Selective Breeding in Aquaculture: An Introduction Reviews:MethodsandTechnologiesinFishBiologyandFisheries VOLUME10 Serieseditor: JenniferL.Nielsen U.S.GeologicalSurvey, AlaskaScienceCenter Anchorage,Alaska Forfurthervolumes: http://www.springer.com/series/6481 · Trygve Gjedrem Matthew Baranski Selective Breeding in Aquaculture: An Introduction 123 TrygveGjedrem MatthewBaranski NofimaMarin NofimaMarin 1432Aas 1432Aas Norway Norway trygve.gjedrem@nofima.no ISSN1571-3075 ISBN978-90-481-2772-6 e-ISBN978-90-481-2773-3 DOI10.1007/978-90-481-2773-3 SpringerDordrechtHeidelbergLondonNewYork LibraryofCongressControlNumber:2009928426 (cid:2)c SpringerScience+BusinessMediaB.V.2009 Nopartofthisworkmaybereproduced,storedinaretrievalsystem,ortransmittedinanyformorby anymeans,electronic,mechanical,photocopying,microfilming,recordingorotherwise,withoutwritten permissionfromthePublisher,withtheexceptionofanymaterialsuppliedspecificallyforthepurpose ofbeingenteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework. Coverillustration:LarvaeofAtlanticCodbySaskiaMennen,Nofima Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Thefoundationofquantitativegeneticstheorywasdevelopedduringthelastcentury and facilitated many successful breeding programs for cultivated plants and ter- restrial livestock. The results have been almost universally impressive, and today nearly all agricultural production utilises genetically improved seed and animals. Theaquacultureindustrycanlearnagreatdealfromtheseexperiences,becausethe basictheorybehindselectivebreedingisthesameforallspecies. The first published selection experiments in aquaculture started in 1920s to improve disease resistance in fish, but it was not before the 1970s that the first family based breeding program was initiated for Atlantic salmon in Norway by AKVAFORSK.Unfortunately,thesubsequentimplementationofselectivebreeding on a wider scale in aquaculture has been slow, and despite the dramatic gains that havebeendemonstratedinanumberofspecies,lessthan10%ofworldaquaculture productioniscurrentlybasedonimprovedstocks.Forthelong-termsustainability of aquaculture production, there is an urgent need to develop and implement effi- cient breeding programs for all species under commercial production. The ability foraquaculturetosuccessfullymeetthedemandsofaneverincreasinghumanpop- ulation, will rely on genetically improved stocks that utilise feed, water and land resources in an efficient way. Technological advances like genome sequences of aquaculturespecies,andadvancedmolecularmethodsmeansthattherearenewand excitingprospectsforbuildingonthesewell-establishedmethodsintothefuture. Themainpurposeofthisbookistodemonstratethesuccessthatselectivebreed- ingprogramshaveachievedsofarinaquaculture,andtohighlightthetremendous potentialthistechnologyoffersforefficientandproductiveaquacultureproduction inthefuture. Themainsectionsofthebookare: • Whyimproveproductiontraitsinfishandshellfish? • Whathasbeenaccomplishedinselectivebreedingprogramsinaquaculture? • Abriefoutlineofthetheoryofquantitativegenetics • Establishingandrunningbreedingprograms • Integrationofmoleculargenetictools v vi Preface The book is primarily written for aquaculture students with selective breeding as a subject, farmers, advisory consultants and farm managers. Students specialis- inginselectivebreedingmayalsofinditusefultoconsultthebook‘Selectionand breedingprogramsinaquaculture’(Springer,2005),whichprovidesamorein-depth coverageofthetopicsdiscussedhere. We hope that this book will stimulate aquaculture industries to consider the use of improved stocks in their production of fish and shellfish. The development and implementation of breeding programs must be driven by industry, with the support of scientists, farmers organisations and governments. The benefits will be farreaching. Ås,Norway TrygveGjedrem February2009 MatthewBaranski Acknowledgements We express our sincere appreciation to our employer, Nofima Marin, Ås, for their continuous support and financial contribution to the publication of this book. It has been inspiring to work together with the skilled scientists at the institute. We are particularly grateful to Dr. Solveig van Nes, Reidun Lilleholt and Grethe Tuven for technical help. Furthermore, we thank the director of AKVAFORSK Genetics Center AS (AFGC), Dr. Morten Rye, for his valuable contribution to the manuscript.Finally,wewouldliketothankDr.HansB.Bentsen,Dr.BjarneGjerde andDr.NicholasRobinsonfortheirvaluablesupport. Ås,Norway TrygveGjedrem February2009 MatthewBaranski vii Contents 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 HistoricDevelopmentofAquaculture . . . . . . . . . . . . . . 1 1.2 DefinitionofaBreedingProgram . . . . . . . . . . . . . . . . 