphysiologyandproductquality.Inordertosecuresufficientgeneticvariation,theavailablevariationshouldbefullyexploited.Inruminantsthisgoesthroughimplementationofglobalmanage-mentincommercialbreedsandsystematicscreeningofendangeredbreeds.Inpigsandpoultrythisshouldbedoneviain-housemanagementofdiversityinbreedingcompanies.

Lastbutnotleast,breedersshouldshowhowtheoutcomeofthebreedingprogrammesismeetingtheneedsofsociety,whetherthepropertraitswereindeedincluded.Moreover,know-ledgeaboutsuccessfulbreedingneedstobedisseminated.

InordertoaccomplishalloftheaboveandtoenhancethecompetitivenessoftheEuropeananimalbreedingsector,anappro-priateandworkablelegalandregulatoryframeworkisnecessary,whichstimulatesbothenterprisesandtheresearchinfrastructure.


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- EUEquus.2001.ThehorseindustryintheEuropeanUnion.Finalreport.SkaraandSolvalle,Sweden.

- EuroStat,varioustables:http://epp.eurostat.ec.europa.eu/portal/page/portal/agriculture/data/main_tables

-EnvironmentalIssuesandOptions.FoodandAgricultureOrganisationoftheUnitedNations,Rome.http://www.fao.org/docrep/010/a0701e/a0701e00.htm

- FarmAnimalBreedingandSociety-Neeteson-vanNieuwenhoven,A.M.,Merks,J.W.M.,Bagnato,A.,Finocchiaro,R.,Sandøe,P.,Christiansen,S.,Noiville,C.,VanGenderen,A.,deVriend,H.1999.Thefuturedevelopmentsinfarmanimalbreedingandreproductionandtheirethical,legalandconsumerimplications.Report.ProjectFarmAnimalBreedingandSociety.EU-QLRT-1999-130pp.http://www.effab.info.

- FABRE-TPStrategicResearchAgenda2008.

- FarmAnimalIndustrialPlatform.2000.TheFutureofGenomicsinFarmAnimals.Positionpaper.http://www.effab.info. 13 pp.

- FoodandAgricultureOrganisation.2007.TheFirstInternationalTechnicalConferenceonAnimalGeneticResourcesforFoodandAgriculture,1-7September2007,Interlaken,Switzerlandhttp://www.fao.org/AG/againfo/programmes/en/genetics/ITC_forum.html

- Gamborg,C.,Sandoe,P.2003.Breedingandbiotechnologyinfarmanimals–ethicalissues.In:Levinson,R.,Reiss,M.(Eds),KeyIssuesinEthics.RoutledgeFalmer,London,pp133-142.

- Gjedrem,T.1997.Selectivebreedingtoimproveaquacultureproduction.WorldAquaculture.33-45.

- HumeD.A.,WhitelawC.B.A.,ArchibaldA.L.(2011)J.Agric.Sci.149:9.

- Interbull.Geneticevaluation.Informationonevaluationsforproduction,


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conformation,udderhealth,longevityandcalvingtraits.http://www.interbull.org/index.php?option=com_wrapper&view=wrapper&Itemid=61

- InternationalCommitteeforAnimalRecording.2005.InternationalAgreementofRecordingPractices.http://www.icar.org/Documents/Rules%20and%20regulations/Guidelines/Guidelines_2011.pdf

- Kasanmoentalib,S.,Visser,T.,Zwart,H.(eds.),RecognizingtheIntrinsicValueofNature(Assen:VanGorcum,1999).41-53.

- Kulak,K.,Nielsen,H.M.,Strandberg.E.2004.EconomicValuesforProductionandNon-productionTraitsinNordicDairyCattlePopulationsCalculatedbyStochasticSimulation.ActaAgric.Scand.,Sect.A,AnimalSci.54:127-138.

- Laughlin,K.2007.TheEvolutionofGenetics,BreedingandProduction.TempertonFellowshipReportNo.15.HarperAdamsUniversityCollege.London.

- Liinamo,A.E.,Neeteson-vanNieuwenhoven,A.M.2003.TheeconomicvalueoflivestockproductionintheEuropeanUnion.

- Liinamo,A.E.,Flock,D.K.,deGreef,K.,Komen,H.,Nieuwhof,G.,2005.Sustainablefarmanimalbreedingandreproduction:scenariobuildingasatooltoimprovecommunicationbetweensocietyandthefoodindustry.http://www.effab.info

- Meyer,G.,Gamborg,C.,Sandø,P.2005.Ethicaldeliberation:principles.Secondreportonethicalandsocietalaspects.EADGENE.http://www.eadgene.info/AboutEADGENE/EthicsSociety/tabid/211/Default.aspx 35pp.

- Musschenga,A.W.2002.Naturalness:beyondanimalwelfare.JournalofAgriculturalandEnvironmentalEthics.15:171-186.

- OECD/FAO(2011),OECD-FAOAgriculturalOutlook2011-2020,OECDPublishing.http://dx.doi.org/10.1787/agr_outlook-2011-enChapter7:Meatconsumption.http://dx.doi.org/10.1787/888932427094Chapter8:Fishconsumption.http://dx.doi.org/10.1787/888932427189

- Rutgers,B.,Heeger,R.1999.InherentWorthandRespectforAnimalIntegrity.In:Dol,M.,FentenervanVlissingen,M.,

- Schroten,E.,1997.Animalbiotechnology,publicperceptionandpublicpolicyfromamoralpointofview.In:Nilsson,A.(Ed.),

- Steinfeld,H.;P.Gerber;T.Wassenaar;V.Castel;M.Rosales;C.deHaan.2007.Livestock’sLongShadow

- TransgenicAnimalsandFoodProduction.KSLA,Stockholm,Sweden.Pp151-156.

- UnitedNations,WorldPopulationProspects:the2010Revision.http://esa.un.org/unpd/wpp/Analytical-Figures/htm/fig_1.htm

- VanderSteen,H.A.M.,Prall,G.F.W.Plastow,G.S.,(2005).Applicationofgenomicstotheporkindustry.,JournalofAnimalScience83(Esuppl.),E1–E8.


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AarhusUniversitet http://www.agrsci.dk ABC(AgriculturalBiotechnologyCenter) http://www.abc.huABI(AgroBioInstitute-Sofia) http://www.abi.bg ACOS(AssociaçãodeCriadoresdeOvinosdoSul) http://www.acos.ptADR(ArbeitsgemeinschaftDeutscherRinderzüchter) http://www.adr-web.deA.I.AAssociazioneItalianaAllevatori http://www.aia.itUniversityofTechnologyandLifeSciences-Bydgoszcz http://www.utp.edu.pl/AltaGenetics http://www.altagenetics.nl ANAS(AssociazioneNazionaleAllevatoriSuini) http://www.anas.itANPS(AsociaciónNacionaldeCriadoresdeGanadoPorcinoSelecto) http://www.anporse.esAPEZ(PortugueseAssociationofAnimalScienceEngineering) http://www.apez.pt AristotleUniversityofThessaloniki http://www.auth.gr AquaGen http://www.aquagen.noAviagen http://www.aviagen.comBBSRC(BiotechnologyandBiologicalSciencesResearchCouncil) http://www.bbsrc.ac.ukBioTalentumLtd. http://www.biotalentum.hu BKTN https://ktn.innovateuk.org/web/biosciencesktnBUT(BritishUnitedTurkeys) http://www.but.co.uk CESTR(CzechFleckviehBreedersAssociation) http://www.cestr.czCFConsultingFinanziamentiUnioneEuropea http://www.cf-consulting.itCherryValley http://www.cherryvalley.co.ukCITA/GobiernodeAragón http://www.aragon.es CobbEurope http://www.cobb-vantress.com CONVISHerdbuchServiceElevageetGénétiqueLuxembourg http://www.convis.lu/COPA-COGECA http://www.copa-cogeca.beCRA(ConsiglioperlaRicercaelaSperimentazioneinAgricoltura) http://www.ispave.it/CRVHolding http://www.crvholding.nlCECAV(ResearchCenterofAnimalandVeterinarianSciences) http://home.utad.pt/~cecav/prodcient.html DanskeSlagterier http://www.lu.dkDeutscheReiterlicheVereinigung(GermanEquestrianFederation;FN) http://www.pferd-aktuell.deDGfZ(DeutscheGesellschaftfürZüchtungskunde) http://www.dgfz-bonn.deEAAP(EuropeanAssociationforAnimalProduction) http://www.eaap.orgEAS(EuropeanAquacultureSociety) http://www.easonline.orgEFFAB(EuropeanForumofFarmAnimalBreeders) http://www.effab.infoEstonianPigBreedingAssociation(EestiTousigadeAretushustu) http://www.estpig.eeEscuelaTécnicaSuperiordeIngenierosAgrónomos http://www.etsia.upm.es Europabio http://www.europabio.orgEuropeanDevelopmentGroupMontenegro AnimalProductionServiceandHealthDivisionofFAO http://www.fao.orgFEAP(FederationofEuropeanAquacultureProducers) http://www.feap.infoFIBL(ForschungsinstitutfürbiologischenLandbau) http://www.fibl.orgFBNDummerstorf http://www.fbn-dummerstorf.deFugato http:// www.fugato-forschung.deULgUniversitédeLiègeGemblouxAgro-BioTech http://www.gxabt.be/Gentec http://www.gentecweb.comGenusPIC http://www.genusbreeding.co.uk /pic.comHendrixGenetics http://www.hendrix-genetics.comHubbard http://www.hubbardbreeders.com HungarianSocietyofAgriculturalSciences http://www.mae-kozpont.huIAH(InstituteforAnimalHealth) http://www.iah.bbsrc.ac.uk IBABSA http://www.ibabsa.netIBBA,IstitutodiBiologiaeBiotecnologiaAgraria http://www.ibba.cnr.it IBNA(InstitutuldeBiologiesiNutritiAnimala) http://www.ibna.roICAR(InternationalCommitteeforAnimalRecording) http://www.icar.orgICBF(IrishCattleBreedingFederation) http://www.icbf.comINIA(InstitutodeInvestigaciónyTecnolog’iaAgrariayAgroalimentaria) http://www.inia.esINRA(InstitutNationaldelaRechercheAgronomique) http://www.inra.fr

