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Omics in Plant
Breeding
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Omics in Plant
Breeding
Editedby
Aluízio Borém
UniversityofViçosa,Viçosa,MG,Brazil
Roberto Fritsche-Neto
UniversityofSãoPaulo/ESALQ,Piracicaba,SP,Brazil
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1 2014
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Contents
ListofContributors ix
Foreword xiii
1 Omics:Openingupthe“BlackBox”ofthePhenotype 1
RobertoFritsche-NetoandAlu´ızioBorém
ThePost-GenomicsEra 3
TheOmicsinPlantBreeding 4
Genomics,PrecisionGenomics,andRNAInterference 5
TranscriptomicsandProteomics 8
MetabolomicsandPhysiognomics 8
Phenomics 9
Bioinformatics 10
Prospects 10
References 10
2 Genomics 13
AntônioCostadeOliveira,LucianoCarlosdaMaia,
DanieldaRosaFarias,andNacieleMarini
TheRiseofGenomics 13
DNASequencing 13
DevelopmentofSequence-basedMarkers 18
GenomeWideSelection(GWS) 25
StructuralandComparativeGenomics 27
References 28
3 Transcriptomics 33
CarolinaMunariRodrigues,ValériaS.Mafra,andMarcos
AntonioMachado
MethodsofStudyingtheTranscriptome 34
ApplicationsofTranscriptomicsApproachesforCrop
Breeding 46
ConclusionsandFutureProspects 51
Acknowledgements 51
References 51
4 Proteomics 59
IlaraGabrielaF.Budzinski,Tha´ısRegiani,MônicaT.Veneziano
Labate,SimoneGuidetti-Gonzalez,DanielleIzilda
v
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vi Contents
R.daSilva,MariaJulianaCalderanRodrigues,Janainade
SantanaBorges,IvanMiletovicMozol,andCarlosAlbertoLabate
History 59
DifferentMethodsfortheExtractionofTotalProteins 60
SubcellularProteomics 64
Post-TranslationalModifications 66
QuantitativeProteomics 69
Perspectives 72
References 73
5 Metabolomics 81
ValdirDiola(inmemoriam),DanilodeMenezesDaloso,and
WernerCamargosAntunes
Introduction 81
MetabolomicandBiochemicalMolecules 83
TechnologiesforMetabolomics 83
MetabolomicDatabaseAnalysis 86
MetabolomicsApplications 89
Metabolomics-assistedPlantBreeding 91
AssociativeGenomeMappingandmQTLProfiles 95
Large-scalePhenotypingUsingMetabolomics 97
ConclusionandOutlook 98
References 99
6 Physionomics 103
FredericoAlmeidadeJesus,AgustinZsögön,andLázaro
EustáquioPereiraPeres
Introduction 103
EarlyStudiesonPlantPhysiologyandtheDiscoveryof
Photosynthesis 104
BiochemicalApproachestoPlantPhysiologyandthe
DiscoveryofPlantHormones 104
GeneticApproachestoPlantPhysiologyandthe
DiscoveryofHormoneSignalTransductionPathways 106
AlternativeGeneticModelsforOmicsApproachesin
PlantPhysiology 112
“Physionomics”asanIntegratorofVariousOmicsfor
FunctionalStudiesandPlantBreeding 117
Acknowledgements 121
References 121
7 Phenomics 127
RobertoFritsche-Neto,Alu´ızioBorém,andJoshuaN.Cobb
Introduction 127
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Contents vii
ExamplesofLarge-scalePhenotyping 128
ImportantAspectsforPhenomicsImplementation 134
MainBreedingApplications 141
FinalConsiderations 144
References 144
8 Electrophoresis,Chromatography,andMass
Spectrometry 147
Tha´ısRegiani,IlaraGabrielaF.Budzinski,Simone
Guidetti-Gonzalez,MônicaT.VenezianoLabate,Fernando
Cotinguiba,FelipeG.Marques,Fabr´ıcioE.Moraes,
andCarlosAlbertoLabate
Introduction 147
Two-dimensionalElectrophoresis(2DE) 148
Chromatography 150
MassSpectrometry 155
DataAnalysis 161
References 164
9 Bioinformatics 167
J.MiguelOrtegaandFabr´ıcioR.Santos
Introduction 167
The“Omics”MegadataandBioinformatics 167
HardwareforModernBioinformatics 169
SoftwareforGenomicSequencing 170
SoftwareforContigAssembling 172
AssemblyUsingtheGraphTheory 173
NewApproachesinBioinformaticsforDNAandRNA
Sequencing 174
Databases,IdentificationofHomologousSequences
andFunctionalAnnotation 175
AnnotationofaCompleteGenome 179
ComputationalSystemwithChainedTasksManager
(Workflow) 181
ApplicationsforStudiesinPlants 182
FinalConsiderations 183
References 184
10 PrecisionGeneticEngineering 187
ThiagoJ.Nakayama,Alu´ızioBorém,LucimaraChiari,Hugo
BrunoCorreaMolinari,andAlexandreLimaNepomuceno
Introduction 187
ZincFingerNucleases(ZFNs) 190
TranscriptionActivator-likeEffectorNucleases(TALENs) 193
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viii Contents
Meganucleases(LHEs:LAGLIDADGHoming
Endonucleases) 194
ClusteredRegularlyInterspacedShortPalindromic
Repeats(CRISPR) 195
ImplicationsandPerspectivesoftheuseofPGEinPlant
Breeding 197
References 202
11 RNAInterference 207
FranciscoJ.L.Aragão,AbdulrazakB.Ibrahim,
andMariaLaineP.Tinoco
Introduction 207
DiscoveryofRNAi 208
MechanismofRNAInterference 209
ApplicationsinPlantBreeding:NaturallyOccurringGene
SilencingandModificationbyGeneticEngineering 211
ResistancetoViruses 215
Host-inducedGeneSilencing 218
InsectandDiseaseControl 218
ImprovingNutritionalValues 219
SecondaryMetabolites 220
Perspectives 220
References 222
Index 229