3 2 DomesticationandtheApplicationofGeneticImprovement inAquaculture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.1 DomesticationofAnimals . . . . . . . . . . . . . . . . . . . . 5 2.2 SelectiveBreeding . . . . . . . . . . . . . . . . . . . . . . . . 6 2.3 QualityTraits . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.4 BetterUtilizationofResources . . . . . . . . . . . . . . . . . . 7 2.5 GeneticImprovementisAccumulative. . . . . . . . . . . . . . 7 2.6 GeneticImprovementProducesPermanentGains . . . . . . . . 8 2.7 InitiatingaSelectiveBreedingProgram . . . . . . . . . . . . . 9 2.8 SelectiveBreedingProgramsinAquaculture . . . . . . . . . . 10 2.9 PrerequisitesforaBreedingProgram . . . . . . . . . . . . . . 11 3 TheSuccessofSelectiveBreedinginAquaculture . . . . . . . . . . 13 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.2 AtlanticSalmon . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.3 RainbowTrout . . . . . . . . . . . . . . . . . . . . . . . . . . 15 3.4 CohoSalmon . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 3.5 Tilapia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 3.6 Carp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 3.7 ChannelCatfish . . . . . . . . . . . . . . . . . . . . . . . . . . 19 3.8 SeaBream . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 3.9 Shrimp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 3.10 Oysters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 3.11 Scallops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 3.12 GeneticImprovementinAquaticSpeciesComparedto TerrestrialLivestockSpecies . . . . . . . . . . . . . . . . . . . 22 3.13 SummaryandConclusion . . . . . . . . . . . . . . . . . . . . 22 4 TheTheoreticalBasisforBreedingandSelection . . . . . . . . . . 25 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 4.2 TheCell. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 ix x Contents 4.3 BasicGenetics . . . . . . . . . . . . . . . . . . . . . . . . . . 26 4.3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . 26 4.3.2 Genes . . . . . . . . . . . . . . . . . . . . . . . . . . 26 4.3.3 EffectofGenes . . . . . . . . . . . . . . . . . . . . . 29 4.4 Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 4.4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . 29 4.4.2 SingleGeneTraits. . . . . . . . . . . . . . . . . . . . 30 4.4.3 QuantitativeTraits. . . . . . . . . . . . . . . . . . . . 30 4.4.4 VariationinQuantitativeTraits . . . . . . . . . . . . . 31 4.4.5 VariationBetweenSpecies . . . . . . . . . . . . . . . 32 4.4.6 VariationWithinSpecies . . . . . . . . . . . . . . . . 33 4.5 EstimationofVariationandCovariation . . . . . . . . . . . . . 33 4.5.1 MeanandStandardDeviation . . . . . . . . . . . . . . 33 4.5.2 VarianceofaSum . . . . . . . . . . . . . . . . . . . . 35 4.5.3 GeneticVariance . . . . . . . . . . . . . . . . . . . . 36 4.5.4 Heritability . . . . . . . . . . . . . . . . . . . . . . . 36 4.5.5 EnvironmentalVariance . . . . . . . . . . . . . . . . . 38 4.5.6 CorrelationsBetweenTraits. . . . . . . . . . . . . . . 40 4.5.7 Regression . . . . . . . . . . . . . . . . . . . . . . . . 42 4.6 InbreedingandRelatedness . . . . . . . . . . . . . . . . . . . 43 4.6.1 GeneticRelationship . . . . . . . . . . . . . . . . . . 43 4.6.2 Inbreeding . . . . . . . . . . . . . . . . . . . . . . . . 44 4.6.3 EffectivePopulationSize . . . . . . . . . . . . . . . . 47 4.6.4 EffectofInbreedingonGeneticVariance . . . . . . . . 48 4.6.5 InbreedingDepression . . . . . . . . . . . . . . . . . 48 4.7 Crossbreeding . . . . . . . . . . . . . . . . . . . . . . . . . . 50 4.7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . 50 4.7.2 Heterosis . . . . . . . . . . . . . . . . . . . . . . . . 50 4.8 Purebreeding . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 4.9 Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 4.9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . 52 4.9.2 NaturalSelection . . . . . . . . . . . . . . . . . . . . 53 4.9.3 ArtificialSelection . . . . . . . . . . . . . . . . . . . 53 4.9.4 PredictingSelectionChange . . . . . . . . . . . . . . 54 4.9.5 MultipleTraitSelection . . . . . . . . . . . . . . . . . 56 4.9.6 CorrelatedResponsetoSelection . . . . . . . . . . . . 57 4.9.7 EffectofSelectiononGeneticVariance . . . . . . . . 58 4.9.8 MethodsofSelection . . . . . . . . . . . . . . . . . . 58 4.9.9 SelectionLimits . . . . . . . . . . . . . . . . . . . . . 59 5 InitiatingBreedingPrograms . . . . . . . . . . . . . . . . . . . . . 63 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 5.2 TheFundamentalBasisofaBreedingProgram . . . . . . . . . 64 5.3 EstablishmentofaBasePopulation . . . . . . . . . . . . . . . 65