Stakeholders


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InstituteofAnimalScience,Kostinbrod,Bulgaria http://iasbg.hit.bgInstituteofBiologyandImmunologyofReproduction,Bulgaria http://ibir.bas.bgInstytutZootechnikiPanstwowyInstytutBadawczy http://izoo.krakow.pl IPG,InstituteforPigGenetics http://www.ipg.nlIRTA(InstitutdeRecercaiTecnologiaAgroalimentàries) http://www.irta.esIsitutoSperimentalePerLaZootecnia http://www.isz.it/ita/index.aspITP(InstitutTechniqueduPorc) http://www.itp.asso.fr KULeuven http://bio.kuleuven.be/KingFaisalUniversity http://www.kfu.edu.sa/en/pages/home.aspxLohmannTierzucht http://www.ltz.deMarineHarvest http://www.marineharvest.comMarineInstitute,ForasnaMara http://www.marine.ieMerial http://www.merial.com MLC(MeatandLivestockCommission) http://www.mlc.org.ukMTTAgrifoodResearchFinland http://www.mtt.fiNAGREF(NationalAgriculturalResearchFoundation) http://www.nagref.grNEIKER-Tecnalia http://www.neiker.net ParcoTecnologicoPadano http://www.tecnoparco.orgNofima http://www.nofima.noNorwegianSchoolofVeterinaryScience http://www.veths.noNorsvin http://www.norsvin.no/ PASEGES http://www.paseges.grPfizerAnimalHealth http://www.pfizerah.comPigResearchCentre http://eng.vsp.lf.dkPolishAcademyofSciences-InstituteofGeneticsandAnimalBreeding http://www.ighz.edu.plSAC(ScottishAgriculturalCollege) http://www.sac.ac.ukSemenitaly http://www.semenitaly.comSIGRA http://www.sigra.lv SlovakAgriculturalResearchAuthority SlovakAgriculturalUniversityinNitra http://www.spu.skSlovenianHolsteinBreedingOrganisation SperiVet,DipartimentodiScienzeSperimentalVeterinarie http://www.sperivet.unipd.it/StonebridgeBreedingLtd http://www..stonebridgeg.com SwedishDairyAssociation http://www.svenskmjolk.seSUISAG http://www.suisag.ch SYSAAF(SyndicatdesSélectionneursAvicolesetAquacolesFrancais) http://www.sysaaf.org/Teagasc http://www.teagasc.ieTOPIGS http://www.TOPIGS.comUCL-Facultéd’IngénierieBiologique,AgronomiqueetEnvironmentale http://www.agro.ucl.ac.beULgUniversitédeLiégeFacultédeMédecineVétérinaire http://ulg.ac.be/fmv UNCEIA http://www.unceia.frUniversitaCattolicaPiacenza http://www.unicat.it UniversityofMilan-VeterinaryScienceandTechnologyforfoodsafety http://www.vsa.unimi.itUniversityofPadua-DipartimentodiScienzeSperimentaliVeterinarie http://www.sperivet.unipd.itUniversityofPalermo-Dipartimento(S.En.Fi.Mi.Zo) http://www.unipa.it/UniversityofBologna http://www.unibo.itUniversityBonn/InstituteofAnimalScience http://www.itw.uni-bonn.deUniversitáDegliStudiDiTeramo http://www.unite.it UniversityofCórdoba http://www.uco.esUniversityofCopenhagen,facultyofLifeSciences http://www.ku.dk/english/UniversityofBedfordshire http://www.beds.ac.uk UniversityofLjubljana http://www.uni-lj.siUniversityofNewcastle http://www.ncl.ac.uk/afrdUniversityofPerugia http://www.unipg.itUniversityofSevilla http://www.investigacion.us.es UniversityofStirling,InstituteofAquaculture http://www.external.stir.ac.ukVikingGenetics http://www.vikinggenetics.com/en/WAAP(WorldAssociationforAnimalProduction) http://www.waap.it/site/WCHIRZ http://www.wchirz.plWorld’sPoultryScienceAssociationFederationofEuropeanBranches http://www.wpsa.comWUR(WageningenUniversityandResearchCenter) http://www.wur.nlZDS(ZentralverbandderDeutschenSchweineproduktion) http://www.zds-bonn.de

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Annex: exPeRt GROuP RePORtSTECHNOLOGIES 1 -Genetics 22 2 -Genomics 24 3 -Reproduction 26

THEMES 4 -FoodQualityandSafety 28 5 -DiversityandDistinctiveness 30 6 -Robustness 32

SPECIES 7 -Aquaculture 34 8 -Cattle 36 9 -Horses 3810 -Honeybees,fur-andcompanionanimals 4011 -Pigs 4212 -Poultry 4413 -SheepandGoats 46


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Genetics

• Breedinggoalsmustbere-evaluatedtoaccountforchangesinconsumerandsocietalopinion,includingtheecologicalfootprint.Thisincludesincorporationof(i)traitswithuncertaineconomicvalues,(ii)thesocialinteracti-onsingroupsofanimalsthatareimportantforproperfunc-tioningofthegroup,and(iii)exploitationofgeneticdifferencesinenvironmentalsensitivityofanimals.

• Increasedinterestincross-breedingandcombiningabilityrequiresindexestorankanimalsbasedonpredictedperformanceincludingnon-additivegeneticeffects.Genomicinformationoffersnewpossibilitiestoestimateandexploitsucheffects.

• Quantifytheimpactofcurrentbreedingschemesandfordesignofnewones.Thismustexploitdevelopmentsinnewbiotechnologiesandpreservegeneticdiversity.

• Buildingtools,infrastructure,andimplementationguidelinesforbreedingstrategiesinpopulationswithpoorinfrastructure.Thisappliesto

specieswithalimitedmarket,orthatarestillintheprocessofdomesticationanddonotcurrentlyhaveabreedingschemeincludingbreedingschemesindevelopingcoun-tries.

GapanalysisandchallengesSomeoftheabovechallengesrequireincreasedknowledge,improvedtechnologiesandadditionalresourcesincluding:• Howtoexploitincreasingcom-plexityinphenotypes(e.g.,highnutritionalvalue,host-pathogeninteractions,longevitytraits,andbehaviouralorsocialinteractionsamonganimalsingroups)andincreasingvolumeofgenomicdata,andefficientcomputeralgorithmsinbree-dingvalueestimation.

• Thegenomesequenceof“minor”speciessuchasduck,quailandaquaculturespecies,aswellassequenceinformationonfounderanimalsoflargebreeds.

TheEuropeanbreedingindustryhasahightechnologicallevelthatensuresthevalueofitsproductsanddeterminesitsleadingroleintheworldmarket.Theindustryiswellpositionedtoadoptnoveltechnologiesbutthisrequiresacontinuousandsub-stantialre-searchinvestment.Accessto/useofgenomicinformation(inparticulargenesequencelinkedtophenotypicvariability)couldbelimitedinthefuture,becauseofaperceivedshort-termcompetitiveadvantageofretainingownership(particu-larlywhengenotypingcostishighrelativetothevalueoftheanimal).Itmaybecircumventedthroughinternationalconsortia.

OpportunitiesandchallengesKeyopportunitiesaretheEuropeanstrengthinpopulationandquantitativegenetics,withaccesstoawiderangeofgeneticresourcesofhighvalueandtoworld-classbreedinginfrastructure.Europeiswellpositionedtorapidlytransferscientificdevelop-mentstoamoreprofitableandsustainableagricultureandaqua-culture.Keychallengesconcern(i)quantificationoffactorscon-tributingtogeneticvariationand(ii)developmentofbreedingschemesthatmakeoptimaluseofgeneticvariationwhileres-trictinglossofgeneticdiversity:• Improvementsinbreedingvalueestimationtoincludedevelopmentsinstatistics,computeralgorithms,accesstophenotypesofpurebredsandcrossbredsinawiderangeofenvironments,andtoincrea-singgenomicdatavolume.Phenotypeswillincreaseanddiversify,e.g.fordiseaseresi-stance,behaviour,robustness;alsodevelopmentsinsensortechnology.Genotypicandsequencedatawillsoonbeavailableformanyanimalsinmanyspecies;dittofortrans-criptomics,metabolomics,proteomicsandepigenomics.

To enhance competitiveness and sustainability of animal food production, breeding pro-grams should focus on sustainable exploitation of genetic variation between animals to:• produce better-quality, healthy, affordable, diverse

food offering consumers real options for improving their quality of life;

• promote a more sustainable agriculture and aquaculture, in terms of producer profitability, biodiversity, environmental footprint, animal welfare, animal health, public health, food safety and food security.

• include emphasis on non-food functions (pleasure, leisure, use in the medical area);

Advances in genomic technologies and reproductive techniques require reassessment for breeding value estimation, breeding programs and germplasm dissemination strategies.

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Longerterm• Toolstoimprovebreedingvalueestimationincorporating“omic”data

• Estimateandexploitnon-additivegeneticvariation.

• Implementationoftoolstoselectfordesireddegreeofenviron-mentalsensitivityorspecialistsindifferentenvironments,and

toselectforcombiningability• Developmentofschemesincor-poratinglargescalegenotypingattheembryolevel.

• Betterutilisegenomicinforma-tiontoexploitdifferenttypesofDNAvariation

Short,mediumandlongtermopportunities/needsforresearchFirst5years• Breedingvalueestimation: oOptimalincorporationof

“omic”information oStatisticalprogramming

adaptedtonewtraitsandnewphenotypes

• Breedinggoals: oFindinganeconomically

viablewaytoincludetraitsofincreasingconsumerconcernincludingthosewithuncertaineconomicvalue

oToolstoexploitgeneticsoftraitsinfluencedbysocialinteractions.

oAccountingforlargeenviron-mentalvariationandenviron-mentalsensitivity

• Breedingplans: oToolstoachievesustainable

long-termgeneticgain,avoidundesirablesideeffects,andsecuresufficientgeneticvariation

oExploitationofnewdevelop-mentsinothertechnologies(e.g.,reproduction)


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Genomics

Short,mediumandlong-termopportunities/needsforresearch

FiveyearsGenomics,sequencingandgenomicvariation:Sequencecharacterisationofthegenomes,andvariationtherein,ofecono-micallyimportantspecies,popu-lationsandindividualsiscriticalto21stcenturyselectiveanimalbreeding.• “Finished”qualitygenomesequences,togetherwithmas-sivediscoveryofvariants,formostrelevantspecies.

• Metagenomicsequencingmicrobialcommunities,e.g.,inthegastrointestinaltract.

• ToolsforgenotypingDNAvari-ants,includingSNPsandCNVsathighdensity.characterizationofepigenomicsvariationacrossarangeoftissues.

Transcriptomics,proteomicsandmetabolomics:Knowledgeofsystemsatthelevelofthetranscriptome,proteomeandmetabolomecancontributetounderstandingthelinksbetweenthegenomeandthetraitsofinterest.• Refinetranscriptomictools(arrays,RNA-seq)anddevelopproteomicstechnologiesforhighthroughputanalysesinfarmedanimal.

• Developcomprehensiveimmu-nological,metabolomictoolkitsforhighthroughputassaysofforallmajorfarmedanimalspecies.

• Developsystemsforhighthroughputgeneticmodificati-on,includingRNAi-basedgeneknock-downincell-basedsystems.

Phenomics–Thephysicalandbiochemicaltraitsoforganisms:Assequencingandgenotypingcostscontinuetofall,effectivecaptureofphenotypicinformationhasbecomethebot-tleneck.• Establishstandardphenotypictraitontologiesforthemajorfarmedanimalspeciestoencompassproductiontraitsanddiseasetraits(metabolic,inheritedandinfectious).

• Co-ordinateandstandardisetheacquisitionofdiseasesur-veillancedataatapan-Europe-anlevelEncouragetheuseofcommercialpopulationsforhighresolutiongeneticanaly-sesinfarmedanimalspecies.

Bioinformatics,statisticsandcomputerscience:Effectiveexploitationoftheopportunitiespresentedby‘omicstechnologiesrequiressubstantialdevelop-mentsinbioinformatics,statisticsandcomputing.

The growing awareness of the finite nature of the planet’s resources means that changes are needed in many economic sectors, including animal production systems, to address environmental issues and more generally sustainability. The scientific strategy for sustainable animal breeding and reproduction needs to address ‘animal as systems and ani-mals in systems’. The development and testing of models lie at the heart of systems biology research. The extent to which a model is predictive determines its value in under-standing the system of interest. Such models have been the foundation of quantitative genetics and genetic improvement of plants and animals for decades. Thus, adapting the 21st century vision of systems biology to the needs of sustainable animal breeding and reproduction is about ensuring that the technologies and information systems customised for the target species and systems are put in place.In the next five years many new genomes and transcripto-mes (species and individuals) will be sequenced. Significant developments in statistical and computing tools, along with improvements in capturing phenotypic data, will be required to realise the potential of genomics to deliver information that will be useful to design improvements in sustainable animal production. The key agenda items to deliver geno-mics-driven improvement in animal breeding and production are set out below.

