Functional Genomics in Aquaculture

423 Pages·2012·5.93 MB·English

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Functional Genomics in Aquaculture
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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
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Functionalgenomicsinaquaculture/editedbyMarcoSarogliaandZhanjiang(John)Liu.
p.cm.
Includesbibliographicalreferencesandindex.
ISBN978-0-470-96008-0(hardcover:alk.paper) 1.Fishes–Breeding. 2.Shellfish–Breeding.
3.Genomics. 4.Aquaculture. I.Saroglia,Marco. II.Liu,Zhanjiang.
SH155.5.F862012
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2012007484
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1 2012
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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
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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
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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)
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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
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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”
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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
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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
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