Maize: Methods and Protocols

232 Pages·2018·4.699 MB·English

by  L. Mark Lagrimini (eds.)

Methods in
Molecular Biology 1676
L. Mark Lagrimini Editor
Maize
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences,
University ofHertfordshire,
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Maize
Methods and Protocols
Edited by
L. Mark Lagrimini
Department of Agronomy and Horticulture, University of Nebraska – Lincoln,
Lincoln, NE, USA
Editor
L.MarkLagrimini
DepartmentofAgronomyandHorticulture
UniversityofNebraska–Lincoln
Lincoln,NE,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7314-9 ISBN978-1-4939-7315-6 (eBook)
DOI10.1007/978-1-4939-7315-6
LibraryofCongressControlNumber:2017952059
©SpringerScience+BusinessMediaLLC2018
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Preface
More maize is grown more than any other food crop worldwide with production at nearly
1 billion metric tons/year. In the USA, corn yield has increased at a steady 1.6 bushels/
acre/year since the 1930s, realized through combined genetic and crop management
improvements.Thedemandforgreateryieldsandmoresustainableproductionwillincrease
dramatically as population increases, the amount of arable land shrinks from urban sprawl
andsalinization,andthethreatfrombioticandabioticstressorsincreasesasaconsequence
of climate change. Looking ahead, the theoretical yield potential for maize is estimated at
300%ofthatwhichisachievedintoday’sbesthybrids,makingthiscropafruitfulsubjectfor
molecular biology studies and genetic improvement. Unlike laboratory models such as
ArabidopsisandBrachypodium,thereisadirectpathfromthelaboratorytocropimprove-
ment. Also, unlike the model plants maize is a highly productive C plant with its own
4
specializedarchitectureandphysiology.Thishighsocialandcommercialvalueformaizehas
ledtosignificantresearchdevelopmentsinprivateindustryandgovernment-fundedlabora-
tories.ThefirstcommercialsaleoftransgenicmaizewasintheUSAin1995(Btgene,insect
resistance).Thesequenceforthemaizegenomewaspublishedin2009.By2014,93%ofthe
cornplantedintheUSAwasgeneticallymodified.
ThisvolumeintheMethodsinMolecularBiologyseriesprovidesacollectionofrelevant
protocols for the molecular characterization of maize. The objective of the book is to
provide the experimentalist with practical methods to successfully carry out each of the
protocols.Eachchapterprovidesadescriptionofthetheorybehindtheprotocol,alistingof
the materials required, and a step-by-step protocol. The book is organized into four parts:
(I) Cell, tissue and organ culture and maize transformation (Chapters 1–4), (II) Gene
silencingandgenerationofmutantpopulations(Chapters5–8),(III)Plantgeneexpression
(Chapters 9–12), and (IV) Plant metabolic networks (Chapters 13). The methods cover a
broad range of topics enabling the reader to grow and propagate maize in the laboratory,
greenhouse,andfield;developandscreenmutagenicpopulations;characterizethegenome
and transcriptome; characterize protein and metabolic regulatory networks; and generate
transgenicplantsforgeneknock-outandoverexpressionpurposes.
We would like to thank the authors for their contributions. The methods they present
were either developed or used effectively in their own laboratories. It is our intention that
thisvolumewillprovideyouwithareadyresourceforallofyour maizeresearch.
Lincoln,NE,USA L.MarkLagrimini
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I CELL, TISSUE, AND ORGAN CULTURE AND MAIZE
TRANSFORMATION
1 UseofInVitroKernelCulturetoStudyMaizeNitrogenand
CarbohydrateMetabolism ............................................... 3
JuliannR.SeebauerandFrederickE.Below
2 Agrobacterium-andBiolistic-MediatedTransformation
ofMaizeB104Inbred................................................... 15
JenniferA.Raji,BronwynFrame,DanielLittle,TriJokoSantoso,
andKanWang
3 AdvancesinAgrobacterium-mediatedMaizeTransformation................. 41
HengZhong,SivamaniElumalai,SamsonNalapalli,
LeeRichbourg,AnnaPrairie,DavidBradley,ShujieDong,
XiujuanJennySu,WeiningGu,TimStrebe,LiangShi,and
