Molecular Markers in Plants PDF
Preview Molecular Markers in Plants
BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 Molecular Markers in Plants BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 Molecular Markers in Plants Editor Robert J. Henry QueenslandAllianceforAgricultureandFoodInnovation UniversityofQueensland Brisbane,Queensland,Australia A John Wiley & Sons, Inc., Publication BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 Thiseditionfirstpublished2013(cid:2)C 2013byJohnWiley&Sons,Inc. Wiley-BlackwellisanimprintofJohnWiley&Sons,formedbythemergerofWiley’s globalScientific,TechnicalandMedicalbusinesswithBlackwellPublishing. Editorialoffices: 2121StateAvenue,Ames,Iowa50014-8300,USA TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UK 9600GarsingtonRoad,Oxford,OX42DQ,UK Fordetailsofourglobaleditorialoffices,forcustomerservicesandforinformation abouthowtoapplyforpermissiontoreusethecopyrightmaterialinthisbookplease seeourwebsiteatwww.wiley.com/wiley-blackwell. 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Designationsusedbycompaniestodistinguishtheirproductsareoftenclaimedas trademarks.Allbrandnamesandproductnamesusedinthisbookaretradenames, servicemarks,trademarksorregisteredtrademarksoftheirrespectiveowners.The publisherisnotassociatedwithanyproductorvendormentionedinthisbook.This publicationisdesignedtoprovideaccurateandauthoritativeinformationinregardto thesubjectmattercovered.Itissoldontheunderstandingthatthepublisherisnot engagedinrenderingprofessionalservices.Ifprofessionaladviceorotherexpert assistanceisrequired,theservicesofacompetentprofessionalshouldbesought. LibraryofCongressCataloging-in-PublicationData Molecularmarkersinplants/editor,RobertJ.Henry. p.cm. Includesbibliographicalreferencesandindex. ISBN978-0-470-95951-0(hardback:alk.paper) 1. Plantbreeding. 2. Geneticmarkers. 3. Plantgenetics. 4. Cropimprovement. I. Henry,RobertJ. SB123.M582013 (cid:3) 634.956–dc23 2012019771 AcataloguerecordforthisbookisavailablefromtheBritishLibrary. Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthat appearsinprintmaynotbeavailableinelectronicbooks. CoverdesignbyModernAlchemyLLC (cid:2) Setin9.5/12.5ptPalatinobyAptaraR Inc.,NewDelhi,India 1 2013 BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 Contents Contributors ix Preface xiii 1 EvolutionofDNAMarkerTechnologyinPlants 3 RobertJ.Henry Introduction 4 EarlyMarkerTechnologies 4 EvolvingRangeofApplicationsofDNAMarkersinPlants 12 Applications 13 FutureDevelopments 15 References 15 2 Whole-GenomeSequencingforMarkerDiscovery 21 MarkEdwards SequencingStrategies 22 SequencingTechnologies 23 EpigeneticMarkers 31 Genome-WideSelection 32 DataAnalysisResources 32 References 33 Colorplatesectionlocatedbetweenpages34and35. 3 AmpliconSequencingforMarkerDiscovery 35 TimothyR.SextonandFrancesM.Shapter Introduction 36 Background 36 MaximizingEfficiencyThroughSamplePooling 38 LimitationsofAmplicon-BasedMPS 44 Bioinformatics 51 ConcludingRemarks 52 Acknowledgments 52 References 53 4 TranscriptomeSequencingforMarkerDiscovery 57 SusanGillies Introduction 58 BasicApproach 58 v BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 vi Contents Conclusions 64 References 64 5 MolecularMarkersinPlantImprovement 67 PeterJ.Prentis,EdwardK.Gilding,AnaPavasovic, CelineH.Frere,andIanD.Godwin Introduction 68 PlantDomesticationandTraditionalBreeding 68 ApplicationofMolecularMarkerstoBreeding 70 Next-GenerationApproachestoQTLDiscovery 75 Conclusion 77 References 78 6 ApplicationsofMolecularMarkersinPlantConservation 81 MaurizioRossettoandPaulD.Rymer Introduction 82 TraditionalApproaches 86 TheWayForward 91 Conclusion 95 References 96 7 MolecularMarkersforPlantBiosecurity 99 AndrewD.W.Geering Introduction 100 ThePresent—PCRforSpecificDiagnosisandforDNA Barcoding 101 TheFuture—Next-GenerationSequencingMethodsto RevolutionizePlantQuarantineDiagnostics 105 Conclusions 110 Acknowledgments 111 References 111 8 MolecularMarkersforHarnessingHeterosis 119 GopalaS.Krishnan,A.K.Singh,DanielL.E.Waters, andRobertJ.Henry Introduction 120 MolecularMarkersforUnderstandingtheGenetic BasisofHeterosis 122 MolecularDiversityandHeterosis—Molecular MarkersforPredictingHeterosis 123 Conclusion 131 References 132 BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 Contents vii 9 GeneticVariantDiscoveryandItsUseinGenome CharacterizationofAgronomicallyImportantCropSpecies 137 Ste´phaneDeschampsandMatthewA.Campbell Introduction 138 SangerResequencing 140 SingleFeaturePolymorphisms 140 Next-GenerationSequencing 143 High-DensityGenotypingusingtheIlluminaGoldenGate Platform 153 