P1:SFK/UKS P2:SFK BLBS108-fm Saroglia May17,2012 9:49 Trim:246mm×189mm Functional Genomics in Aquaculture i P1:SFK/UKS P2:SFK BLBS108-fm Saroglia May17,2012 9:49 Trim:246mm×189mm Functional Genomics in Aquaculture Editedby Marco Saroglia DepartmentofBiotechnology andMolecular Sciences AnimalBiotechnologyandAquacultureUnit UniversityofInsubria ViaJ.H. Dunant3Varese I-21100 Italy and Zhanjiang (John) Liu TheFishMolecularGeneticsandBiotechnology Laboratory DepartmentofFisheriesandAlliedAquaculturesand ProgramofCellandMolecularBiosciences AquaticGenomicsUnit AuburnUniversity Auburn,AL36849 USA A John Wiley & Sons, Inc., Publication iii P1:SFK/UKS P2:SFK BLBS108-fm Saroglia May17,2012 9:49 Trim:246mm×189mm Thiseditionfirstpublished2012©2012byJohnWiley&Sons,Inc. Wiley-BlackwellisanimprintofJohnWiley&Sons,formedbythemergerofWiley’sglobal Scientific,TechnicalandMedicalbusinesswithBlackwellPublishing. 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(cid:2) Setin10/12ptDutch801BTbyAptaraR Inc.,NewDelhi,India Disclaimer Thepublisherandtheauthormakenorepresentationsorwarrantieswithrespecttotheaccuracyor completenessofthecontentsofthisworkandspecificallydisclaimallwarranties,includingwithout limitationwarrantiesoffitnessforaparticularpurpose.Nowarrantymaybecreatedorextendedby salesorpromotionalmaterials.Theadviceandstrategiescontainedhereinmaynotbesuitablefor everysituation.Thisworkissoldwiththeunderstandingthatthepublisherisnotengagedin renderinglegal,accounting,orotherprofessionalservices.Ifprofessionalassistanceisrequired,the servicesofacompetentprofessionalpersonshouldbesought.Neitherthepublishernortheauthor shallbeliablefordamagesarisingherefrom.ThefactthatanorganizationorWebsiteisreferredto inthisworkasacitationand/orapotentialsourceoffurtherinformationdoesnotmeanthatthe authororthepublisherendorsestheinformationtheorganizationorWebsitemayprovideor recommendationsitmaymake.Further,readersshouldbeawarethatInternetWebsiteslistedinthis workmayhavechangedordisappearedbetweenwhenthisworkwaswrittenandwhenitisread. 1 2012 i P1:SFK/UKS P2:SFK BLBS108-fm Saroglia May17,2012 9:49 Trim:246mm×189mm Contents ListofContributors vii Preface xi Chapter1. FunctionalGenomicsResearchinAquaculture:PrinciplesandGeneral Approaches 1 ShikaiLiu,YuZhang,FanyueSun,YanliangJiang,RuijiaWang,ChaoLi, JiarenZhang,andZhanjiang(John)Liu Chapter2. GenomicResourcesforFunctionalGenomicsinAquacultureSpecies 41 JiarenZhang,YanliangJiang,FanyueSun,YuZhang,RuijiaWang,ChaoLi, ShikaiLiu,andZhanjiang(John)Liu Chapter3. Production,Growth,andInsulin-LikeGrowthFactor-I(IGF-I)Gene ExpressionasanInstantaneousGrowthIndicatorinNileTilapia OreochromisNiloticus 79 ChristopherL.Brown,EmmanuelM.VeraCruz,RemediosB.Bolivar, andRussellJ.Borski Chapter4. GeneExpressionPatternduringEuropeanSeaBassLarvaeDevelopment: ImpactofDietaryVitamins 91 DavidMazurais,MariaDarias,IgnacioFernandez,ChantalCahu, EnricGisbert,andJose-LuisZambonino-Infante Chapter5. TranscriptomicsoftheCompensatoryGrowthinEuropeanSeaBass Dicentrarchuslabrax 113 GencianaTerova,SamuelaCora,TizianoVerri,RosalbaGornati, GiovanniBernardini,andMarcoSaroglia Chapter6. FunctionalGenomicAnalysisoftheNutritionalandHormonalRegulation ofFishGlucoseandLipidMetabolism 129 SandrineSkiba-Cassy,SergioPolakof,IbanSeilez,andSt´ephanePanserat Chapter7. GenomicResponsestoStressChallengesinFish 147 LluisTortandMarianaTeles Chapter8. FunctionalGenomicAnalysisofSexDeterminationandDifferentiation inTeleostFish 169 FrancescPiferrer,PaulinoMart´ınez,LaiaRibas,AnaVin˜as,andNoeliaD´ıaz Chapter9. FunctionalGenomicsofStress:MolecularBiomarkersfor EvaluatingFishCNSActivity 205 ChiaraTognoli,RosalbaGornati,MarcoSaroglia,GencianaTerova, andGiovanniBernardini