Table Of Content

Andriy Bilichak John D. Laurie Editors Accelerated Breeding of Cereal Crops S P H PRINGER ROTOCOLS ANDBOOKS Forfurther volumes: http://www.springer.com/series/8623 SpringerProtocols Handbooks collects adiverse range ofstep-by-steplaboratorymethods andprotocolsfromacrossthelifeandbiomedicalsciences.Eachprotocolisprovidedinthe Springer Protocol format: readily-reproducible in a step-by-step fashion. Each protocol openswithanintroductoryoverview,alistofthematerialsandreagentsneededtocomplete theexperiment,andisfollowedbyadetailedproceduresupportedbyahelpfulnotessection offeringtipsandtricksofthetradeaswellastroubleshootingadvice.Withafocusonlarge comprehensive protocol collections and an international authorship, Springer Protocols Handbooksareavaluableadditiontothelaboratory. Accelerated Breeding of Cereal Crops Edited by Andriy Bilichak Agriculture and Agri-Food Canada, Morden, MB, Canada John D. Laurie Agriculture and Agri-Food Canada, Lethbridge, AB, Canada Editors AndriyBilichak JohnD.Laurie AgricultureandAgri-FoodCanada AgricultureandAgri-FoodCanada Morden,MB,Canada Lethbridge,AB,Canada ISSN1949-2448 ISSN1949-2456 (electronic) SpringerProtocolsHandbooks ISBN978-1-0716-1525-6 ISBN978-1-0716-1526-3 (eBook) https://doi.org/10.1007/978-1-0716-1526-3 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2022 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. 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Preface Growing world population and increased threats associated with a warming climate place high demands on plant breeders to rapidly develop resilient crops with stable yields across different environments. To meet global food demand, growers need to double crop production by 2050, a seemingly unrealistic goal with the current yield increase. Maize, rice, and wheat provide 60% of the energy intake for people around the globe. Although crops likericeandmaizehaveseensignificantdevelopmentofgenomicresourcesandunderstand- ingofgeneticcausesforagronomicallyimportanttraits,hexaploidwheatlagsinthisregard. The large genome of wheat has hampered progress, but its polyploid nature offers great untapped potential for the creation of functional variation. With advances in omics tech- nologiesand theadventofgeneediting, biotechnologyincerealcropsisacceleratingat an incrediblepace. Leading scientists with expertise ranging from cereal biotechnology and genomics to conventional breeding provide in this book either up-to-date methods used in respective programs or an overview of their research fields. In a stepwise manner, the reader is introduced to well-established and emerging techniques that can potentially streamline the discovery of genes responsible for agriculturally important traits in crops. We start withtherecentprogressingenomicsofselectedcropsfromthePoaceaefamily,highlighting approachesundertakentocreatethefirstpangenomeforbreadwheatandwhatcanbedone to streamline mining for genetic variation. Methods that utilize this variation are increas- ingly crucial for breeders. The reader is introduced to techniques widely used in conventional breeding, such as marker-assisted selection and mapping of quantitative trait loci, as well as recent advancements of genome-wide association studies. Next, we show how artificial intelligence can help with breeding by using machine learning for genomic selection. Technologies that speed-up the breeding process, such as the production of doubled haploid plants through microspores, are of great interest to breeders. In addition to the variationthatoccursnaturally,welookatinducedmutagenesisthroughtheuseofchemicals, radiation, and transposable elements. Rapid high-throughput detection of natural and induced variations can be accomplished using PCR and Targeting Induced Local Lesions in Genomes (TILLING). Transcription factors play an essential role in regulating gene expression; therefore, the precise mapping of their position using methods such as DNA affinity purification sequencing (DAP-seq) is vital for functional genomics studies. With rapid advancements in gene editing, this technology is now making it into the breeders’ hands. Included methods describe approaches to construct CRISPR/Cas expression cas- settes for monocots using modular assembly systems and genome editing in wheat. A manifestation of genomic sequence at the phenotypic level is performed through proteins and their posttranslational modifications. Therefore, quantitative proteomics in cereals is gainingmomentumforacomprehensiveunderstandingofcropgenetics.Finally,phenotyp- ing is a crucial component of plant breeding, integrating crop development, growth, and yield.High-throughputphenomicsoffersapowerfultoolforbreederstoselecttraitsthatare eitherchallengingtoseeor notdetectablebytheeye. Overall,thisbookprovidesacollectionofmethodsthat,webelieve,willbeofinterestto plant breeders, researchers, postdoctoral fellows, and students working in functional v vi Preface genomicsfor thedevelopmentofthenextgenerationofcropplants.Finally,wewouldlike to gratefully acknowledge the authors for their valuable contribution to this book, the associate editor for Springer protocols, Monica Suchy, and Springer Nature for the invita- tiontocontribute. Morden,MB,Canada AndriyBilichak Lethbridge,AB,Canada JohnD.Laurie Contents Preface ..................................................................... v Contributors................................................................. ix 1 RecentAdvancesinSequencingofCerealGenomes......................... 