Barley: Methods and Protocols

316 Pages·2019·11.938 MB·English

by  Wendy A. Harwood

Methods in
Molecular Biology 1900
Wendy A. Harwood Editor
Barley
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
Barley
Methods and Protocols
Edited by
Wendy A. Harwood
Crop Transformation Group, Department of Crop Genetics, John Innes Centre, Norwich, UK
Editor
WendyA.Harwood
CropTransformationGroup
DepartmentofCropGenetics
JohnInnesCentre
Norwich,UK
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8942-3 ISBN978-1-4939-8944-7 (eBook)
https://doi.org/10.1007/978-1-4939-8944-7
LibraryofCongressControlNumber:2018962159
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Preface
Barleyistheworld’sfourthmostimportantcereal,bothintermsofareaandproduction,as
wellas oneoftheworld’sfirstdomesticatedcrops.Inaddition tobeinganimportant crop
forbothfoodandfeed,itisalsoavaluablediploidmodelcereal.Barleyhasextensivegenetic
resources,continuallyadvancinggenomicresources,andarangeofefficientbiotechnologi-
caltools.
In this volume, we start with review chapters that introduce barley as both crop and
model,andconsider thehistoryandimportanceofmutationbreedinginthedevelopment
ofthecrop.Protocolchaptersthencoverpracticaltechniquessuchascrossingbarley,arange
oftissueculturemethods,thepreparationofbarleytissuesfordifferentformsofmicroscopy,
and the assessment of sensitivity to abiotic stresses. Efficient protocols are provided for
transformation,TILLING,virus-inducedgenesilencing,andgenomeediting.Thereisalso
particular emphasis on a range of protocols for genotyping and for the analysis of gene
expression.
Thisbookshouldbeavaluablereferencevolumeforcerealresearchersandbreedersby
providingdetailedprotocolscoveringimportanttraditionalskillssuchascrossingandtissue
culturethroughtothelatesttechnologiesforgenotyping,expressionanalysis,andgenome
editing.
Norwich,UK WendyA.Harwood
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 AnIntroductiontoBarley:TheCropandtheModel........................ 1
WendyA.Harwood
2 MutationBreedinginBarley:HistoricalOverview .......................... 7
LudmilaOhnoutkova
3 APracticalGuidetoBarleyCrossing ...................................... 21
WilliamT.B.Thomas,HazelBull,AllanBooth,RuthHamilton,
BrianP.Forster,andJeromeD.Franckowiak
4 BarleyAntherCulture................................................... 37
LudmilaOhnoutkova,TomasVlcko,andMentewabAyalew
5 IsolatedMicrosporeCultureinBarley..................................... 53
PatricioEstevesandFranc¸oisJ.Belzile
6 TILLINGinBarley ..................................................... 73
MatthiasJost,MiriamSzurman-Zubrzycka,KatarzynaGajek,
IwonaSzarejko,andNilsStein
7 Virus-InducedGeneSilencing(VIGS)forFunctional
CharacterizationofDiseaseResistanceGenesinBarleySeedlings ............. 95
LokanadhaR.Gunupuru,AlexandrePerochon,ShahinS.Ali,
StevenR.Scofield,andFionaM.Doohan
8 Agrobacterium-MediatedTransformationofBarleyImmature
Embryos............................................................... 115
AlisonHinchliffeandWendyA.Harwood
9 Methodsfor theSimpleandReliableAssessmentofBarley
SensitivitytoAbioticStressesDuringEarlyDevelopment.................... 127
AgataDaszkowska-Golec,AnnaSkubacz,MarzenaKurowska,
MichałSłota,DorotaSwiergolik,andIwonaSzarejko
10 PreparationofBarleyRootsforHistological,Structural,
andImmunolocalizationStudiesUsingLightandElectron
Microscopy ............................................................ 153
MarekMarzecandMichaelMelzer
11 PreparationofBarleyPollenMotherCellsforConfocal
andSuperResolutionMicroscopy......................................... 167
SybilleMittmann,MikelArrieta,LukeRamsay,RobbieWaugh,
andIsabelleColas
12 MicroarraysforHigh-ThroughputGeneExpressionAnalysis
ofBarley............................................................... 181
JennyA.MorrisandPeteE.Hedley
vii
viii Contents
13 GenomeEngineeringUsingTALENs..................................... 195
GoetzHenselandJochenKumlehn