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Fifteenyears• Integrationofmulti-level‘omicsdata(genomesequence,trans-criptomics,proteomics,metabo-lomics)foreffectivedissectionofthelinkbetweenthegenomeandendtraitsofinterest.

• Useadvancedtechnologiestoacquirehighqualityphenotypicdataforlargenumbersofanimals(livingand/orpost-morteminslaughterhousesorpackingplants).

• Userfriendly,customizableandyetsophisticatedstatisticaltoolsandwebbasedsystemstomakethemostofgenomicandphenomicinformation.

• Exploitlatestcomputingandcommunicationstechnologiesformoreeffectiveformoreeffectivedatastorage,sharing,integrationandanalysis.

Twenty-fiveyearsDeveloparangeofstemcellsfromfarmedanimalspeciestofacilitatecell-basedinvitrofunc-tionalgenomicsresearch,inclu-dinggeneticmanipulation.Developsystemsforhighthrou-ghputgeneticmodification,inclu-dingRNAi-basedgeneknock-downincell-basedsystems.Developadvancedtechnologiesforgeneticmanipulationinfarmanimalspecies,includingthecapabilityforprecisiongeneticmodificationusinghomologousrecombinationinappropriatestemcells,useofzinc-fingernucleasesandRNAi-basedgeneknockdown.

• Supportforcontinuedannotati-onandmaintenanceofgenomedatabasescustomisedforfar-medanimalspecies(needforcontinuityrequiresinclusionin15and25yearagendas)

• Developdatasharingpoliciestomaximisethevaluetobeextractedfromcomplexdatasetswithoutcompromisinglegitimatecommercialinte-rests.

• Exploitdistributedcomputingtechnologies(GRID,Cloud)formoreeffectivedatastorage,sharing,integrationandanaly-sis(cf.iPlant).Developscala-blebioinformaticstoolstohandlehighthroughput‘omicsandtraitdata,e.g.,genomicselectionproceduresorinfe-renceofgenomewidediversityparameters.


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Reproduction

organsortissuedonorsarealreadyonthemarketandwillgrowfastinimportance.Inspeciessuchaspig,sheep,goat,cattleandrabbit,efficientproductionoftheseveryhighlyvaluableanimalswouldrequireimprovedreproductivetechnologies(Assistedreproductivetechnology(ART),nucleartransfer,gametebanking).Althoughtransgenicfarmanimalsarenotessentialforfoodsecurity,theneedforspecificRTishighandtheanimalproductionforfoodsecuritycanbenefitfromdevelopmentsandresearchinthisarea.Thereforeclosecollaborationbetweenteamswithdifferentareasofexpertiseisnecessary.

GapanalysisandgoalsettingIInordertomeettheseoppor-tunitiesandchallengesthereisaneedtoimproveefficiencyofRTingeneral,butthisneedmaybeevenmoreimportantforspecificlocalandendangeredbreedsorspecies.Thegapisduetodiffe-rencesinanatomyandphysiologyamongdifferentspecies,alackofcoordinationintheresearchanddifferencesinthelevelofdevelopmentinthefieldwhichhamperpracticalapplicationofRTindifferentspeciesorbreedspresentinEU.Thereforeitisimportantnotonlytofillthegapsofknowledgeandfurtherdeveloppracticalmethodsinordertofacilitatetheuseofbotholdand

newreproductivetechniquesbutalsotoinvestincoordinationinresearchandapplicationwithintheEUwithrespecttotheseRT.AcoherentandflexibleEuropeanresearchagendainanimalbree-dingandreproductionthereforeisamusttoachievethefollowinggoals:

1.Improvetheefficiencyofreproductivetechniques(includingART)topreservegeneticdiversity,

2.Identifythecriticalnetworksofgenesinvolvedinfertilitythroughreproductivephysiologyandgeneexpressionstudies

3.Identifythroughaccessto“omictechnologies”newphe-notypicandgeneticmarkersforfertilityformultitraitselectionandpreventionofdiseases.Thisaspectwillbeverycriticaltoimproveperfor-manceandcompetitivenessofthebreedingindustryinEuropekeepingupthequalityofdairyandmeatproducts.

4.Improvereproductivetechni-questolowerecologicalfoot-print

5.Increasefoodsecurityinrelationwithglobalwarmingandglobalincreaseinhumanpopulation.

6.ImproveefficiencyofRTtofillthegapsinhumanARTinrelationtotheuseofanimalmodels,investigationofepige-neticeffectsanddevelopmentofnewtherapeuticapproaches.

TheproblemofstasisIfnoresearchanddevelopmenttakesplaceintheareaofRT,therateoffurtherdevelopmentsinanimalbreedingwillbedrasticallyreduced.Thiswillnegativelyinfluencetheevaluationanddis-seminationofspecificgenesofhighimportancefortheimprove-mentofanimalhealthandwelfareaswellasforthechangesneces-

OpportunitiesandchallengesTherapiddevelopmentsinmoleculargenetics,and“omictechnologies”(genomics,proteo-mics,metabolomics)andgenomicselectionhaveprovidednewopportunitiestoreducegenera-tionintervalsandenhancefertilityandbreedingefficiency.EffectiveuseofRTisimportanttoreapthemaximumbenefitsofgenomicselection.Thiswillenablepro-ductionofmoreoffspring(largerlittersizeforsomespecies),andgeneticallymoreefficientanimalstoreducecostsandguaranteeefficientfoodproduction.Suchdevelopmentsrepresentamajoropportunityforbothsecurefoodproductionandforapplicationsinhumanaswellasveterinarymedicine.Thereareseveralchal-lengesinoptimisationofexistingRTespeciallytoimprovetheirpracticality,todevelopnewtech-niquesandtoimplementRTovermultiplespeciesforasecure,diverseandsustainablefoodsupplyforEuropeancitizensandforapplicationintheareaofveterinaryaswellashumanmedicine.Partofthechallengeistoovercomelackofknowledgeandcircumventtheanatomicalandphysiologicallimitationsinsomeofthespeciesthroughdedicatedresearchanddevelopment.Interdisciplinaryopportunities:Transgenicfarmanimalsgeneratedforuseinnewmedicalapproa-chesasmodels,bioreactorsor

Reproduction techniques (RT) are almost indispensable and essential components of modern animal breeding. They have been used for decades to enable safe and efficient breeding and to ensure improved efficiency in food production. Several reproduction techniques are available but their application in animal breeding schemes differs between countries and regions in Europe as well as between the different species. Relatively new is the application of RT in the area of human medicine, for example for transgenesis in relation to xeno-transplantation or for use of animal models in pharmaceutical research.

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selectiongoalswillrequiredisse-minationofgenesfromveryfewelitesiresthroughinnovativeandefficientRT(e.g.Embryotypingpriortotransfer).

Themostrelevantresearchactivi-tiesasaresultofthegapanalysisandprioritysettingexercisearesummarisedinTable1(appendix).Duringthisprocess,wefirstdiscussedforeachresearchissuehowmuchitcontributedto:

efficientfoodproduction,environ-ment,animalhealthandwelfare,sustainabilityandhumanapplica-tions.Thenresearchissueswererankedbasedontheirprioritieswithinthecategoriessub-catego-ries.Themaincategorieswere:RTresearchingeneral,artificialinsemination(AI),embryotrans-fer(ET),AssistedReproductiveTechnologyinanimalsforhumanmedicine,Nucleus/Genetransfer.

Researchactivity PriorityTimeframe(years)

Efficientsemensexing High 5

Diseasetransferthroughsperms/oocytes/embryos/nuclei/genes:-detection,relevanceanddestructionofpathogens. High 5-15

Gametedevelopment,maturationandembryodevelopmentincludingmaternalinteraction=epigeneticsandfetalgrowthregulation High 5-15

Optimizationofestrussynchronization,ovulationinduction,superovulationresponse,minimizingtheuseofhormones High 5-15

Improvedinvitroembryoproduction High 5-15

ART/NT/GTtechnologydevelopmentforinstancetocompletefunctionalvalidationofthenovelcandidategenespotentiallyaffectingfertilityandothereconomicallyimportanttraits High 5-15

Rearingofefficientbreedinganimals High 5-25

Influenceofphysicalenvironmentandanimalinteractiononreproductionincludingfeedcomposition. High 5-25

(Cryo)preservationofgametes,embryosandsomaticcellsforgenebankingpurposesandreproduction High 15-25

Improvementofimagingmethods:Ultrasonographytoanalyzeovarianstate,earlydetectionofpregnancyandfetusabnormalities. Medium 5-15

Evaluationofrelevantbreedingsoundness Medium 5-15

Developmentofaccurateovulationdetectionmethodsfortimedinsemination Medium 5-15

Lowdoseinsemination Medium 5-15

Improvementofmethodsforprocessing,handlingofembryo’sinordertoenhancesurvival/quality Medium 5-15

Investigationofthefertilizationprocess Medium 5-15

DevelopmentofAItechniqueswithimprovedpracticalityandlaborefficiencyforallspecies Medium 5-15

Semenpreservation:developmentofnewextenders,slowreleasesemenincl.liquidsemen Medium 5-15

Non-surgicaltransferofembryos Medium 5-15

Embryoquality:developmentofdiagnostictestsforrelevant(genetic)characterizationofembryoquality Medium 5-15

Noninvasivesexingofembryos Medium 5-15

Estruscycle:investigationoftheestruscycleforsomespeciesorendogenousbreeds Medium 5-25

Femalefactorse.g.reproductivediseasesassociatedwiththedecreaseinfertilityandpregnancyloss Medium 5-25

Developmentofmilkornonmilkbasedindicatorsforestrusandpregnancy Medium 5-25

Improvementofefficiencyandsafetyofgenetransfermethods Low 5-15

Developmentoftransgenicanimalmodelsfornewapplicationsinthemedicalarea Low 5-15

Farmanimalproductionforanimalmodels Low 5-25

DevelopmentofadvancedNTprotocols Low 5-15

Establishmentofcellulardifferentiationandtransplantationmethods Low 5-15

Farmanimalproductionforbiomedicalapplication Low 5-25

Developmentofmethodsforderivationandmaintenanceoflivestockembryonicandadultstemcells Low 5-25

Riskassessment/researchcommunication Low 5-25

saryfortruesustainabilityinagri-cultureandaquaculture.Inthenewcontextofgenomicselection,reproductiveefficiencymaybeco-meabottleneckinselectionforproductiontraitsaswellasfunctio-naltraitsandforthenewtraitsofimportancetolimitenvironmentalfootprints.Atthesametime,selectingforaverylargenumberoftraitsofinterestmayleadtoincreasedinbreedingandtoreducedgeneticdiversity.Such

Table1:Researchactivitiesandpriorities


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Food Quality and SafetyNutritionalquality:Thenutritionalvalueoffoodsofanimaloriginisdrivenbymacroandmicrocom-position.Thereisanopportunitytoimprovegeneralnutritionalvalueandmaintainandfurtherdevelopnicheproducts,throughbetterunderstandingofthegeneticsandgenomicsofproductcomposition.

GapAnalysisThemaingapsare:a)theneedtoidentifytheDNApolymorphisms(andtheirmodeofaction,SNP,CNV,etc.),theirinteractionswitheachotherandtheenvironmentcontrollingtheheritablecomponentofrelevanttraits;b)theneedforthedevelopmentofbetter,cheaperandlessinvasivetoolsformeasuring(deep)phenotypesasabasisforbreedingvalueestimationandpaymentsystemsandc)theintegrationofa)andb)toaddgenomicselectionfornoveltraitsrelatedtofoodqualityandsafetytogeneticimprovementprogrammes.New‘gaps’inrela-tiontosafetymaybecreatedbylegislativechanges(e.g.antibioticban).Also,changesinfuturedis-tributionoflivestockproduction,

spatialandtemporalandconsi-deringscaleandtype(e.g.,freerangevsintensiveindoors),islikelytohaveanimpactonthe“risks”tofoodsafety,butcouldalsoprovideopportunities.

