Joanna Jankowicz-Cieslak · Thomas H. Tai Jochen Kumlehn · Bradley J. Till Editors Biotechnologies for Plant Mutation Breeding Protocols Biotechnologies for Plant Mutation Breeding Joanna Jankowicz-Cieslak (cid:129) Thomas H. Tai (cid:129) Jochen Kumlehn (cid:129) Bradley J. Till Editors Biotechnologies for Plant Mutation Breeding Protocols Editors JoannaJankowicz-Cieslak ThomasH.Tai PlantBreedingandGeneticsLaboratory CropsPathologyandGeneticsResearchUnit JointFAO/IAEADivisionofNuclear USDA-ARS TechniquesinFoodandAgriculture Davis Vienna,Austria California,USA JochenKumlehn BradleyJ.Till PlantReproductiveBiology PlantBreedingandGeneticsLaboratory LeibnizInstituteofPlantGeneticsand JointFAO/IAEADivisionofNuclear CropPlantResearch(IPK) TechniquesinFoodandAgriculture Gatersleben,Germany Vienna,Austria ISBN978-3-319-45019-3 ISBN978-3-319-45021-6 (eBook) DOI10.1007/978-3-319-45021-6 LibraryofCongressControlNumber:2016959193 ©InternationalAtomicEnergyAgency2017.ThebookispublishedopenaccessatSpringerLink.com. 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Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAGSwitzerland In memory of Dr Pierre J.L. Lagoda (1961–2016) for his tireless efforts and endless enthusiasm for plant mutation breeding. Preface Sustainable global food security remains a serious challenge. The compounding factors of a growing population, a changing climate and finite and dwindling natural resources mean that food production needs to increase dramatically in the coming decades. Genetic improvement of crops has historically led to vast gains in yields and subsequently has reduced famine. Variation is the source of all breeding, and inducing mutations is an important and successful approach for generating novel variation and developing new crop varieties that are climate smartandnutritiousandincreasefarmer’sincomes. The use of induced mutations dates back to the 1920s, and today there are over3200mutantcropvarietiesregisteredinadatabasecuratedbytheFAO/IAEA. The process can be improved through the development, adaptation and transfer of technologies for optimizing the density of induced mutations and increasing the efficiency of phenotypic and genotypic screening of large mutant plant populations. Towards this end, the Joint FAO/IAEA Programme of Nuclear Techniques for Food and Agriculture initiated a collaborative Coordinated Research Project (CRP) titled “Enhancing the Efficiency of Induced Mutagenesis through an Integrated Biotechnology Pipeline“. The project brought together researchers from developing and developed countries with the aim to develop protocols and guidelines to improve the efficiency of the different steps of the plant mutation breeding process. This book provides protocols resulting from this CRP. A range of methods are provided suitable for those new to the field The views expressed in this text do not necessarily reflect those of the IAEA or FAO or governments oftheirMember States.Thementionofnamesofspecific companiesorproducts does not imply an intention to infringe on proprietary rights, nor should it be construed as an endorsementorrecommendationonthepartofIAEAorFAO. vii viii Preface as well as to those seeking more advanced phenotypic and genotypic screening techniques. To guarantee high scientific quality, all chapters of this book have been peer reviewed. We are thankful to the participants of the CRP, authors of the chapters and also to all the reviewers (for list, see overleaf) who donatedtheirtimetoimprovethechapters. Vienna,Austria BradleyJ.Till Acknowledgements We thank the participants of the IAEA Coordinated Research Project (CRP) D24012 for the valuable input into the project which stimulated this book. We alsothankmanyPBGandPBGLstaffpastandpresentwhosupportedactivitiesand initiated new thinking about novel biotechnology approaches for increasing effi- cienciesinmutation inductionand detection. Specifically,wewouldliketothank Dr Chikelu Mba for the preparation of the Coordinated Research Programme proposal. Funding for this work was provided by the Food and Agriculture Orga- nization of the United Nations and the International Atomic Energy Agency through their Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture. ix Contents PartI Introduction 1 MutagenesisforCropBreedingandFunctionalGenomics. . . . . . . 