GenotypingbySequencing 155 GenomeCharacterizationandHaplotypes 157 ConclusionsandPerspectives 159 References 160 10 FutureProspectsofMolecularMarkersinPlants 169 ReyazulR.MirandRajeevK.Varshney Introduction 170 MolecularMarkers:ThePast 172 MolecularMarkers:ThePresent 173 MolecularMarkers:TheFuture 175 NovelApproachesorPlatformsforPlantBreeding 180 Conclusions 183 Acknowledgments 184 References 184 Index 191 BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 Contributors MatthewA.Campbell DuPontPioneer Johnston,Iowa,UnitedStates Ste´phaneDeschamps DuPontAgriculturalBiotechnology ExperimentalStation–P.O.Box80353 200PowderMillRoad Wilmington,DE19880-0353 MarkEdwards SouthernCrossPlantSciences SouthernCrossUniversity Lismore,Australia CelineH.Frere SchoolofAgriculturalandFoodSciences UniversityofQueensland Brisbane,Australia AndrewD.W.Geering CooperativeResearchCentreforNationalPlantBiosecurityandthe QueenslandAllianceforAgricultureandFoodInnovation TheUniversityofQueensland EcosciencesPrecinct Brisbane,Queensland,Australia EdwardK.Gilding SchoolofAgriculturalandFoodSciences UniversityofQueensland Brisbane,Australia SusanGillies SouthernCrossPlantSciences SouthernCrossUniversity Lismore,Australia ix BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 x Contributors IanD.Godwin SchoolofAgriculturalandFoodSciences UniversityofQueensland Brisbane,Australia RobertJ.Henry QueenslandAllianceforAgricultureandFoodInnovation UniversityofQueensland Brisbane,Queensland,Australia PavanaJ.Hiremath InternationalCropsResearchInstitutefortheSemi-AridTropics Hyderabad,India GopalaS.Krishnan DivisionofGenetics IndianAgriculturalResearchInstitute NewDelhi,India AnaPavasovic SchoolofBiomedicalScience QueenslandUniversityofTechnology Brisbane,Australia PeterJ.Prentis SchoolofEarth,EnvironmentalandBiologicalSciences QueenslandUniversityofTechnology Brisbane,Australia OscarRiera-Lizarazu InternationalCropsResearchInstitutefortheSemi-AridTropics Hyderabad,India MaurizioRossetto NationalHerbariumofNSW RoyalBotanicGardensandDomainTrust Sydney,Australia ReyazulR.Mir InternationalCropsResearchInstitutefortheSemi-AridTropics Hyderabad,India PaulD.Rymer HawkesburyInstitutefortheEnvironment UniversityofWesternSydney Richmond,Australia BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 Contributors xi TimothyR.Sexton DepartmentofForestSciences TheUniversityofBritishColumbia Vancouver,BritishColumbia,Canada FrancesM.Shapter SouthernCrossPlantSciences SouthernCrossUniversity Lismore,Australia A.K.Singh DivisionofGenetics IndianAgriculturalResearchInstitute NewDelhi,India RajeevK.Varshney InternationalCropsResearchInstitutefortheSemi-AridTropics Hyderabad,India; CGIAR-GenerationChallengeProgramme Mexico; SchoolofPlantBiology FacultyofNaturalandAgriculturalSciences TheUniversityofWesternAustralia Crawley,Australia DanielL.E.Waters SouthernCrossPlantScience SouthernCrossUniversity Lismore,Australia BLBS114-fm BLBS114-Henry Trim:244mm×172mm September18,2012 10:40 Preface Plantsarefundamentaltolife,beingthebasisofourfoodproductionand an essential part of the global ecosystem on which life on earth depends. Plants have been used as a source of a wide range of materials, but the threat of exhaustion of fossil oil supplies has resulted in a renewed eval- uation of plants as a source of energy and biomaterials. Molecular anal- ysis of plants has found many applications in plant improvement, in the managementofplantproduction,andtheconservationofplantresources. Molecularmarkersareroutinelyusedtoidentifyplantsforforensicorin- tellectualpropertyapplications.Moleculartoolshavebecomekeycontrib- utors to the management of wild plant populations helping to conserve biodiversity.Therelentlessneedforthecontinuousdevelopmentofgeneti- callyimprovedcropstosatisfythedemandsofaglobalhumanpopulation growinginnumberandaffluenceisnowstronglysupportedbymolecular markertechnology. RecentdramaticadvancesinDNAsequencingarenowprovidingcost- effective options for the discovery of very large numbers of markers for anyplant species.Thesedevelopmentssignificantlychangethe approach tomarkerdiscoveryandanalysisinplantsandgreatlyexpandthepoten- tialrangeofapplications.Thisbookoutlinesthetechnologiesformolecular analysisofplantsinsupportofplantbreeding,production,andconserva- tion.Thetechniquesthathavebeenusedinthepastarereviewedinrela- tiontorecentdevelopmentsandfuturepotential.Thisbookupdatesearlier volumesonthistopicfeaturingsignificantadvancesinboththetechnology andapplicationofmarkers. RobertHenry UniversityofQueensland xiii
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