TheproblemofstasisWithoutrelevantresearchonproductsafetyandqualitywithinEuropewewillnotbeabletosatisfytheincreasingdemandofconsumersfordiversefoodsofhighsafetyandqualityproducedinatransparentandtraceableway.Weriskthatanimalbreederselsewhereintheworldgaininmarketshare,andalsomissoutontheopportunitytodevelopdifferentiatedvalue-addedproductstohelpEuropeanfarmerscompetewithlower-costimports.

Priorityproblemsandopportunities.Consumerandretailersexpecta-tionsfornutritionsourcedfromlivestockinEuropearechangingveryquicklyandmoreandmoreinformationontheprovenance,qualityandsafetyofthefoodisrequired.Theanimalbreedingsectorneedstobeabletoadjustselectiongoalsconsistentlytomeettheseexpectationsandtoprovidenewproduct/marketopportunitiesthroughselection.Therearesignificantopportunitiestoimprovesafety,qualityandconsistencyofproductthrough;a)developmentofbettertoolstomeasure/predictphenotypesandb)genomicsresearchtodevelopmoleculargeneticselectiontools.FoodSafety:Weneedtobetterunderstandandexploitgeneticvariationinresistancetoinfectionby(currentandemergent)zoon-oticorganismsasoneofseveraltechnologiesneededtoensurefoodsafety.

Productquality:Thesafedisse-minationofgeneticimprovementalsohasaroletoplayinensuringfoodsafetyandquality.

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andthoseunderdevelopment.Weneedtodeveloptoolstorou-tinelyphenotypeanimalsforthesetraitsandprogressfromQTLtoidentifiedpolymorphisms.Thesearerequisitesforintegra-tingfoodsafetyandqualityrelatedtraitsinfuturegenomicselectionprogrammes.Weneedtodeveloptoolstoaidinthecollection,collationandqualityassuranceofrelevantdatainthefoodchainandacrossborders.Theprovisionofinteroperabilityofdifferentdatabasesandtoenableeasydata-exchangesshallbearesearchtask,aswell.

15yearsContinuedworkonthetraitslistedunder5-yearstogetherwithincreasingattentiontootherzoonoses(especiallyVTEC,Staphylococcusinmilkandviralinfectionsofshellfish),foodflavourcharacteristics,proteinqualityvariation,processingcharacteristics(weexpectimpor-tantdevelopmentsinprocessinginthistimescale),micronutrientcompositionandconsistencyofthedesiredfood/processingqualityattributes.

By15yearsweshouldhavesuf-ficientknowledgeofimportantgenesforqualityandsafetytraitsandtheprioritywillbetoresearchtheinteractionsofthesemajoreffectsinrelationtothesustai-nabilityofspecificlivestockpro-ductsandsystems.Advanceswillalsobeneededingeneticevalua-tionsystemsthatcombinenovelphenotypes,multiplegeneticmarkersand/orcompletegenomestoinformselectiondecisionsandproductdifferentiation.Also,foodqualityislikelytoexpandtoincludefunctionalattributesoftheproductratherthansensoryattributesalone.Ashighlightedthiswillbeatraitthatanimalbreederswillchasebutfoodresearchislikelytodevelopanimalfeeds(oradditives)whichwillconveythedesiredfunctionalattributeintheanimalproduct

(i.e.,functionalfeedsleadingtofunctionalfood).Withthecombi-nationoftoolsavailableitwillbeimportanttounderstandthegenotype*dietinteractionforthedesiredattributes.Asaresultofglobalchangecompetitionforresourcesmaychangethecom-positionoflivestockdiets(e.g.,availabilityofgrainforanimalfeed,useofnewproteinresources)whichcouldimpactonanimalperformance,productqualityandconsistency.Animalbreedersmayneedtoexplorefuturegenotype*futurediet(andsystem)inter-actionsfortraitsofinterest.

25YearsInthistimescalepriorityshouldbegiventoanimalfitnessandadaptationtoglobalchangeasacomponentofperceivedquality.Theknowledgeofthefunctionalgeneticelementsrelatedtofoodsafetyandqualitytraitswillhavegrownsignificantlyandresearchwillbedrivenbypredictivebiolo-gicalapproachesthatseektomodeltheinteractionsofgenesandproductionsystemstomeetspecificmarketneeds.Fromimprovedunderstandingofthegenomicsofhost-pathogeninter-actions,researchshouldincludenovelapproachestosafety,inclu-dingimprovedvaccinesandpos-siblyGMapproachestoresistance.

RESEARCHNEEDS

First5yearsAnimalbreedingcanhelptosup-portantibioticreductionpolicybyimprovingselectionforgeneticresistanceandbetterunderstan-dingofimmunesystemespeciallythenon-specificpartofit.Havinginmindthattheuseofantibioticsinlivestockproductionwillbedecreasedinthefuture,thosegenotypesthatrequirelessadmi-nistrationofpharmaceuticswillbecomethepreferredones,pre-ferredbyproducersandconsumers.Theprioritiesare:Campylobacter

infectionofpoultrymeat,Myco-bacteriumaviumsubspeciesparatuberculosis(MAP)inbovines,MRSAandESBLproducingbacteriainintensiveproductionsystemsandrelevanceforhumanhealth,Salmonellainfectionofpoultryandpigmeatandeggs,ListeriamonocytogenesinReady-To-Eatfoods,innateimmunity,generalanimal“fitness”,identifiedtaintsoffoods(especiallyboartaints),tendernessofbeefandpork,shellqualityofeggs,lipid/antioxidantcontentandcompositionofallanimalfoods,storagestabilityoffishandmilk.Understandingtherolethatgeneticsplaysintheresponseofanimalstovaccineswillhelptoidentifyanimalsthatrespondbesttovaccines,current


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Diversity and Distinctiveness

gementofthegeneticvariationofworldwidedistributedcommercialbreeds,inordertoavoidlossesduetotheuseoftoonarrowgeneticbasis.

• Tominimizethenegativeimpactofimprovedselectionprocessessuchasgenomicselectiononthegeneticdiver-sityofbreeds.

• WithEUenlargement,numberoffarmshasmorethandoubled.InthisprocessnewbreeddiversityhasalsoenteredinEU.AcrossallEurope,stillexistingdiversityisatriskofbeingexposedtotheerosionprocessthatgenerallyaccom-paniesintensificationofpro-ductionsystems.

1.2Keyopportunities• Breeddiversityisoftenthoughtjustassourceofgeneticvaria-tiontoensurefuturegeneticimprovement.However,itisalsovaluableforfoodproductdiversificationandquality,formaintenanceofdiversityofnaturalagro-ecosystemsandruralcultureandfornewrolesupraisefordomesticanimals,includingsport,leisure,tourism,companion,hobby.

• AwarenessforfarmanimalgeneticresourceshasbeenraisedinthelasttwodecadeswithinEU.

• Genomicresearchismakingpossibletolocaliseandcharac-terisegenesandtheirfunctions.Breedswithextremephenotypesareprovingtobeparticularlyusefulatthisrespect.Then,breeddiversityoffershigh

1.Challenges,opportunities,gaps

1.1Challenges• Tomaintainwithintheproductionsystemsalargevarietyofbreedseconomicallycompetitive.Thisincludesdevelopingsustainablelocalbreeds.

• Todevelopmethodsandstrategiestofurtherexploitavailablegeneticvariationinlivestockandatthesametimeimplementandfurtherdevelopmethods/strategiestomaintainfarmanimalgeneticdiversity.

• Toachieveawiderparticipationofthestakeholdersontheissuesofanimalgeneticresourcessustainableuseandconser-vation,includingtheindustry.

• ToachieveabetterincorporationofAnGRcriteriainpolicies.

• Todeveloplowcoststrategiesforanimalgeneticresourcesinventories,conservationanddevelopment.

• Todevelopandimplementstrategiesforacommonmana-

Introduction: exploitation and conservation of genetic diversityFarm animal genetic resources are sources of genetic variation of fundamental importance to ensure future genetic improve-ment, to satisfy possible future changes in the markets and in the production environment, and to safeguard against disasters that give an acute loss of genetic resources. In many areas, local breeds adapted to harsh conditions are unique sources of income for the rural communities. The link between local breeds and the environment where they were developed makes them key components for the management and con-servation of the European agro-ecosystems diversity, and important elements of cultural diversity, as they reflect a history of symbiosis of relatively long periods with mankind. Diversity of breeds and their farming systems highly contribute to European food products quality and diversity. Then, farm animal genetic resources are opportunities to maintain a vital countryside. European breeding organisations are strong players in the global competition. It is crucial for Europe that the breeding sector maintains and further develops its leading role. At this respect, sustainable utilisation and conservation of the European breed (and production system) diversity can play an important role.

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Strategiesshouldbebasedonatotaleconomicvalueofbreeds.

• Strategiesforminimizinggeneticloss(inbreeding)underimprovedselectionprocesses(e.g.genomicselection).

2.Theproblemofstasis:whatwillhappenifnoresearchordevelopmentoccurs

• Lossoffarmanimalgeneticdiversityandofopportunitiesforfuturedevelopmentoffarmanimalpopulations.

• Lossofopportunitiesforkeepingavitalcountryside.

3.Short,mediumandlong-termneedsforresearch

3.1Fiveyearshorizon• TodevelopstrategiesatthecountryandEuropeanleveltohalterosionoffarmanimaldiversity,withinandbetweenbreeds.

• Todevelopmodelsandstrate-gies,attheEuropeanandgloballevels,forthemanagementofgeneticdiversitywhenbreedingisnotcentralisedinordertoavoidtheriskthatatoonarrowgeneticbasiswillbeused.

• Todevelopenhancedrepro-duction,moleculargeneticandstatistictoolsforpreservinggeneticdiversity.

• Toincreaseefficiencyand

profitabilityoflessintensiveorsmall-scaleanimalfarming,oftenassociatedtolocalendangeredbreeds.

• Todevelopstrategiestobalanceimprovedselectionprocesses(genomicselection)withminimizingthelossofgeneticdiversity.

3.2Fifteenyearshorizon• Tostudyefficiencyofstrategiestohalterosionoffarmanimalgeneticresources.

• Tounderstandandexperimenttheroleofanimalfarmingagri-cultureincludingtheassociatedlocalbreedsinsustainableruraleconomiesandenvironments.

• Todevelopmechanismsinordertohavemarketsrecognisingthenon-marketservicesoffarming,includingtheenviron-mentalandculturalroles.

• Toimplementknowledgeondifferencesinthegeneticstructuresofbreeds.

• Todeveloptechniquesfortheregenerationofindividualsfromcryoconserveddiploidcellsinoviparousspecies

3.3.Twenty-fiveyearshorizon• Todevelopmodelsusingbreeddiversitytounderstandgenomestructureandfunctions.

opportunitiesforunderstandinggenomestructureandfunctionoffarmanimals,anddevelop-mentopportunities.

• Breedswithseeminglylimitedcompetitivebenefitmayharboursinglegenes(e.g.diseaseresi-stance)ofpotentialhighvaluewithrespecttoeconomicsandanimalwelfare,whichcanbetransferredthroughtraditionalbreedingstrategiesortransgenictechniquesinhighefficiencybreeds.

• Europeanresearchleadershipinthefarmanimalgeneticresourcesissuecanprovideusefulexpertiseforotherpartsoftheworld.