QiudengQue
4 ABriefHistoryofPromoterDevelopmentforUseinTransgenic
MaizeApplications...................................................... 61
MichaelL.Nuccio
PART II GENE SILENCING AND GENERATION OF MUTANT POPULATIONS
5 DeletionMutagenesisandIdentificationofCausativeMutations
inMaize ............................................................... 97
ShangangJia,AixiaLi,ChiZhang,andDavidHolding
6 SelectiveKnockdownsinMaizebySequence-SpecificProtein
Aggregation............................................................ 109
CamillaBetti,JoostSchymkowitz,FredericRousseau,and
EugeniaRussinova
7 Virus-InducedGeneSilencinginMaizewithaFoxtailmosaicvirusVector..... 129
YuMeiandStevenA.Whitham
8 UseofaVirusGeneSilencingVector forMaizeFunctional
GenomicsResearch ..................................................... 141
TaoZhou,XuedongLiu,andZaifengFan
PART III PLANT GENE EXPRESSION
9 Laser-CaptureMicrodissectionofMaizeKernelCompartments
forRNA-Seq-BasedExpressionAnalysis ................................... 153
ShanshanZhang,DhirajThakare,andRaminYadegari
vii
viii Contents
10 RibosomeProfilinginMaize............................................. 165
PrakitchaiChotewutmontri,NicholasStiffler,
KennethP.Watkins,andAliceBarkan
11 DetectionofDNAMethylationbyWhole-Genome
BisulfiteSequencing..................................................... 185
QingLi,PeterJ.Hermanson,andNathanM.Springer
12 PlantGeneRegulationUsingMultiplexCRISPR-dCas9
ArtificialTranscriptionFactors............................................ 197
LeviG.Lowder,AimeeMalzahn,andYipingQi
PART IV PLANT METABOLIC NETWORKS
13 CellularandSubcellularLevelLocalizationofMaizeLipids
andMetabolitesUsingHigh-SpatialResolutionMALDI
MassSpectrometryImaging.............................................. 217
MariaEmiliaDuen˜as,AdamD.Feenstra,AndrewR.Korte,
PaigeHinners,andYoungJinLee
Index ...................................................................... 233
Contributors
ALICEBARKAN (cid:1) DepartmentofBiology,InstituteofMolecularBiology,UniversityofOregon,
Eugene,OR,USA
FREDERICKE.BELOW (cid:1) DepartmentofCropSciences,UniversityofIllinois
atUrbana–Champaign,Urbana,IL,USA
CAMILLABETTI (cid:1) DepartmentofPlantBiotechnologyandBioinformatics,GhentUniversity,
Ghent,Belgium;Center forPlantSystemsBiology,VIB,Ghent,Belgium
DAVIDBRADLEY (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,
NC,USA
PRAKITCHAICHOTEWUTMONTRI (cid:1) DepartmentofBiology,InstituteofMolecularBiology,
UniversityofOregon,Eugene,OR,USA
SHUJIEDONG (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,
NC,USA
MARIAEMILIADUEN˜AS (cid:1) DepartmentofChemistry,IowaStateUniversityofScience
andTechnology,Ames,IA,USA;AmesLaboratory,U.S.DepartmentofEnergy,Ames,IA,
USA
SIVAMANIELUMALAI (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,
NC,USA
ZAIFENGFAN (cid:1) StateKeyLaboratoryforAgro-BiotechnologyandDepartmentofPlant
Pathology,ChinaAgriculturalUniversity,Beijing,China
ADAMD.FEENSTRA (cid:1) DepartmentofChemistry,IowaStateUniversityofScienceand
Technology,Ames,IA,USA;AmesLaboratory,U.S.DepartmentofEnergy,Ames,IA,USA
BRONWYNFRAME (cid:1) DepartmentofAgronomy,IowaStateUniversity,Ames,IA,USA;
Center forPlantTransformation,PlantSciencesInstitute,IowaStateUniversity,Ames,
IA,USA
WEINING GU (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,NC,
USA
PETERJ.HERMANSON (cid:1) DepartmentofPlantBiology,MicrobialandPlantGenomics
Institute,UniversityofMinnesota,SaintPaul,MN,USA
PAIGEHINNERS (cid:1) DepartmentofChemistry,IowaStateUniversityofScienceandTechnology,
Ames,IA,USA
DAVIDHOLDING (cid:1) DepartmentofAgronomyandHorticulture,Center forPlantScience
Innovation,BeadleCenter forBiotechnology,UniversityofNebraska–Lincoln,Lincoln,
NE,USA
SHANGANGJIA (cid:1) DepartmentofAgronomyandHorticulture,Center forPlantScience
Innovation,BeadleCenter forBiotechnology,UniversityofNebraska–Lincoln,Lincoln,
NE,USA
ANDREWR.KORTE (cid:1) DepartmentofChemistry,IowaStateUniversityofScience
andTechnology,Ames,IA,USA;AmesLaboratory,U.S.DepartmentofEnergy,Ames,
IA,USA