3 JoannaJankowicz-Cieslak,ChikeluMba,andBradleyJ.Till PartII MutationInductionandChimeraDissociation 2 ChemicalandPhysicalMutagenesisinJatrophacurcas. . . . . . . . . 21 FatemehMaghuly,SouleymaneBado,JoannaJankowicz-Cieslak, andMargitLaimer 3 ChemicalMutagenesisandChimeraDissolutioninVegetatively PropagatedBanana. . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . 39 JoannaJankowicz-CieslakandBradleyJ.Till 4 MutationInductionUsingGammaIrradiationandEmbryogenic CellSuspensionsinPlantain(Musaspp.). . . . . . . . . . . . . . . . . . . . 55 JorgeLo´pez,Ayme´ Rayas,ArletysSantos,V´ıctorMedero, YoelBeovides,andMilagrosBasail 5 OptimisationofSomaticEmbryogenesisinCassava. . . . . . . . . . . . 73 KennethE.DansoandWilfredElegba 6 CreationofaTILLINGPopulationinBarleyAfterChemical MutagenesiswithSodiumAzideandMNU. . . . . . . . . . . . . . . . . . . 91 IwonaSzarejko,MiriamSzurman-Zubrzycka,MalgorzataNawrot, MarekMarzec,DamianGruszka,MarzenaKurowska, BeataChmielewska,JustynaZbieszczyk,JanuszJelonek, andMiroslawMaluszynski 7 Site-DirectedMutagenesisinBarleybyExpressionofTALE NucleaseinEmbryogenicPollen. . . . . . . . . . . . . . . . . . . . . . . . . . . 113 MaiaGurushidze,StefanHiekel,IngridOtto,G€otzHensel, andJochenKumlehn xi xii Contents 8 DoubledHaploidyasaToolforChimaeraDissolution ofTALEN-InducedMutationsinBarley. . . . . . . . . . . . . . . . . . . . . 129 MaiaGurushidze,HannesTrautwein,PetraHoffmeister,IngridOtto, AndreaM€uller,andJochenKumlehn PartIII PhenotypicScreening 9 FieldEvaluationofMutagenizedRiceMaterial. . . . . . . . . . . . . . . 145 SydneyD.Johnson,DennisR.Taylor,ThomasH.Tai, JoannaJankowicz-Cieslak,BradleyJ.Till,andAlphaB.Jalloh 10 RootPhenotypingPipelineforCerealPlants. . . . . . . . . . . . . . . . . 157 MichalSlota,MiroslawMaluszynski,andIwonaSzarejko 11 BreedingNewAromaticRicewithHighIronUsingGamma RadiationandHybridization. . .. . . . .. . . .. . . .. . . .. . . . .. . . .. 173 PhuongTanTranandCuaQuangHo 12 UtilisingNIRSforQualitativeandNon-destructiveIdentification ofSeedMutantsinLargePopulations. . . . . . . . . . . . . . . . . . . . . . 193 JohannVollmannandJoannaJankowicz-Cieslak 13 ProteomeAnalysesofJatrophacurcas. . . . . . . . . . . . . . . . . . . . . . 203 FatemehMaghuly,GorjiMarzban,EbrahimRazzazi-Fazeli, andMargitLaimer PartIV GenotypicScreening 14 Low-CostMethodsforDNAExtractionandQuantification. . . . . . 227 OwenA.Huynh,JoannaJankowicz-Cieslak,BanumatySaraye, BernhardHofinger,andBradleyJ.Till 15 AProtocolforBenchtopExtractionofSingle-Strand-Specific NucleasesforMutationDiscovery. . . . . . . . . . . . . . . . . . . . . . . . . . 241 BernhardJ.Hofinger,OwenA.Huynh,JoannaJankowicz-Cieslak, andBradleyJ.Till 16 AProtocolforValidationofDoubledHaploidPlantsbyEnzymatic MismatchCleavage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 BradleyJ.Till,BernhardJ.Hofinger,Ays¸eS¸en,OwenA.Huynh, JoannaJankowicz-Cieslak,LikyeleshGugsa,andJochenKumlehn 17 Bioinformatics-BasedAssessmentoftheRelevanceofCandidate GenesforMutationDiscovery. . . . . . . . . . . . . . . . . . . . . . . . . . . . 263 MichalSlota,MiroslawMaluszynski,andIwonaSzarejko 18 MutationDetectionbyAnalysisofDNAHeteroduplexes inTILLINGPopulationsofDiploidSpecies. . . . . . . . . . . . . . . . . . 281 MiriamSzurman-Zubrzycka,BeataChmielewska,PatrycjaGajewska, andIwonaSzarejko