1.3GapanalysisBasictechnologytomeetexistingchallengesandopportunitiesisalreadyavailable,butneedsfurtherdevelopmentinparticularinthefollowingareas:• systematicscreeningofpotentialuniquegeneticstructuresin(endangered)breeds,basedonfarmanimalsequences,highthroughputgenotypingandcomparativegenomics;

• reproductivetechnologiesforcommercialandconservation(exsitu)purposes;

• strategiesforkeepingavitalcountryside,includingthecha-racteristicanimalproductionsystemsandassociatedbreeds.


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Robustness

titorsandEUcitizenswillnotfindthequalityofproductsandpro-ductioncircumstancestheyaspireto.Givenalreadyknownandprobablygeneralisednegativegeneticcorrelationsbetweenpro-ductionandhealthtraits,lackofresearchinthisareawillleadtocontinueddeterioratingfunctio-nalityofanimalsandthedecreaseofanimalwelfarebecauseofthelackofadaptationtoproductioncircumstances.

Short,mediumandlong-termopportunitiesandneedsforresearch5yeartimehorizonbygroupoftopics:• Improvedperformance,environmentalimpact,healthandwelfarerecordingfordiversecommerciallyandsoci-allyimportanttraitsincluding:

oSustainableperformancerecording(e.g.,usefulinformation,geneticandnon-genetic,goingbackquicklytofarmersstimulatingandmaintaininginterest)linkedtogenotypicdata.

oBiologicalefficiencyandenvironmentalsustainability(e.g.,waste,diets,green-housegases).

oAnimalhealth(e.g.,recordingcoveringallanimals,notonlydiseased).

oAnimalwelfare(e.g.,indicationofwelfareaspectsoftraitsinbreedingprogrammes,developingandrecordingofobjective(heritable)welfareindicators,welfarebeingthebalanceofthevariousaspectsinbreedingprogramme,andappropriatemanagement).

oLinkingofexistingdatabases,easierdataexchange,onaherd-level,regionally,nation-allyandEUwidetogetherwithpublic-privatecooperationinthisfield.

oObtainingdatainenvironmentsclosertocommercialuseinallspeciesandforalltraits.

• Improvedgeneticevaluationsforperformance,healthandwelfaretraitsincluding:

oDevelopmentofroutinecom-binedgeneticevaluationofanimalsbasedonphenotypicandgenomicinformation,sustainingresearchtowardsgenomicselection.

oAdvancedgeneticevaluationsusingoptimallyexistingdatabasesonaherd,regional,

ProblemofstasisExpertsidentifiedthatstasisinthefieldsof“Health,Welfare,andPerformance”(Robustness)willincreasethegapbetweenavailableandneededanimalsinthefuture,aswellasthegapbetweentechnologicalpossibilitiesandadequateuseofthem.ImpactontheindustryandEUcitizenswillbeverysubstantial.Industrywillbeunabletoadaptandfacechallengesfromcompe-

Robustness comprises many components but in general is the way animal can cope with its environment and potential changes in this environment. Climate change is one of these potential changes and can have large effect on disease challenge, in fodder and water availability, and land degra-dation. Given the current evolution of the European agriculture and the demand for environmental friendly production systems; adapted breeding for low input and industrial pro-duction systems will be needed. Environments will become less “optimised” due to welfare consideration (e.g, extensi-fication, open air, more diverse feedstuff), genetic characte-ristics need to be adapted in order to avoid decrease in fitness and therefore efficiency. This should be considered also in relation to the climate change, as extensive systems maybe more susceptible to some negative effects of climate change. Shift to selection for increased product quality, healthy and safe products is considered a major challenge in all species from poultry to buffalos. To achieve such goals, all methods to develop adequate multiple trait selection tools in breeding strategies should be encouraged. More automatic on-farm performance recording (e.g., milk ingre-dients and hygienic status), interaction between recording protocols and modelling of genetic and non-genetic goals are key opportunities and challenges.

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productqualityandanimalrobustnesstraitswillbewidespread.

oAdvancedmodellingfornewandpotentiallymassivedata(e.g.,longitudinaldatarecor-dedon-farmautomatically)willbeneeded.

oIntegrationofGxEinteractioninroutinegeneticevaluations,selectinganimalsforanenvi-ronment,notcreatingproperenvironmentsfortheanimals.Thiswillbeespeciallyimportantinlessoptimisedproductionsystemsandfor

developingcountries. oInteraction,dataexchange,

distributedcomputingandexpert-systemswillbedeve-lopedonaherd,regional,nationalandEUwidelevel.

oMajorresearchindevelopmentofgeneticsolutionstodisea-ses,leadingtodevelopmentofgeneralisedimmunity.Thiswillbeaccompaniedbyinvestigationsofthemolecularorpolygenicgeneticmecha-nismsspecifictoindividualdiseases.

oMoleculargeneticscouldplayamajorroleincludingtheuseoflaboratoryspecies(e.g.,mouse)toidentifydiseaseresistancecandidategenes.

25yeartimehorizonDevelopmentsoftechnologieshavethepotentialtochangeradicallythedirectionofanimalbreedingforperformance,healthandwelfare,mostinfluentialshouldbeincreasedcapabilities:• Monitorbiologicalprocessestogainnewinsideintoanimals

• Acquiremolecular,gene-expressionandothernoveltypesofdata

• Analyzedataandtopredictgeneticmeritandnon-geneticmanagementrelatedvalues

nationalandEUwidelevel,takingintoaccountgenotype-environmentinteractions.

oStrengtheningresearchongeneticevaluationmethodo-logy,inparticularfornoveltraitsasproductqualityandanimalfitnessandrobustness.

oDevelopmentofEUwidecooperationoncommonbreedinganimalcomparisons.

• Improvedbreedingprogrammesforperformance,environmentalimpact,productquality,healthandwelfare:

oBreedingforimprovedpro-ductsandimprovedproduc-tioncircumstanceswillaffectcurrentbreedingprogrammes.

oImportanceofhealth,envi-ronmentalimpact,andwel-faretraitsandreproductionwillincreasewithbroadeningofbreedingobjectives.

oSocialconsiderationswillenterbreedingprogrammes.

15yeartimehorizon: oNewwaysofgettingtraitsof

animals,whichareclosertothegenesandphysiologyoftheanimal-biological/physiologicalknowledgeoftheanimalwillbeusedtogetbetterphenotypesandbreedingprogrammes.

oSelectionforalternative


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Aquaculture

Challengesandopportunitiesforbree-dinginaquacultureReducingtheenvironmentalimpact• Feedsource:manyaquacul-turespeciesarecarnivorousbutaremoreandmorefedwithfatandproteinofplantorigintosubstituteforthisfromwildfishorigin.Selectivebreedinghasthepotentialtoacceleratethisdevelopmentconsiderably.

• Productionefficiency:Thereissignificantgeneticpotentialforimprovementsinproductionefficiencytraits:growthrate,feedefficiency,nutrientretention,processingyield,sexualmaturityandsurvival.Producingmorefishwithfewerinputsandlesswastewillreducetheenvironmentalfoot-printandincreasecompetitive-nessoftheindustry.Greaterchallengesarearisingforthesetraitsasaresultofclimatechange.

• Escapees:Escapeesfromaquaculturestockscontinuetoposeamajorlimitationtoaquacultureproductioninopen

Aquaculture is an important food sector in the EU, which provides healthy, nutritional products of high quality. It is strategically important for Europe, especially in view of our heavy reliance on imports of seafood. The EU-27 total fisheries capture in 2007 was 31 % less than in 1995, while aquaculture production increased by 10.5 % to 2.142.600 metric tonnes (EuroStat Fishery statistics 2009).

Aquaculture production systems and technology will have to address climate change and contribute to sustainable food security. The EU Commission requested, in communication (SEC(2009) 453 and 454) to the EU parliament and EU Council, an increased focus on aquaculture and to acknow-ledge the importance of sustainability in this regard. Selective breeding and reproduction are important knowledge areas for further development of the industry in a sustainable and ethical manner, where research is needed for the industry to be able to develop and to meet market demands and need for fish products in Europe.

environments,mostlybecauseoftheunknowngeneticimpactofescapedfishfromgeneticallyimprovedstrainsonwildstocks.Quantificationoftheimpactofescapeesonthegeneticstructureofwildpopulationsisurgentlyneeded.Noveltechni-quesareneededtocontrolpubertyandmaturationandmethodstoincorporatetheseintobreedingpractices.

Improvingfishhealthandwelfare• Robustness:Robustnesscanbesimplydefinedastheabilityofanimalsorstrainstocontinuetoperformunderchallengingorchangingconditions.Aquacultureisincloserelationtotheenvironmentintermsoftemperature,oxygen,feedandpathogens.Climatechangewill

emphasizethechallengeasrearingenvironmentsarebeco-mingmorevariableandextreme.Thetechnologicalgapistodefi-nerobustnesstraits,thatcanbeincludedinbreedingschemes,andtodevelopmethodstoselectforthese.Theirrelationtoproductiontraitsmustbeestablishedunderdifferentrearingsystems.

• Diseaseresistance:Existingandnewdiseaseserodeproductivityandhenceprofita-bilityanddevelopmentoftheindustry.Preventionandtreat-mentrelyonvaccination(wherefeasible)anduseofdrugsandchemicals.Thelatterhaveanegativeimpactontheenvironmentandthepublicimageofaquaculture.Animalswithbetterresistancetospecificdiseasesforeachspeciesareneededtoensureahealthyandmoresustainableindustry.Breedingforbetterresistancetoinfectiousdiseaseshavebeenimplementedinseveralbreedingprograms,mainlyinsalmonids.Furtherresearchinotherspeciesandpathogensshouldbeencouraged.

• Productquality:AquacultureproductsrepresentalargeandincreasingpartoftheEUaquaticproductconsumptionTherefore,itisofparamountimportancethatEuropeanaquacultureproductssustainthehighestqualitylevelforappearance,organolepticandnutritionalvalue.Importantproductqualitytraitsare;processingtraits,skinandmeatcolour,texture,fatcontentanddistribution,nutritionalprofile(especiallyhealthpromotingfattyacids),abilityforconser-vation,smokingorcookingandfleshflavourandtaste.Thescientificbasisforincludingproductqualityinbreedingprogramsisscarce.

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• Newaquacultureproducts:Europeanaquacultureproduc-tionisdominatedbyalimitednumberofspeciesfarmedregi-onallyusingimprovedjuveniles(salmon,trout,seabream,seabass,carp).Initiationofrationaldomesticationandbreedingprogramsisneededforotherspeciesforthelongtermandsustainabledevelopmentoftheseproductions,withspecialattentiontoherbivorous/omnivorousspecies.Fordes-criptionofstateoffarmingdevelopmentforeachspeciesseewww.aquabreeding.eu.

Generictopics• Genomics:Today,thereisagrowingamountofgenomicinformationavailable(geneticmarkers,geneticmaps,QTL,transcriptomeandgenomesequencedata,etc),buttherearelargedifferencesbetweenspecies.Thisinformationshouldbeexpandedandmethodshavetobedevelopedtoincludetheminthebreedingprogrammes.

• Knowledgetransfer:Verylittleknowledgeongeneticsandbreedingisbeingtransferredtotheaquacultureindustryandtodevelopingcountries.Thisisparticularlytrueformarkerassistedandgenomicselection.Itisimportanttofacilitateedu-cationofstudentsandindustryrepresentativesintheareaofbreedingandgenetics.