1 SeanWalkowiak,CurtisJ.Pozniak,andKirbyT.Nilsen 2 MappingQuantitativeTraitLociinWheat:HistoricPerspective, Tools,andMethodsforAnalysis.......................................... 31 RamanDhariwalandHarpinderSinghRandhawa 3 IntroductiontoMarker-AssistedSelectioninWheatBreeding................ 77 SudhakarPandurangan,ClareWorkman,KirbyNilsen, andSantoshKumar 4 Genome-WideAssociationStudies(GWAS)inCereals....................... 119 BraulioJ.Soto-Cerda,AkshayaVasudevan,Andre´Laroche, andRajaRagupathy 5 CropGBM:AnUltra-EfficientMachineLearningToolbox forGenomicSelection-AssistedBreedinginCrops.......................... 133 YuetongXu,JohnD.Laurie,andXiangfengWang 6 DoubledHaploidProductionthroughMicrosporeCulture .................. 151 TheiaJensen,KyleBodell,FengyingJiang,andJohnD.Laurie 7 ChemicalandPhysicalMutagenesisApproachesforIdentification ofHerbicideandDroughtToleranceTraitsinWheat........................ 167 NehaVaid,MarcusA.Samuel,SateeshKagale, andRajuSoolanayakanahally 8 UsingTILLINGLinesforFunctionalGenomicsinWheat................... 181 LiangChenandYin-GangHu 9 ATransposon-BasedActivationTagSystemforFunctionalGenomics inCereals:DetectionofMping-BasedActivationTagMobilizationinWheat... 195 AngelaN.Plemmons,AmandaR.Askins,SarahM.Mendoza, andC.NathanHancock 10 AModularCloningToolkitforGenomeEditinginCereals.................. 209 FlorianHahn,LauraSanjurjoLoures,andVladimirNekrasov 11 GenomeEditingandIdentificationofTargetedHeritableMutations inWheat............................................................... 225 MatthewJ.MilnerandEmmaJ.Wallington 12 AGenotypingProtocoltoIdentifyCRISPR/Cas9-EditedEvents inHexaploidWheat..................................................... 239 JohannSchernthaner,MargaretBalcerzak,JhadeswarMurmu, andRajagopalSubramaniam vii viii Contents 13 qPCRMethodsfor theQuantificationofTransgeneInsertCopy NumberandZygosityUsingtheComparativeCtMethodinTransgenic SorghumbicolorL.Moench .............................................. 251 JoelHague,KimberlyNelson,AlexYonchak,andAlbertP.Kausch 14 ARoadMapforUndertakingQuantitativeProteomicsinPlants: NewOpportunitiesforCerealCrops...................................... 269 IbrahimKhodabocus,QiaomuLi,DevangMehta,andR.GlenUhrig 15 DNAAffinityPurificationSequencing(DAP-Seq)forMapping Genome-WideTranscriptionFactorBindingSitesinPlants.................. 293 MiaomiaoLiandShao-ShanCarolHuang 16 BasicsofSensor-BasedPhenotypinginWheat.............................. 305 EmilyThoday-Kennedy,NathanGood,andSuryaKant Index ...................................................................... 333 Contributors AMANDAASKINS • DepartmentofBiologyandGeology,UniversityofSouthCarolinaAiken, Aiken,SC,USA MARGARETBALCERZAK • OttawaResearchandDevelopmentCentre,Ottawa,ON,Canada KYLEBODELL • LethbridgeResearchandDevelopmentCentre,AgricultureandAgri-Food Canada,Lethbridge,AB,Canada;TheDepartmentofBiologicalSciences,Universityof Lethbridge,Lethbridge,AB,Canada LIANGCHEN • StateKeyLaboratoryofCropStressBiologyforAridAreas,Collegeof Agronomy,NorthwestA&FUniversity,Yangling,Shaanxi,China RAMANDHARIWAL • AgricultureandAgri-FoodCanada,LethbridgeResearchand DevelopmentCentre,Lethbridge,AB,Canada NATHANGOOD • AgricultureVictoria,GrainsInnovationPark,Horsham,VIC,Australia JOELHAGUE • DepartmentofCellandMolecularBiology,UniversityofRhodeIsland,West Kingston,RI,USA FLORIAN HAHN • PlantSciencesDepartment,RothamstedResearch,Harpenden,UK C.NATHAN HANCOCK • DepartmentofBiologyandGeology,UniversityofSouthCarolina Aiken,Aiken,SC,USA YIN-GANGHU • StateKeyLaboratoryofCropStressBiologyforAridAreas,Collegeof Agronomy,NorthwestA&FUniversity,Yangling,Shaanxi,China;InstituteofWater SavingAgricultureinAridRegionsofChina,NorthwestA&FUniversity,Yangling, Shaanxi,China SHAO-SHAN CAROLHUANG • Center forGenomicsandSystemsBiology,Departmentof Biology,NewYorkUniversity,NewYork,NY,USA FENGYINGJIANG • LethbridgeResearchandDevelopmentCentre,AgricultureandAgri-Food Canada,Lethbridge,AB,Canada SATEESHKAGALE • NationalResearchCouncilCanada,Saskatoon,SK,Canada SURYAKANT • AgricultureVictoria,GrainsInnovationPark,Horsham,VIC,Australia; CentreforAgriculturalInnovation,SchoolofAgricultureandFood,FacultyofVeterinary andAgriculturalSciences,TheUniversityofMelbourne,Melbourne,VIC,Australia ALBERTP.KAUSCH • DepartmentofCellandMolecularBiology,UniversityofRhodeIsland, WestKingston,RI,USA IBRAHIMKHODABOCUS • DepartmentofBiologicalSciences,UniversityofAlberta,Edmonton, AB,Canada SANTOSHKUMAR • BrandonResearchandDevelopmentCentre,AgricultureandAgri-Food Canada,Brandon,MB,Canada ANDRE´ LAROCHE • AgricultureandAgri-FoodCanada,LethbridgeResearchand DevelopmentCentre,Lethbridge,AB,Canada JOHND.LAURIE • LethbridgeResearchandDevelopmentCentre,AgricultureandAgri- FoodCanada,Lethbridge,AB,Canada MIAOMIAOLI • Center forGenomicsandSystemsBiology,DepartmentofBiology,NewYork University,NewYork,NY,USA QIAOMU LI • DepartmentofBiologicalSciences,UniversityofAlberta,Edmonton,AB, Canada ix