170mmx244mmBorem ffirs.tex V3-05/08/2014 5:21P.M. Page2 170mmx244mmBorem ffirs.tex V3-05/19/2014 11:57A.M. Page1 Omics in Plant Breeding 170mmx244mmBorem ffirs.tex V3-05/19/2014 11:57A.M. Page2 170mmx244mmBorem ffirs.tex V3-05/19/2014 11:57A.M. Page3 Omics in Plant Breeding Editedby Aluízio Borém UniversityofViçosa,Viçosa,MG,Brazil Roberto Fritsche-Neto UniversityofSãoPaulo/ESALQ,Piracicaba,SP,Brazil 170mmx244mmBorem ffirs.tex V3-05/19/2014 11:57A.M. Page4 Thiseditionfirstpublished2014©2014byJohnWiley&Sons,Inc. Editorialoffices:1606GoldenAspenDrive,Suites103and104,Ames,Iowa50010,USA TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UK 9600GarsingtonRoad,Oxford,OX42DQ,UK Fordetailsofourglobaleditorialoffices,forcustomerservicesandforinformation abouthowtoapplyforpermissiontoreusethecopyrightmaterialinthisbookplease seeourwebsiteatwww.wiley.com/wiley-blackwell. 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Coverimages:iStock ©pawel.gaul,iStock ©Vladimirovic,iStock ©emyerson Typesetin9.5/12.5ptPalatinobyLaserwordsPrivateLimited,Chennai,India 1 2014 170mmx244mmBorem ftoc.tex V3-05/08/2014 5:30P.M. Pagev 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 170mmx244mmBorem ftoc.tex V3-05/08/2014 5:30P.M. Pagevi 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 170mmx244mmBorem ftoc.tex V3-05/08/2014 5:30P.M. Pagevii 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 170mmx244mmBorem ftoc.tex V3-05/08/2014 5:30P.M. Pageviii 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