• Crossbreedingandexploita-tionofheterosis:Crossbreedingisanacceptedmethodologyfortheprotectionofgeneticallyimprovedstrains,byexploringhybridvigour.Inmanyaquaculturespecies,hybridisationbetweenrelatedspeciesispossible,producingsterileormonosexoffspring.Thus,moreknowledgeisnee-dedontheuseofcrossbreedingforbreedingprogramsandforpreventinggeneticpollution.

• Reproductiontechnologiesandsexdetermination:Efficientreproductiontechnolo-

giesareimportantforbreedingprogrammes,astheyfacilitatedirectedmatingsofparents.Cryopreservationcanbeanessentialtooltosecureandmanageefficientbreedingpro-grammes.Inparallel,inmanyfishspecies,sexdeterminationisamixtureofgeneticandenvironmentalfactors,leadingtounbalancedsex-ratiosinaquaculturestocks(e.g.seabass,sole).Knowledgeaboutsuchfactorsisneededformanyspecies(rainbowtrout,cod,seabass,halibutandmolluscs)astheyhavethepotentialto

improveproductionefficiencyandproductqualitythroughbreedingofmono-sexpopulati-ons,possiblywithouttheuseofhormonaltreatments.


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Cattle and Buffaloinenvironmentalfootprintandfoodsafetyandquality,includingnutritionalandorganolepticqua-lity,andimprovedanimalhealthandwelfare,areintensifying.Nationalbreedingprogrammesofthefuturemustreadjusttoreflecttheseinternationaltrends.

GapstobefilledThefieldsoffutureresearchcanbedividedintothreecategories:I)trait-orientatedresearch;II)optimalexploitationofdevelopingtechnologiesincattle;andIII)otherissuesincludinggeneticdiversity.I.Intrait-orientatedresearch,

onemainfocusshouldbethedevelopmentofcost-effectiveprotocolsfortherecordingoftraitsespeciallyassociatedwithhealth,welfare,animalfuncti-onalityandproductquality.Thistraitorientatedresearchisespeciallyimportantfortheexploitationofgenomicselectionforthesetraits.

II.‘-omic’technologiesaredeve-lopingrapidlyandwholegenomesequence(mainlythroughimputation)availableonallanimalswillsoonbethenorm.Theoptimalexploi-tationofthisinformationin

geneticevaluationandbree-dingprogramsiscurrentlynotknown.

III.Simulationstudiesclearlyshowthatgeneticgainis

expectedtorapidlyincreasewiththeapplicationofgenomicselectiontobreedingprograms.Thismayhaveseriousimpli-cationsforgenetictrendofselectedpopulation(changesinbreedinggoals)andgene-ticdiversitybothwithinbreedbutalsoacrossbreed.Nichemarketshelpedbylocalisedbreedsmayvanishasbreedsforwhichaccurategenomicpredictionsareavailabletakeover.

TheproblemofstasisWithstasisfirstly,cattlefarminginEuropewillloseitsinternatio-nalcompetitivenessasothercountriesdevelopandexploitnewtechnologies.InsomepartsofEuropetheoccupationoflandiscloselylinkedtolivestockpro-ductionandinthissituationalossofcompetitivenesswillhaveaverystrongnegativesocietalimpact.Secondly,thissituationwilleventuallyleadtoadrasticincreaseinimportsoflivestockproductsandcreatelongertermdependencies.Thirdly,sinceani-malbreedingalreadyisaglobalbusiness,scenariosinwhichonlyveryfewbreedingorganizationstakeovertheentiremarket,asisalreadythecaseinpoultrybree-ding,maybeenvisaged.Finally,

Keyopportunitiesandchallenges-TheroleofresearchanddevelopmentInmostEuropeancountries,effortsundertakeninthepastusinganimalbreedingtechnolo-gieshavefocusedonincreasedoutputperanimal.Recently,breedingprogrammeshavebeenmodifiedtoincreasinglyfocusonprofitabilityandtoincludefuncti-onalityandproductqualitytraits.However,Europe’scattleproduc-tionisincreasinglybecomingaglobalmarketwithtwoaspects:thethreatcausedbyimportsofcheaperproductsfromSouthAmerica(mainlybeef)butalsotheopportunitiesofemergingcountriesincreasingdairyandbeefconsumption(Asia).Thereisaneedtoimproveefficiencyofproduction(ratherthanproducti-vity)butalsotheopportunitytoexporthighvaluegeneticstonewmarketsaswellashighvalueani-malproducts(e.g.dairyproducts).Furthermore,acrosscountrygeneticevaluationsprovideincre-asingaccesstodiversegenetics.Additionally,toolsandalgorithmsareconstantlyimprovingtoexploittherapidadvancesingenomictechnologies.Consumerinterest

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(datatransfer,databasestructure,cloudcomputing)

-Evaluationofwholegenomesequencedataasasourceofinformationindairyandbeefcattlebreedingprograms

-Internationalgenomicevaluations-Implementationofconceptsformaintaininggeneticdiversityincludinggenomicinformationc)Otherissues-Economicalassessmentofnewtechnologiesandtheirassociatedrisks

15-yearhorizona)Trait-orientatedresearch-Mechanismsofdiseaseresistance-Physiologicaltraitsasalternativeindicators;metabolomicsb)Technology-GenotypexEnvironmentinter-

actionandepigeneticsincludinggenomicinformationc)Otherissues-Localbreedsandspecificregionsissues

25-yearhorizonForthishorizon,itmaybeverydifficulttospeculateaboutfutureresearchneeds,sometopicscouldbe:-Efficientpredictionandcapturingfromgenexgeneandgenexenvironmentinteractions

-Expertsystemsforon-farmaswellasnetworkedgeneticevaluations

-Designerfood(milk,beef)fromtransgenicanimals

-Useofstemcelltechnologyforreproduction

newtechnologies,beitbiotech-nology,ormolecularapproaches,orothers,beartheultimatechanceforincreasedqualityofproduction(cattleandbuffaloproducts),foodsafetyandwel-fareofanimals.

Short,mediumandlong-termopportunities/needsforresearch5-yearhorizona)Trait-orientatedresearch-Improvementsfortherecordingofhealth,functionality,andproductqualitytraitswithinte-grationofmolecularapproacheslikemetabolomicsandproteo-mics;

-Managementofphenotypicandgenomicdataforbestuse(i.e.,comparativephenomicsandgenomicsacrossspecies).b)Technology-Moreresearchontheoptimalimplementationofgenomicdataintogeneticevaluations

-Improvementsinreproductivetechnologieslikesemensexingandembryotechnologiesandhowtheycanbeexploitedincattlebreeding

-Embryonicselection-Developmentoftoolsformana-gingSNPandsequencingdataforindividualgenomicselection


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Horses

GapanalysisandgoalsettingIfnoresearchordevelopmentoccursinEurope,itisexpectedthattheEUwilllooseitsinterna-tionalleadershipinsporthorsebreedingandcompetition,willloosebreedsandwillbeconfrontedwithshrinkageofthehorsebree-dingindustry,especiallyinCEEcountries.Reducedanimalwel-fare,lesscontributionofhorsestosustainablefarmingandsocio-culturallifeandeconomiclossesinbreedingindustryaretobeexpected

Researchinequinesisneededtoimproveperformance(suchasgaits,jumpingability,velocity,endurance),functionaltraits(e.g.longevity,fundamentalstability)andtoinvestigatethepotentialofdiseaseresistance.Furthermore,researchonfertility,behavior(e.g.temperament)andhereditarydiseasesisneeded.Thesectorshouldpreserveitspositiveimagebyanticipatingonsignalsofnegativeeffectsofselectiononhealthandcharacter.

The economic impact of the horse industry in the EU has been estimated at 100 billion euro per year providing 400 000 full time jobs. It plays a leading role internationally. The horse sector is very diverse and horses fulfill a wide range of functions to serve mankind. This has resulted in a diversity of horse breeds and related activities. Importantly, horses have a very positive image towards society.

The diversity of the sector in itself is a challenge and requires efforts to raise standards of education of breeders and owners to the same level within all EU-member states. Knowledge and technology transfer between EU countries should be extended. Traditionally, there is a tight relationship between equine science and horse breeding organisations. This facilitates a quick and efficient adoption of new know-ledge into horse breeding programs.

Short,mediumandlongtermopportunitiesandneedsforresearch

Shortterm• IdentificationandparentagecontrolusingnewtoolsintegratedinaEuropeanidentificationsystem;

• DevelopmentanduseofDNA-teststoselectagainstdiseases

• Recordingmoreprecisepheno-typesusingconventionalandmoderntools;

• Definingreliablebreedingobjectivesfocusedonperfor-mance,behaviorandhealthresistance,evaluatedwithmoderntechnicalandbiologicaldataandthenimplementedgeneticanalysis;

• Analysisofinteractionsbetweengenotypeandenvironmentandbetweenhorseandhuman;

• Developingstatisticalmodelsthatcanhandletypicalhorsedata(ranksorcompetitionresults);

• Improvinginformationonhorsegenome;

• Identifygenesforthemaingenetic(hereditary)diseases;

• Strategiestocopewithlimitedsizereferencepopulationin

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genomicselectionprograms;• Controlofeffectivepopulationsizeofthehorsebreeds;

• Buildingahorsebreedinventory,estimationandmanagementofbiodiversityof

• Studysub-fertilityofstallionsandmaresduetotheirusageassporthorse;

• Knowledgeofstallionandmarereproductivephysiology;

• Studyofenvironmentalfactors(pesticides)witheffectsonfertilityanddevelopmentoftoolsfordiagnosisandtherapyoffertilityproblems;

Longterm• developtoolsforselectionwhichcombinegenomictesting(onmultipleloci)andphenotypicdataformanytraitssimul-taneouslysuchasperformance(gaits,jumpingability),temperament,fertility,growthdevelopment;

• Identifyofgeneswhichplayaroleinthemaingenetic(here-ditary)diseases;

• Developearlyandreliablepre-dictorsforlongevity;

• Developbasicknowledgeinthemainbiologicalfunctionstodeciphermuscle,skeletonandnervedevelopmentandphysiology;

• Developbioinformaticspipelinestoanswerscientificquestionsandimplementtraceability;

• Studygeneticaspectsofqualityofhorsemilkandmeat;

• Developbreedingsystemsinclu-dingnewtraits:biomechanics,performance,temperament,growthandfertilityability,andtheeffectsoftraining,welfareandhorsejudgingsystems;

• Studygeneticvariationofhorsebehaviorandimplementknow-ledgeinbreeding;

• Improvereproductionefficiency(animalandbreeders’welfare),

predictfertilityofstallionsperejaculate(frozenorchilled);

• Improveefficiencyofoocytefreezingtechniques;

• Investigatefactorsduringgestationandneonatallytominimizebonedisordersandneonataldiseases;

• Identifygenesforfertilitytraits;

• Improveknowledgeandunderstandingoftechnologiesforsemensexingandcloning.


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Honeybees, fur- and companion animals

redundant.Infuranimalsandrabbits,stasiswillgiveothercoun-tries,suchasChina,theopportu-nitytoincreasethemarketshareattheexpenseofEurope.ThisthreatenstheEuropeanproductioncharacterizedbyhighqualityandsafetyofanimalproductsandhighanimalwelfare.Inhoneybees,thereareverylargelossesduetodiseases.Aseriousconsequenceisthelossofpollinationofagri-culturalcropsandwildflora.Unintendedcrossingofimportedbreedstoindigenoushoneybeeracesresultsinalossofbiodiver-sityandmoreaggressivehybridcolonies.Furthermore,theindi-genousracesconstituteanimpor-tantexportproducttocountriesoutsideEurope.