YOUNGJINLEE (cid:1) DepartmentofChemistry,IowaStateUniversityofScienceandTechnology,
Ames,IA,USA;AmesLaboratory,U.S.DepartmentofEnergy,Ames,IA,USA
AIXIALI (cid:1) DepartmentofAgronomyandHorticulture,CenterforPlantScienceInnovation,
BeadleCenter forBiotechnology,UniversityofNebraska–Lincoln,Lincoln,NE,USA
ix
x Contributors
QINGLI (cid:1) NationalKeyLaboratoryofCropGeneticImprovement,HuazhongAgricultural
University,Wuhan,Hubei,China;DepartmentofPlantBiology,MicrobialandPlant
GenomicsInstitute,UniversityofMinnesota,SaintPaul,MN,USA
DANIELLITTLE (cid:1) DepartmentofAgronomy,IowaStateUniversity,Ames,IA,USA;
Center forPlantTransformation,PlantSciencesInstitute,IowaStateUniversity,Ames,
IA,USA
XUEDONGLIU (cid:1) StateKeyLaboratoryforAgro-BiotechnologyandDepartmentofPlant
Pathology,ChinaAgriculturalUniversity,Beijing,China
LEVIG.LOWDER (cid:1) DepartmentofBiology,EastCarolinaUniversity,HowellScience
Complex,Greenville,NC,USA
AIMEEMALZAHN (cid:1) DepartmentofPlantScienceandLandscapeArchitecture,University
ofMaryland,CollegePark,MD,USA
YUMEI (cid:1) DepartmentofPlantPathologyandMicrobiology,IowaStateUniversity,Ames,IA,
USA
SAMSONNALAPALLI (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,
NC,USA
MICHAELL.NUCCIO (cid:1) InariAgriculture,Inc.,Cambridge,Massachusetts,MA,USA
ANNAPRAIRIE (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,NC,
USA
YIPINGQI (cid:1) DepartmentofPlantScienceandLandscapeArchitecture,Universityof
Maryland,CollegePark,MD,USA
QIUDENG QUE (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,NC,
USA
JENNIFERA.RAJI (cid:1) DepartmentofAgronomy,IowaStateUniversity,Ames,IA,USA;
Center forPlantTransformation,PlantSciencesInstitute,IowaStateUniversity,Ames,
IA,USA
LEERICHBOURG (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,NC,
USA
FREDERIC ROUSSEAU (cid:1) SwitchLaboratory,VIB,Leuven,Belgium;DepartmentforCellular
andMolecularMedicine,KatholiekeUniversiteitLeuven(KULeuven),Leuven,Belgium
EUGENIARUSSINOVA (cid:1) DepartmentofPlantBiotechnologyandBioinformatics,Ghent
University,Ghent,Belgium;Center forPlantSystemsBiology,VIB,Ghent,Belgium
TRIJOKO SANTOSO (cid:1) DepartmentofAgronomy,IowaStateUniversity,Ames,IA,USA;
Center forPlantTransformation,PlantSciencesInstitute,IowaStateUniversity,Ames,
IA,USA; IndonesianCenter forAgriculturalBiotechnologyandGeneticResources
ResearchandDevelopment(ICABIOGRAD-IAARD),Bogor,Indonesia
JOOSTSCHYMKOWITZ (cid:1) SwitchLaboratory,VIB,Leuven,Belgium;DepartmentforCellular
andMolecularMedicine,KatholiekeUniversiteitLeuven(KULeuven),Leuven,Belgium
JULIANNR.SEEBAUER (cid:1) DepartmentofCropSciences,UniversityofIllinoisatUrbana–
Champaign,Urbana,IL,USA
LIANGSHI (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,NC,USA
NATHANM.SPRINGER (cid:1) DepartmentofPlantBiology,MicrobialandPlantGenomics
Institute,UniversityofMinnesota,SaintPaul,MN,USA
NICHOLASSTIFFLER (cid:1) DepartmentofBiology,InstituteofMolecularBiology,
UniversityofOregon,Eugene,OR,USA
TIMSTREBE (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,NC,USA
XIUJUANJENNYSU (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,NC,
USA
Contributors xi
DHIRAJTHAKARE (cid:1) SchoolofPlantSciences,UniversityofArizona,Tucson,AZ,USA
KANWANG (cid:1) DepartmentofAgronomy,IowaStateUniversity,Ames,IA,USA;Center for
PlantTransformation,PlantSciencesInstitute,IowaStateUniversity,Ames,IA,USA
KENNETHP.WATKINS (cid:1) DepartmentofBiology,InstituteofMolecularBiology,Universityof
Oregon,Eugene,OR,USA
STEVENA.WHITHAM (cid:1) DepartmentofPlantPathologyandMicrobiology,IowaState
University,Ames,IA,USA
RAMINYADEGARI (cid:1) SchoolofPlantSciences,UniversityofArizona,Tucson,AZ,USA
CHI ZHANG (cid:1) SchoolofBiologicalSciences,Center forPlantScienceInnovation,Beadle
Center forBiotechnology,UniversityofNebraska–Lincoln,Lincoln,NE,USA
SHANSHANZHANG (cid:1) SchoolofPlantSciences,UniversityofArizona,Tucson,AZ,USA
HENG ZHONG (cid:1) SyngentaCropProtection,LLC.,ResearchTrianglePark,Durham,
NC,USA
TAOZHOU (cid:1) StateKeyLaboratoryforAgro-BiotechnologyandDepartmentofPlant
Pathology,ChinaAgriculturalUniversity,Beijing,China