v P1:SFK/UKS P2:SFK BLBS108-fm Saroglia May17,2012 9:49 Trim:246mm×189mm vi Contents Chapter10. TheSoLuteCarrier(SLC)FamilySeriesinTeleostFish 219 TizianoVerri,GencianaTerova,AlessandroRomano,AmilcareBarca, PaolaPisani,CarloStorelli,andMarcoSaroglia Chapter11. Next-GenerationSequencingandFunctionalGenomicAnalysis inRainbowTrout 321 MohamedSalem Chapter12. FunctionalGenomicsResearchofAtlanticCodGadusmorhua 339 MatthewL.Rise Chapter13. CatfishFunctionalGenomics:ProgressandPerspectives 349 EricPeatman Chapter14. FunctionalGenomicsinShrimpDiseaseControl 361 ArunK.DharandRefugioRobles-Sikisaka Chapter15. ApplicationsofFunctionalGenomicsinMolluscsAquaculture 377 A.Figueras,M.M.Costa,andB.Novoa Index 397 ColorPlatesappearafterpage403 P1:SFK/UKS P2:SFK BLBS108-bcontrib Saroglia May11,2012 7:27 Trim:246mm×189mm List of Contributors AmilcareBarca FishNutritionLaboratory DepartmentofBiologicalandEnvironmental Plouzan´e29200,France SciencesandTechnologies(DBEST) SamuelaCora LaboratoryofGeneralPhysiology UniversityofSalento DepartmentofBiotechnologyandLife ViaProvincialeLecce-Monteroni Sciences LecceI-73100,Italy UniversityofInsubria ViaJ.H.Dunant3 GiovanniBernardini VareseI-21100,Italy DepartmentofBiotechnologyandLife M.M.Costa Sciences InstitutoInvestigacionesMarinas(IIM) UniversityofInsubria ConsejoSuperiordeInvestigaciones ViaJ.H.Dunant3 Cientificas(CSIC) VereseI-21100,Italy EduardoCabello6 and Vigo36208,Spain Inter-UniversityCentreforResearchin ProteinBiotechnologies“TheProtein EmmanuelM.VeraCruz Factory” CentralLuzonStateUniversity PolytechnicUniversityofMilanand ScienceCityofMun˜oz3120,ThePhilippines UniversityofInsubria ViaJ.H.Dunant3 MariaDarias VareseI-21100,Italy IRTA CentredeSantCarlesdelaR`apita RemediosB.Bolivar (IRTA-SCR) CentralLuzonStateUniversity UnitatdeCultiusExperimentals ScienceCityofMun˜oz Crta.delPobleNous/n NuevaEcija3120,ThePhilippines SantCarlesdelaR`apita43540,Spain RussellJ.Borski ArunK.Dhar DepartmentofBiology ViracineTherapeuticsCorporation NorthCarolinaStateUniversity Columbia,MD21046,USA Raleigh,NC27695,USA NoeliaD´ıaz ChristopherL.Brown InstitutdeCi`enciesdelMar USDepartmentofCommerce ConsejoSuperiordeInvestigaciones NOAAAquacultureandEnhancement Cient´ıficas(CSIC) Division Barcelona,Spain TheMilfordLaboratory IgnacioFernandez Milford,CT06460,USA IRTA ChantalCahu CentredeSantCarlesdelaR`apita Ifremer (IRTA-SCR) vii P1:SFK/UKS P2:SFK BLBS108-bcontrib Saroglia May11,2012 7:27 Trim:246mm×189mm viii ListofContributors UnitatdeCultiusExperimentals DepartmentofFisheriesandAllied Crta.delPobleNous/n AquaculturesandProgramofCelland SantCarlesdelaR`apita43540,Spain MolecularBiosciences AquaticGenomicsUnit A.Figueras AuburnUniversity InstitutoInvestigacionesMarinas(IIM) Auburn,AL36849,USA ConsejoSuperiordeInvestigaciones ShikaiLiu Cientificas(CSIC) EduardoCabello6 TheFishMolecularGeneticsand Vigo36208,Spain BiotechnologyLaboratory DepartmentofFisheriesandAllied EnricGisbert AquaculturesandProgramofCelland IRTA MolecularBiosciences CentredeSantCarlesdelaR`apita AquaticGenomicsUnit (IRTA-SCR) AuburnUniversity UnitatdeCultiusExperimentals Auburn,AL36849,USA Crta.delPobleNous/n Zhanjiang(John)Liu SantCarlesdelaR`apita43540,Spain TheFishMolecularGeneticsand BiotechnologyLaboratory RosalbaGornati DepartmentofFisheriesandAllied DepartmentofBiotechnologyandLife AquaculturesandProgramofCelland Sciences MolecularBiosciences UniversityofInsubria, AquaticGenomicsUnit ViaJ.H.Dunant3 AuburnUniversity VereseI-21100,Italy Auburn,AL36849,USA and Inter-UniversityCentreforResearchin PaulinoMart´ınez ProteinBiotechnologies“TheProtein DepartamentodeGen´etica Factory” UniversidaddeSantiagodeCompostela PolytechnicUniversityofMilanand