14 CreatingTargetedGeneKnockoutsinBarley
UsingCRISPR/Cas9 ................................................... 217
TomLawrensonandWendyA.Harwood
15 Genotyping-by-SequencingontheIonTorrentPlatform
inBarley............................................................... 233
AminaAbed,Gae´tanLe´gare´,SoniaPomerleau,Je´roˆmeSt-Cyr,
BrianBoyle,andFranc¸oisJ.Belzile
16 DNAMethylationAnalysisinBarleyandOtherSpecies
withLargeGenomes.................................................... 253
KarolinaChwialkowska,UrszulaKorotko,
andMiroslawKwasniewski
17 High-ResolutionRT-PCRAnalysisofAlternativeBarley
Transcripts............................................................. 269
CraigG.Simpson,JohnFuller,PauloRapazote-Flores,
Claus-DieterMayer,CristianeP.G.Calixto,LindaMilne,
PeteE.Hedley,ClareBooth,RobbieWaugh,andJohnW.S.Brown
18 ExomeCaptureforVariantDiscoveryandAnalysisinBarley ................. 283
MichaBayer,JennyA.Morris,ClareBooth,AllanBooth,
NikiUzrek,JoanneR.Russell,RobbieWaugh,andPeteE.Hedley
Index ...................................................................... 311
Contributors
AMINAABED (cid:1) DepartmentdePhytologieandInstitutdeBiologieInte´grativeetdesSyste`mes
(IBIS),Universite´Laval,Que´bec,QC,Canada
SHAHINS.ALI (cid:1) SPCL,USDA/ARSBeltsvilleAgriculturalResearchCenter,Beltsville,MD,
USA
MIKELARRIETA (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,
Scotland,UK
MENTEWABAYALEW (cid:1) BiologyDepartment,SpelmanCollege,Atlanta,GA,USA
MICHABAYER (cid:1) TheJamesHuttonInstitute,Dundee,Scotland,UK
FRANC¸OIS J.BELZILE (cid:1) De´partementdePhytologieandInstitutdeBiologieInte´grativeetdes
Syste`mes(IBIS),Universite´Laval,Que´bec,QC,Canada
ALLANBOOTH (cid:1) TheJamesHuttonInstitute,Dundee,Scotland,UK
CLAREBOOTH (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,Scotland,
UK
BRIAN BOYLE (cid:1) Plateformed’AnalysesGe´nomiques,InstitutdeBiologieInte´grativeetdes
Syste`mes(IBIS),Universite´Laval,Que´bec,QC,Canada
JOHNW.S.BROWN (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,
Scotland,UK;DivisionofPlantSciences,UniversityofDundeeatTheJamesHutton
Institute,Dundee,Scotland,UK
HAZELBULL (cid:1) JamesHuttonLimited,Dundee,Scotland,UK;SyngentaUKLtd.,Market
Stainton,UK
CRISTIANEP.G.CALIXTO (cid:1) DivisionofPlantSciences,UniversityofDundeeatTheJames
HuttonInstitute,Dundee,Scotland,UK
KAROLINACHWIALKOWSKA (cid:1) CentreforBioinformaticsandDataAnalysis,Medical
UniversityofBialystok,Bialystok,Poland;DepartmentofGenetics,UniversityofSilesiain
Katowice,Katowice,Poland
ISABELLECOLAS (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,
Scotland,UK
AGATADASZKOWSKA-GOLEC (cid:1) DepartmentofGenetics,FacultyofBiologyandEnvironmental
Protection,UniversityofSilesiainKatowice,Katowice,Poland
FIONAM.DOOHAN (cid:1) SchoolofBiologyandEnvironmentalScienceandEarthInstitute,
CollegeofScience,UniversityCollegeDublin,Dublin,Ireland
PATRICIOESTEVES (cid:1) De´partementdePhytologie,Universite´Laval,Que´bec,QC,Canada
BRIAN P.FORSTER (cid:1) BioHybridsInternationalLtd.,Reading,UK
JEROMED.FRANCKOWIAK (cid:1) Agronomy/PlantGenetics,UniversityofMinnesotaTwinCities,
St.Paul,MN,USA
JOHNFULLER (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,Scotland,
UK
KATARZYNAGAJEK (cid:1) FacultyofBiologyandEnvironmentalProtection,Departmentof
Genetics,UniversityofSilesia,Katowice,Poland
LOKANADHAR.GUNUPURU (cid:1) DepartmentofPlant,Food,andEnvironmentalSciences,
DalhousieUniversity,Truro,NS,Canada
RUTHHAMILTON (cid:1) UniversityofDundeeattheJamesHuttonInstitute,Dundee,Scotland,
UK
ix
x Contributors
WENDYA.HARWOOD (cid:1) CropTransformationGroup,DepartmentofCropGenetics,John
InnesCentre,Norwich,UK
PETEE.HEDLEY (cid:1) GenomeTechnology,CellandMolecularSciences,JamesHuttonInstitute,
Dundee,UK
GOETZ HENSEL (cid:1) PlantReproductiveBiology,LeibnizInstituteofPlantGeneticsandCrop
PlantResearch(IPK)Gatersleben,Seeland,Germany
ALISONHINCHLIFFE (cid:1) CropTransformationGroup,DepartmentofCropGenetics,JohnInnes
Centre,Norwich,UK