GapanalysisResearchisrequiredinordertomaintainEurope’sleadingrole.Thiscanbedividedintotwomainareas:1)studyoftraitsandthetechniquesrequiredtodoso,and2)developmentofefficientbree-dingschemes.Table1showsgapsinknowledgeandtechnologyinthespecies.Specificationismadewithrespecttooverallgapsorgapsinsomecountries/breeds.

KeychallengesandopportunitiesandproblemofstasisEuropeisleadingwithinfuranimal,honeybee,andrabbitresearch,breedingandproduction,andplaysgloballyanimportantroleinbreedingofdogsforpolice/army/customs.Despitetheleadingroleforeachofthefourspecies,itisachallengetoincreaseorevenmaintainthepresentEuropeanproductionandmarketshare.Thealreadyinsufficientnumbersofhighqualityworkingdogsisexpectedtoincreasefurtherresultinginhighpricesandlowerquality.Stasiswillgiveotherstheopportunitytofurtherdeveloptheirprofessionalbreedingprograms,makingimportofthegeneticallybetterdogsfromEurope

The species dogs, fur animals, honeybees, and rabbits - were chosen for their organized breeding and/or extensive European economic revenues. An additional report was produced for each species that contains further details.

Table1.Gapsintechnologyandknowledgeindogs,furanimals,honeybees,andrabbits

Species

Dogs Furanimals Honeybees Rabbits

A B A B A B A B

Technology

ApplicationofDNAtechnology X X X X

Geneticevaluation X X X X

Artificialinsemination X X X

Cryoconservation X X X X

Invitrocultivationofsomaticcells X

Knowledge

Educationofbreeders X X X

Reproductionbiology,EmbryoMortality,fertility X X X

Genotype.xEnvironmentInteraction X X X X

Selectioncriteria X X X X

Epigenetics X X X

Geneticparameters X X X X

Efficientbreedingprograms X X X X

Transparencyaboutnewtechnologiestothepublic X X X X

Anxindicatesagapinthatfield.*A=gapingeneral;B=gapinsomecountries/breeds;

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15years:•Technologies:honeybees:developtechnologiesforinvitrocultivationofsomaticcellsforfunctionalgeneticsinbree-dingforresistance;rabbits:invitrocelltechnologyandcryo-bankingofembryosandfemalegametes

•“-Omics”:dogs,furanimals,honeybees,rabbits:useoftranscriptomics,proteomicsandphenomics(e.g.metabo-lomics,etc.)approachesandothertechnologiestounder-standthebiologyofthetraitstounderstandtheconsequencesofselection

•Epigenetics:furanimals,rabbits:studyofepigeneticcontributiontothevariabilityofproductionanddiseasetraits,behaviorandmortality;dogs,honeybees:applicationoftheresultsoftheresearchonepigenetics

•Health:honeybees:developselectionstrategiestoimproveresistanceforparasites;rabbits:investigatethegeneticcompo-nentsforresistancetoimportantdiseases;dogs,furanimals:investigatethegeneticback-groundofhealthrelatedpro-blems

•Ethics:honeybees:investigatetheriskofuseofgenetically

modifiedhoneybees;dogs:investigateethicalaspectsofuseofdogsfornewtasks

•Educationofbreeders:dogs:prioritizationofselectioncriteriaandgeneticevaluation

25years:•Genomics:furanimals:genomicstudiesofbiologyofreproduc-tion,sexualmaturityandmoul-ting;rabbits:developtoolsformanaginggenomicinformation

•Performance:dogs,honey-bees,furanimals,rabbits:selectionforadaptationtochangingclimaticconditions;honeybees:breedinghoney-beesforpollinationingreen-houses

Needsforresearch

5years:•Practicalissues:dogs:improvetherecordingsystemandsetuporganizedbreedingprograms;honeybees,rabbits:developtechniquesforcryo-conservationofsemenandimproverepro-ductivetechnologies

•Genomics:furanimals:constructagenomemapandsequencethegenome;rabbits:improvetheassemblyandannotationoftherabbitgenome;dogs,furanimals,honeybees,rabbits:SNPanalysisandgeno-micselection

•“-Omics”:dogs,furanimals,honeybees,rabbits:develop“–omics”tools

•Health:dogs,furanimals,honeybees,rabbits:investigatethegeneticbackgroundofhealthrelatedproblemsanddevelopselectionstrategiestoimproveresistancetothemostimportantparasitesandimprovediseaseresistance;rabbits:improvequalityofavailablevaccinesusingrecom-binantmarkertechnologies;

•Epigenetics:dogs,honeybees:studyofepigeneticcontributiontothevariabilityofproductionanddiseasetraits,behaviorandmortality

•Performance:dogs:developobjectivemeasuresofbehavior;dogs,furanimals,honeybees,rabbits:estimationofbreedingvaluesfornewtraits

•Biodiversity:honeybees:conservationofgeneticdiversity,developtechniquesformaintai-ningpureraces;furanimals:cryo-conservesemen(alopex-types),livepopulations(mink)

•Ethics:furanimals:publictransparencyoftheproduction;dogs:investigateethicalaspectsofbreedspecifictraits

•Educationofbreedersforallspecies:Showtheimportanceofrecordingsystemsandagree-mentonthebreedinggoals


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Pigs

herdsarethebasisforcross-breedingfortheproductionlevel.Yet,theavailablegeneticvariati-onisstillimmensewitheachbreedingorganisationsowningseveralpurebredlines,eachofthemwith(mostly)50+effecti-velyunrelatedanimals.Thebree-dinggoalshaveevolvedfromhighlyheritabletraitssuchasgrowth,feedefficiencyandcar-casscompositiontosustainabilityrelatedtraitssuchaslittersize,pigletvitality,sowlongevityandmeatquality.Breedinghasbeco-memoreandmoretechnologyintensive,withanincreasinguseofcomputerandinformationtechnologiesforreal-timetreat-mentoflargeamountsofinfor-mation.Researchingeneticsandbree-dinghasbeenrevolutionizedbytheeruptionofmoleculartechno-logies.Sequencingoftheporcinegenomewasvirtuallyfinishedin2010,allowingtomoveforwardtogenomicselection.Finally,increasingresearcheffortshavebeendevotedtothecharacteri-sationandanimprovedmanage-mentofgeneticdiversity.Researchonreproductionhas

alsobeenveryactive,withsigni-ficantprogressonfreshandfro-zensementechnologies,thedevelopmentofembryofreezingandsomaticcellcloning.Breedingobjectiveswillfurtherevolve,withtheneedforanimalsthatarerobust,areeasytomanageinlessconstrainedhou-singsystems,withasfewinter-ventions(treatments,assistance)aspossible,andhaveagoodadaptability,i.e.remainproducti-veandhealthyinawiderangeofproductionenvironments.Pigfeedisnowmoreincompetitionwithhumanfood,thereforemorefocusshouldbeputonsubopti-maldietsmadeofbyproducts,likeDDG’s.

Needforresearchtoremaincompetitive(problemofstasis)Theknowledge-intensiveanimalbreedingsectorincreasinglydependsonnewtechnologies/improvementsofexistingtechno-logiesdirectlystemmingfromresearchthatrequiremoreandmoreinvestmentsaswellasskil-ledpeoplewithastrongscientificbackgroundtounderstandand

1.Context-opportuni-tiesandchallenges

Porkisthemostwidelyconsumedmeatintheworldandwillsteadilyincreaseoverthenextdecades,mainlyindevelopingcountries,whilemeatconsumptioninEuropeandNorthAmericawilltendtoslowlydecrease.Allelementsofthepigcarcassarevaluedinsomeform,creatingaverywiderangeofproducts.Tradersvalueuniformitywithinandbetweenindividualsalespackagesofaspecificproduct.Inmostcases,Europeanporkchainswillneces-sarilytradeonaworldwidebasistocreatemaximumvalueoftheindividualelementsofthepigcarcass.WithinEuropeoranyotherproductionregionthepigshouldadaptasgoodaspossibletothelocalenvironmentintermsofclimate,housingsystem,healthandavailabilityofnutrients.Europeanpigbreedingorganisa-tionsareSMEs.Atrendisvisibleofconcentration,withcurrentlyabout10globalplayersandasignificantnumberofsmallerlocalbreeders.Alimitednumberofpurebredanimalsofspeciali-sedsireanddamlinesinnucleus

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geneticvariabilityofimmunecompetence/diseaseresistance;

• Geneticevaluationforsowlon-gevity,pigletsurvival/mothe-ringability;studiesonsowreservemobilization;

Targetsona15yearhorizon:• Fullyannotatedgenomeofthepigincludingacatalogueofallfunctionalelements;

• Identificationoflargenumbersofcausativepolymorphisms;identificationandmodellingofgenexgeneandgenexenvi-ronmentinteractions;

• Extensiveuseofgenomicinfor-mationatthedifferentlevelsofthebreedingpyramidtoexploitadditiveandnonadditivegene-ticvariation,withresistancetodisease,robustnessandbeha-viourasmajortargettraits

• Exploitationofgenexenviron-mentinteractions(e.g.byvari-ationofthefeed)forproducingvaryingproductqualitiesorproducingundervaryingenvi-ronmentalconditionswithonegenotypeofanimals;

• Useofgenomictools(e.g.herdsanitarystatusevaluation)and

complexmodelstooptimiseherdmanagement;

• Largescaledevelopmentofsemensexing;

• Developmentofmodelsfortheco-evolutionofhostsandpathogens.

• Increaseduseofpigsasamodelinhumanmedicine(e.g.polyfactorialdiseases,tumortherapy).

Targetsona25yearhorizon:• Identificationofcomplexregu-latorynetworksandepigeno-micmechanismsatthewhole-genomelevel;

• Anearcompletecatalogueofdiagnosticsforcurrentlyknowninheriteddiseases;

• Progresstowardsmodellingthelikelyimpactofnewmutations;

• Utilisationofcompletegenomesequencefromallbreedinganimals;

• Fullunderstandingoftheimplementation,impactandconsequencesofgeneticmodi-fication;

• Developmentofageneticidentitycardforeachanimal.

makeanefficientuseofnewtechnologies.IfnoresearchordevelopmentoccursinEurope,onlyveryfewgloballyactingbreedingorganisationswillsurvi-veandtheSMEinpigbreedingwilldisappearandasaconse-quencediversityofbreeds/geno-typessuitedtovariousenviron-mentsandlocalmarketneedswillbelost.ThechallengeistostimulatecooperationacrossfieldswithoutloosingefficiencyintheownSME’s.

3.Short,mediumandlong-termopportuni-ties/needsforresearch

Targetsona5yearhorizon:

1Definitionoftheproductionenvironment,whatisallowedandneeded• Thoroughdefinitionofwelfareindicators.