Lugo27002,Spain UniversityofInsubria ViaJ.H.Dunant3 DavidMazurais VareseI-21100,Italy Ifremer FishNutritionLaboratory YanliangJiang Plouzan´e29200,France TheFishMolecularGeneticsand B.Novoa BiotechnologyLaboratory DepartmentofFisheriesandAllied InstitutoInvestigacionesMarinas(IIM) AquaculturesandProgramofCelland ConsejoSuperiordeInvestigaciones MolecularBiosciences Cientificas(CSIC) AquaticGenomicsUnit EduardoCabello6 AuburnUniversity Vigo36208,Spain Auburn,AL36849,USA St´ephanePanserat INRA,UMR1067NutritionAquacultureet ChaoLi G´enomique TheFishMolecularGeneticsand Saint-P´ee-sur-NivelleF-64310,France BiotechnologyLaboratory P1:SFK/UKS P2:SFK BLBS108-bcontrib Saroglia May11,2012 7:27 Trim:246mm×189mm ListofContributors ix EricPeatman ViaProvincialeLecce-Monteroni TheFishMolecularGeneticsand LecceI-73100,Italy BiotechnologyLaboratory DepartmentofFisheriesandAllied MohamedSalem AquaculturesandProgramofCelland LaboratoryofAnimalBiotechnologyand MolecularBiosciences Genomics AquaticGenomicsUnit DivisionofAnimalandNutritionalSciences AuburnUniversity WestVirginiaUniversity Auburn,AL36849,USA Morgantown,WV26506-6108,USA FrancescPiferrer CarloStorelli InstitutdeCi`enciesdelMar DepartmentofBiologicalandEnvironmental ConsejoSuperiordeInvestigaciones SciencesandTechnologies(DBEST) Cient´ıficas(CSIC) LaboratoryofGeneralPhysiology Barcelona,Spain UniversityofSalento ViaProvincialeLecce-Monteroni PaolaPisani LecceI-73100,Italy DepartmentofBiologicalandEnvironmental SciencesandTechnologies(DBEST) MarcoSaroglia LaboratoryofGeneralPhysiology DepartmentofBiotechnologyandMolecular UniversityofSalento Sciences ViaProvincialeLecce-Monteroni AnimalBiotechnologyandAquaculture LecceI-73100,Italy Unit UniversityofInsubria LaiaRibas ViaJ.H.Dunant3 InstitutdeCi`enciesdelMar VareseI-21100,Italy ConsejoSuperiordeInvestigaciones Cient´ıficas(CSIC) FanyueSun Barcelona,Spain TheFishMolecularGeneticsand BiotechnologyLaboratory MatthewL.Rise DepartmentofFisheriesandAllied OceanSciencesCenter AquaculturesandProgramofCelland MemorialUniversityofNewfoundland MolecularBiosciences A1C5S7,Canada AquaticGenomicsUnit AuburnUniversity RefugioRobles-Sikisaka Auburn,AL36849,USA UniversityofCalifornia DepartmentofPathology GencianaTerova SchoolofMedicine DepartmentofBiotechnologyandLife SanDiego,CA92182,USA Sciences UniversityofInsubria, AlessandroRomano ViaJ.H.Dunant3 DepartmentofBiologicaland VereseI-21100,Italy EnvironmentalSciencesandTechnologies and (DBEST) Inter-UniversityCentreforResearchin LaboratoryofGeneralPhysiology ProteinBiotechnologies“TheProtein UniversityofSalento Factory” P1:SFK/UKS P2:SFK BLBS108-bcontrib Saroglia May11,2012 7:27 Trim:246mm×189mm x ListofContributors PolytechnicUniversityofMilanand Jose-LuisZambonino-Infante UniversityofInsubria Ifremer ViaJ.H.Dunant3 FishNutritionLaboratory VareseI-21100,Italy Plouzan´e29200,France TizianoVerri JiarenZhang DepartmentofBiologicalandEnvironmental TheFishMolecularGeneticsand SciencesandTechnologies BiotechnologyLaboratory LaboratoryofGeneralPhysiology DepartmentofFisheriesandAllied UniversityofSalento AquaculturesandProgramofCelland ViaProvincialeLecce-Monteroni MolecularBiosciences LecceI-73100,Italy AquaticGenomicsUnit AuburnUniversity AnaVin˜as Auburn,AL36849,USA DepartamentodeGen´etica,Facultadde Biolog´ıa(CIBUS) YuZhang SantiagodeCompostela,Spain TheFishMolecularGeneticsand BiotechnologyLaboratory RuijiaWang DepartmentofFisheriesandAllied TheFishMolecularGeneticsand AquaculturesandProgramofCelland BiotechnologyLaboratory MolecularBiosciences DepartmentofFisheriesandAllied AquaticGenomicsUnit AquaculturesandProgramofCelland AuburnUniversity MolecularBiosciences Auburn,AL36849,USA AquaticGenomicsUnit