MATTHIASJOST (cid:1) LeibnizInstituteofPlantGeneticsandCropPlantResearch(IPK),
Seeland,Germany
URSZULA KOROTKO (cid:1) DepartmentofGenetics,UniversityofSilesiainKatowice,Katowice,
Poland
JOCHEN KUMLEHN (cid:1) PlantReproductiveBiology,LeibnizInstituteofPlantGeneticsand
CropPlantResearch(IPK)Gatersleben,Seeland,Germany
MARZENAKUROWSKA (cid:1) DepartmentofGenetics,FacultyofBiologyandEnvironmental
Protection,UniversityofSilesiainKatowice,Katowice,Poland
MIROSLAWKWASNIEWSKI (cid:1) CentreforBioinformatics andDataAnalysis,MedicalUniversity
ofBialystok,Bialystok,Poland;DepartmentofGenetics,UniversityofSilesiainKatowice,
Katowice,Poland
TOMLAWRENSON (cid:1) JohnInnesCentre,Norwich,UK
GAE´TANLE´GARE´ (cid:1) Plateformed’AnalysesGe´nomiques,InstitutdeBiologieInte´grativeetdes
Syste`mes(IBIS),Universite´Laval,Que´bec,QC,Canada
MAREKMARZEC (cid:1) FacultyofBiologyandEnvironmentalProtection,DepartmentofGenetics,
UniversityofSilesia,Katowice,Poland;DepartmentofPhysiologyandCellBiology,Leibniz
InstituteofPlantGeneticsandCropPlantResearch(IPK),Seeland,Germany
CLAUS-DIETER MAYER (cid:1) BiomathematicsandStatisticsScotland,Dundee,UK
MICHAELMELZER (cid:1) DepartmentofPhysiologyandCellBiology,LeibnizInstituteofPlant
GeneticsandCropPlantResearch(IPK),Seeland,Germany
LINDAMILNE (cid:1) InformationandComputationalSciences,TheJamesHuttonInstitute,
Dundee,Scotland,UK
SYBILLEMITTMANN (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,
Scotland,UK;DivisionofPlantSciences,UniversityofDundeeatTheJamesHutton
Institute,Dundee,Scotland,UK
JENNYA.MORRIS (cid:1) GenomeTechnology,CellandMolecularSciences,JamesHuttonInstitute,
Dundee,UK
LUDMILAOHNOUTKOVA (cid:1) FacultyofScience,CentreoftheRegionHanaforBiotechnological
andAgriculturalResearch,DepartmentofChemicalBiologyandGenetics,Palacky
University,Olomouc,CzechRepublic
ALEXANDREPEROCHON (cid:1) SchoolofBiologyandEnvironmentalScienceandEarthInstitute,
CollegeofScience,UniversityCollegeDublin,Dublin,Ireland
SONIAPOMERLEAU (cid:1) Plateformed’AnalysesGe´nomiques,InstitutdeBiologieInte´grativeetdes
Syste`mes(IBIS),Universite´Laval,Que´bec,QC,Canada
LUKERAMSAY (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,Scotland,
UK
PAULORAPAZOTE-FLORES (cid:1) InformationandComputationalSciences,TheJamesHutton
Institute,Dundee,Scotland,UK
JOANNE R.RUSSEL (cid:1) TheJamesHuttonInstitute,Dundee,Scotland,UK
Contributors xi
STEVENR.SCOFIELD (cid:1) CropProductionandPestControlResearchUnit,USDA-ARS,West
Lafayette,IN,USA;DepartmentofAgronomy,PurdueUniversity,WestLafayette,IN,
USA
CRAIGG.SIMPSON (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,
Scotland,UK
ANNASKUBACZ (cid:1) DepartmentofGenetics,FacultyofBiologyandEnvironmentalProtection,
UniversityofSilesiainKatowice,Katowice,Poland
MICHAŁ SŁOTA (cid:1) DepartmentofGenetics,FacultyofBiologyandEnvironmentalProtection,
UniversityofSilesiainKatowice,Katowice,Poland
JE´ROˆMEST-CYR (cid:1) Plateforme d’AnalysesGe´nomiques,InstitutdeBiologieInte´grativeetdes
Syste`mes(IBIS),Universite´Laval,Que´bec,QC,Canada
NILSSTEIN (cid:1) LeibnizInstituteofPlantGeneticsandCropPlantResearch(IPK),Seeland,
Germany
DOROTASWIERGOLIK (cid:1) DepartmentofGenetics,FacultyofBiologyandEnvironmental
Protection,UniversityofSilesiainKatowice,Katowice,Poland
IWONASZAREJKO (cid:1) FacultyofBiologyandEnvironmentalProtection,DepartmentofGenetics,
UniversityofSilesia,Katowice,Poland
MIRIAMSZURMAN-ZUBRZYCKA (cid:1) FacultyofBiologyandEnvironmentalProtection,
DepartmentofGenetics,UniversityofSilesia,Katowice,Poland
WILLIAMT.B.THOMAS (cid:1) TheJamesHuttonInstitute,Dundee,Scotland,UK
NIKIUZREK (cid:1) TheJamesHuttonInstitute,Dundee,Scotland,UK
TOMASVLCKO (cid:1) FacultyofScience,CentreoftheRegionHanaforBiotechnologicaland
AgriculturalResearch,DepartmentofChemicalBiologyandGenetics,PalackyUniversity,
Olomouc,CzechRepublic
ROBBIEWAUGH (cid:1) CellandMolecularSciences,TheJamesHuttonInstitute,Dundee,
Scotland,UK;DivisionofPlantSciences,UniversityofDundeeatTheJamesHutton
Institute,Dundee,Scotland,UK