• BanofboarcastrationinallEuropeancountries,declarationofBrussels

• Insightinenvironmentsensiti-vitytraitsandgenotypexenvi-ronmentinteractions;

2Technology• Availabilityofahighqualityannotatedgenomesequenceofthepig,ofhighdensitySNPpanels,wholegenomelinkagedisequilibriummapsandfullgenomeexpressionarrays;

• Useofmarkerassistedselec-tionbasedonlinkagedisequili-brium,genotypeassistedselec-tionandgenomicselectioninpigbreeding;useofmarkersforthemaintenanceofgeneticvariability;

3Traits• Cooperationbetweenfeedexpertsandbreedingexperts->useofby-products,guthealth

• Cooperationbetweenhumanmedicine,veterinariansandgeneticists;oneworld,onehealth

• Improvedknowledgeonthe


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Poultry

SpeciesGroupsSeveraldistinctspeciesofpoultryarefarmedinEuropeandwhilstthereareseveralsynergiesinresearchtherearealsoanumberofspeciesspecificissues.Thissectorisdrivenbythechickenaboutwhichthereismostexistingdataandwhichismassivelymoreimportantineconomictermsthananyoftheotherspecies.Forclarificationthegroupsareasfollows:Broilerchickens,Layerchickens,Turkeys,Waterfowl:Ducks(Pekinducks,Muscovy

The major part of the poultry industry is at a significantly more mature stage than those of other species both in terms of production systems and specific knowledge in respect of breeding. In part this is a result of basic research carried out in Europe over the last 40 years which also explains a significant concentration of the world commercial poultry breeders in Europe. These companies and industries are significant wealth creators and must be supported to main-tain their European bases. There will be significant spin-off for minor breeds and other species from fundamental work carried out on chickens. For these reasons the approach and needs of the poultry sector may be viewed differently from the other species.

throughputgenotypinghaveenabledthisinformationtobetranslatedintopracticalgenoty-pingtools,atfirstatlowdensityandrecentlyathighdensitytothewholegenome.Againthegenotyping,mathematicalandcomputationaltoolsneedtobeappliedtotheseotherspecies.

A:IssuesInadditiontocontrollinganimaldiseaseandmaintainingwelfare,theenvironmentalimpactandsustainabilityofpoultrysystemswillbethemajorissuesinpoul-try,withanincreasingfocusongeneticsolutionswhichmustbeidentifiedandunderstood.Atthesametimeeconomicefficiencyofproductionsystemsmustbemaintained.

1.1.Animaldisease:inadditiontotraditionaldiseasestherearere-emergingdiseasesasaconse-quenceforexampleofthebanontheuseofantibioticgrowthpromotersandlimitationsofcurrentvaccines.Abetterunder-standingoftherelationshipbetweenhostanditsmicrobiotaanditscontributiontoguthealthisrequired.

ducks,Muleducks)andGeese,Otherpoultry:GuineafowlandQuail,Gamebirds:Pheasants,PartridgeandWildDucks.Currentlytherearereferencesequencesforthewholegenomesofchickenandturkey,genomeanalysesforduckandquailareunderdevelopment.Extensiveknowledgeonthegenomevaria-tion(inparticularSNPs)inchickenpopulationsis/willbeavailableandthesametechniquescanbeappliedtotheseotherspecies.Similarlydevelopmentsinhigh

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1.2.Animalwelfareandbehaviour:WithintheEUimprovementsinAnimalwelfareremainhighpriorities:beaktrim-ming;skeletonandlegstrengthofbroilersandturkeys,foodrestrictionespeciallyofbroilerbreeders;broodinessinturkeys;researchinordernottokillanimalsofonesexatbirthsuchasmaleroostersoflayingstrainsandfemalemuleducks

1.3.Foodqualityandsafety:thisisacriticalissueandthebasisforretaininganimalproductionwithintheEU.Itinvolvesbothmandatoryfoodquality(labora-toryinspection)andthemarketquality(consumers,retailers,etc).Novelingredients(co-products)thatenterthefoodchainwillneedtoensurethattheymeettheserequirements.

1.4.Sustainableproduction:focusonmanagementofgeneticvariabilityandgeneticdiversity,useoflocalresources(strains,rawmaterials)withinthecontextoffoodsecurity,economicviability(marketcostsandpricesstructureacceptability)

1.5.EnvironmentalImpact:theenvironmentalimpactandrecourseuseassociatedwithpoultrysystemswillrequireafundamentalreviewandwouldsolutionstoreducethese.Consistentandholisticmethodo-logiesthatassesstheseimpactsarerequired.

B:Researchpriorities1.Scientificresearchforapplicationinpoultrybreedingprograms:

•Useofgenomicstoolsincludingnextgenerationsequencinginbreedingprograms

oImprovementsinaccesstocost-effectivehighthroughputgenomesequencingandhighperformanceparallelcomputingwillincreaseourknowledgeofthegenomevariation(SNPs,CNVandotherstructuralvari-ants)inchickenpopulations;thisnewknowledgewillunder-pinhighthroughputtoolsforcost-effectivegenotyping1000’sofanimalsfor1,000-1,000,000SNPs;genotypesbasedonwholegenomeswillbeexploitedinbothgenomewideassociationanalysis(GWAS)ofthecontributionofspecificgenescontrollingspecifictraitsandthedevelop-mentofgenomewideselection(GWS)strategiesoftraits;

•Developmentofmethodstoincreasebirdrobustness

•Developmentofmethodstoincreasegeneraldiseaseresi-stance

•Developmentofbreedingmethodstoimproveanimalwel-fare(thisincludesdefinitionofappropriatephenotypesrelatedtoanimalwelfare)

•Developmentofbreedingmethodstoimprovemetabolicanddigestiveefficiencies

2.Impactofgeneticsonsustainabilityofpoultryproductionandfoodsecurity:•Assessmentofenvironmentalimpactandresourceuse

•Rawmaterialsandnovelingredientusage

•Biodiversity•Tuningofbalancedbreedingobjectives

3.Developmentofnewknowledgeandtools:•Advancedmethodstopredictphenotypesfromgenotypes

oAdvancedgenomicstoolswillrequirethedevelopmentofnewcomputationalandstatisticalmethods.

oAdvancesinsystemsbiology.•Reproductivebiotechnologiesincludingtransgenics

•Novelphenotypingmethods oPhenotypingmethodsand

dataacquisitioninnewpro-ductionsystems(electronicIDofanimals)areimportantinitselfbutwillalsobethemajoropportunityinallfutureGWASandGWSstrategies.

•Holistictoolstoassessenviron-mentalimpactofpoultrysystemsincludinglifecycleana-lysis

oAmajorchallengewillbetopredicttheimpactofgeneticselectionstrategies,thiswillincludenewmethodsinLifecycleassessment(LCA)toprovideaholisticviewofimpactsonthelivestock,theenvironment,theclimate,socialandeconomicimpacts,inadditiontheimpactsoftheseonthegeneticpotentialoflivestock.


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Sheep and Goats

programmes.Increasedeconomicandbiologicalefficiencyiscrucialinmostproductionsystemstodecreasethecostsofproductiontoensurethefutureviabilityofsmallruminantproductioninsituationsofdecliningorstaticconsumptionfortheirproduce.Directandindirectmeasuresofemissionsarerequiredtogenerateknowledgeoftheimpactofsheepandgoatproductiontotheenvi-ronmentbutalsofortheimpactofachangingenvironmenttotheproduction.Quantifyingtheimpactofhavingadiversepopula-tionofsheepandgoatsisneededtoestablishacommonsystemofevaluationthatincludesbothmar-ketandnon-market(‘publicgood’)benefitsofkeepingsmallordecli-ningpopulationsofgeneticallydistinctsheepandgoatbreeds.

ProblemofthestatusquoIntheabsenceofresearchanddevelopmentinthesheepandgoatsectorsinEuropeandgivendecreasingsubsidies,andifpro-ductiveefficiencyisnotimproved,theseindustrieswillquicklyloseouttothecompetition(importsanddomesticalternatives)onpriceandquality.Sheepandgoatswillbedisproportionatelyaffectedbyregulationsaimedatlimitinggreenhousegasemissions.Lossofsignificantpartsofthesheepandgoatindustrieswillleadtoneglectoftraditionalland-scapesandlossofincomefortheruralpopulationinless-favouredareas,whilstbiodiversitywillsuf-ferasaresultofsurvivalofonlyafewhighlyselectedbreeds.Europeanconsumerswilldepend

Problems,knowledgegapsandopportunitiesManyquestionsexistforsmallruminantsessentiallyduetothehighcostoftechnologiesinrelationtothevalueoftheanimal.Thereisalackofgoodrecordingsystemsalongthechainwhichfeedbacktotheproducer.Ifthiswouldbesetup,e.g.productqualitycouldbeimproved.Alsothebettercollectionofphenotypeswilltakeadvantageofopportunitiestotacklemajordiseasesthroughquantitativeandmolecularbreeding.Knowledgeofgeneticpropertiesofdiseaseandtheircorrelationswithproductiontraits,eithershouldpreventanydeteriorationfromhappening,ormaycontrolhealthproblemsiftheyareincorporatedintosustai-nablesheepandgoatbreeding

Sheep and goats are among the most extensively farmed livestock species in Europe that often utilise marginal areas which are not suitable for other forms of agricultural pro-duction providing the main source of income for these rural populations. The worrying decline in sheep numbers in the EU in recent years has had knock-on effects for the supporting infrastructure of the industry such as availability of sheep shearers, livestock hauliers and regional abattoirs. This decline impacts upon the social structure and industry in the remote and harshest land areas of the EU. Failure to address the decline in livestock numbers will increase Europe’s dependency on imports of meat and milk products from third countries.

Sheep and goats are generally less efficient than other lives-tock species in the production of meat and milk because of their small size, low reproductive rate and lower yields. With declining subsidies, and in order to stay competitive, sheep and goat producers have sought to create special markets for quality products and to increase their efficiency of pro-duction. However, this approach as a means to increase pro-fitability of sheep and goat enterprises is not having the expected impact, hence focussing on improving the efficien-cy of production is critical for a sustainable industry. In the absence of research and development and given decreasing subsidies, if the efficiency of production is not improved these industries will quickly lose out on price and quality to the competition to imports from third countries or to alter-native domestic species, thereby furthering the existing decline in the demand for lamb meat.

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ourfarmingsystems•GenotypexEnvironmentInteraction,includingproduc-tionandfunctionaltraits

Mediumpriority•Researchinreproductiveandembryotechnology

•Developmentofsheepandgoatproductsadaptedtospecifichumangenomes

Lowpriority•Methodstoimprovequalityofwoolorcreatesheddingorhairsheep

•Adaptormitigatesheepandgoatsandsystemstochangingclimates.Developstrategysothatbreedskeeppacewithglobalwarming

•Developmentofspecificdrugstargetedtodifferentsheepandgoatgenotypes

•Officialanimalidentificationthroughmolecularinformation

onimports,whichmaynotnecessarilycorrespondtotheirrequirementsandmaynotbesustainable.Foreignresearchwillonlyaddresstheseissuestoalimitedextent.

Shortandlong-termopportunitiesandneedsforresearch

ShorttermhorizonHighpriority•Researchonnewtraitscontri•Improvefertility(AIefficiency,a-seasonalbreeding)andprolificacywhilemaintainingfunctionalabilities

Mediumpriority•Researchonroutinemeasuresandgeneticcomponentsofmeatandmilkqualityforhumannutrition

•Finishsheep&goatgenomesequencingandimprovegeneannotation

•Developandimprovetools(genetics,sustainablemanage-ment)tocopewithinternalparasites

•Increasecollaborativeapproachofnewmoleculartechnologyuse

•Implementationofmoreefficienttraceabilityanddiseasemonito-ringsystems,usingEIDandDNAtechnologies

•Howtoovercomebiologicalandenvironmentaltrade-offs(antagonisticbreedinggoals,environmentalbenefitsandbreedinggoals,others)

Lowpriority•Developmentofmethodsandtoolsforconservationofrarebreedsandgeneticvariability

•Developmentofdatabasesonanimaldiseasesandlinkwithselectionprogramsandgenediscoveryresearch

LongtermhorizonHighpriority•Geneticsolutionstodiseases•FavourEuropeansheepandgoatproductioninordertolimitimportationsandsustain

Strategic Research Agenda 2011FABRE Technology Platform ©2011

Address:FABRE-TP SecretariatP.O. Box 766700 AB WageningenThe Netherlands

Website: www.fabretp.infoE-mail address: [email protected] Telephone: +31 317 41 20 06