AuburnUniversity Auburn,AL36849,USA P1:SFK/UKS P2:SFK BLBS108-Preface Saroglia May17,2012 13:33 Trim:246mm×189mm Preface Genomicsasadisciplinehasachievedmorein by mining the datasetsfor valuablebiological lessthan30yearsingeneratingavastamount information. of biological information than the accumula- Functionalanalysesofgenomesinaquacul- tion of all biological information in history. ture include all performance and production Currently, the genetic composition of a large traits such as growth, development, nutrition, number of organisms has been or is being de- sex determination, reproduction, immunity ciphered, including a large number of aqua- anddiseaseresistance,andresponsetovarious culture species. As increased understanding is environmental and physiological conditions. gained with the structure, organization, and Initially, such genome-scale issues can be evolution of genomes, scientists finally come addressed through association of genome to the point to ask some really serious ques- expression with the performance, and then tions concerning gene functions. Genomics is the functions of the genes involved in specific nowundergoingatransitionorexpansionfrom traitscanbecharacterizedintogenepathways. the mapping and sequencing of genomes to Eventually, however, the functions for the anemphasisongenomefunctions.Alongwith vast majority of aquaculture-related traits can the transition, the major goals of genomics be approached by the combination of tran- shift from structural genomics to functional scriptome profiling for expression candidates, genomics. genome-wideassociationstudiesforpositional Functionalgenomicsrepresentsanewphase candidates, comparative genome analysis for of genome analysis. It requires the develop- functional candidates, quantitative genomic mentofinnovativetechnologiesthatmakeuse analysis,and finally,directlytesting the candi- of the vast resource of structural genomics dategenestovalidatetheirfunctions.Because information. Specifically, functional genomics aquaculturespeciesinvolveawidespectrumof refers to the development and application of organisms ranging from invertebrate to verte- genome-wide experimental approaches to as- brateanimals,andmanyoftheinvolvedspecies sess gene functions by making use of the in- haveveryspecialbiologicalcharacteristicssuch formationandresourcesprovidedbystructural asextremelyhighfecundity,extremelyhighand genomics. It is characterized by high through- low tolerance to low dissolved oxygen, among putorlarge-scaleexperimentalmethodologies many others, functional genomics research of combined with statistical and computational aquaculture species will undoubtedly have a analysis of results. The fundamental strategy profoundimpactonbiology. in functional genomics is to expand the scope This book has 15 chapters. The first two ofbiologicalinvestigationfromstudyingasin- chapters provide a general introduction to glegeneorproteins,orafewgenes,tostudying functional genomics and general approaches allgenesorproteinsatonceonagenome-wide for functional genomics research in aquacul- scale.Suchoperationsallowthegenerationof ture, and existing genomic resources for func- tremendously large data sets that demand ad- tional genomics in aquaculture species. Chap- ditional capacities of data analysis to draw in- ters 3–10 are devoted to functional genomics formation relevant to biology. Computational of growth, development, reproduction, nutri- biology will play a critical and expanding role tion,andresponsestostressanddiseases;and in functional genomics, as it is characterized thelastfivechaptersarespecificchaptersthat xi
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