From Plant Genomics to Plant Biotechnology

354 Pages·2013·9.41 MB·English

by  Palmiro Poltronieri

Applied Plant Genomics and Biotechnology
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Woodhead Publishing Series in Biomedicine:
Number 72
Applied Plant Genomics
and Biotechnology
Edited by
Palmiro Poltronieri
Yiguo Hong
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SANFRANCISCO(cid:129)SINGAPORE(cid:129)SYDNEY(cid:129)TOKYO
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Contents
Listoffigures ix
Listoftables xv
Abouttheeditors xvii
Aboutthecontributors xix
Listofabbreviations xxxi
Introduction xxxvii
1 Transgenic,cisgenicandnovelplantproducts:Challenges
inregulation andsafetyassessment 1
PalmiroPoltronieriandIdaBarbaraReca
1.1 GeneticallymodifiedplantproductsintheUnitedStates 1
1.2 GMPproductsinEurope 2
References 14
2 Whatturnsonandoffthecytokininmetabolismsandbeyond 17
EvaJiskrova´,IvonaKubalova´andYoshihisaIkeda
Acronyms 17
2.1 Introduction 17
2.2 Regulationofcytokininbiosynthesis 18
2.3 Applicationofalteredcytokininmetabolismstoimprove
agriculturaltraits 28
Acknowledgement 29
References 29
3 Appleallergensgenomicsandbiotechnology:Unravelling
thedeterminantsofappleallergenicity 35
FedericaSavazzini,GiampaoloRicciandStefanoTartarini
3.1 Introduction:Fruitandappleallergies 35
3.2 Abioticfactors:Influenceofenvironmentandcultivationtechniques 43
3.3 Bioticfactors:Pathogeninfectionandallergenscontent 44
3.4 Post-harvest,foodprocessingandbreedingstrategiestowards
allergeniccontentdecrease 46
3.5 Conclusion 48
References 49
4 Non-foodinterventions:Exploringplantbiotechnologyapplications
totherapeuticproteinproduction 55
MatteoBusconi,MariangelaMarudelliandCorradoFogher
4.1 Introduction 55
vi Contents
4.2 Plantasheterologousexpressionsystemformolecularfarming 56
4.3 Stabletransformation 57
4.4 Transienttransformation 59
4.5 Limitsontheuseofplantsasexpressionsystemsformolecular
farming 60
4.6 Plant-maderecombinantpharmaceuticals 61
4.7 RegulatoryaspectsandclinicalstatusofPMPs 66
References 67
5 Inplantaproducedvirus-likeparticlesascandidatevaccines 73
SlavicaMatic´andEmanuelaNoris
5.1 Introduction 73
5.2 Papillomaviruses 74
5.3 HepatitisBvirus 77
5.4 Humanimmunodeficiencyvirus-1 79
5.5 InfluenzaAvirus 81
References 82
6 BiotechnologyofEuphorbiaceae(Jatrophacurcas,
Manihotesculenta,Ricinuscommunis) 87
FatemehMaghuly,JohannVollmannandMargitLaimer
6.1 Euphorbiaceaecrops 87
6.2 Geneticdiversity 89
6.3 Geneticimprovement 93
6.4 Phytosanitaryimprovement 98
6.5 Concludingremarks 105
Acknowledgement 105
References 106
7 Regulationframeworkforflowering 115
TizianaSgammaandStephenJackson
7.1 Introduction 115
7.2 Gettingreadytoflower:thejuveniletoadulttransition 116
7.3 Frameworkcontrollingflowering 117
7.4 Floweringsensingtheenvironment 117
7.5 Endogenouscuesregulatingflowering 124
7.6 Floweringtimecontrolandmanipulation 127
References 128
8 Epigeneticregulationduringfleshyfruitdevelopmentandripening 133
EmelineTeyssier,LisaBoureauv,WeiweiChen,RuieLui,
CharlotteDegraeve-Guibault,LindaStammitti,YiguoHong
andPhilippeGallusci
8.1 Introduction 133
8.2 AnoverviewofDNAmethylationinplants 134
8.3 Histonemarksarelikelytoplayfundamentalroleinfruitdevelopment 142
8.4 Concludingremarks 145
References 146
Contents vii
9 Tomatofruitqualityimprovementfacingthefunctionalgenomics
revolution 153
DominiqueRolin,EmelineTeyssier,YiguoHongandPhilippeGallusci
9.1 Introduction 153
9.2 Whatismeantbyfruitquality? 154
9.3 Genomics-assistedbreedingforimprovingfruitquality 155
9.4 Futurepotentialoftomatobreedingusingomicsapproaches 157
9.5 Fruitmodellingtoestablishfleshyfruittraitsofinterest 160
9.6 Concludingremarks 161
References 162
10 Ricegenomicsandbiotechnology 167
DaweiXue,HuaJiangandQianQian
10.1 Goldenageofgenomics,biologicalengineeringandpaddyrice 167
10.2 Researchontheimportantagronomictraitsinricebiology 169
10.3 Emergenceofnewtechnologieswillextendthegoldenageofpaddyrice 172
10.4 Ricerequiresfurtherresearchdevelopmenttoremaina
monocotyledonmodelplant 173
References 174
11 Genome-wideDNAmethylationintomato 179
RupertFrayandSilinZhong
11.1 Introduction 179
11.2 MethodstodetectandquantifyDNAmethylation 179
11.3 Distributionof5-methylcytosineintomatogenome 182
11.4 Genome-wideDNAmethylationreprogrammingduringfruitripening 186
11.5 Conclusion 190
Acknowledgements 191
References 191
12 Recentapplicationofbiotechniquesfortheimprovement
ofmangoresearch 195
MohammadSorofUddinandQiCheng
12.1 Introduction 195
12.2 Originanddistribution 196
12.3 Economicimportance 197
12.4 Cytology 197
12.5 Molecularbiotechniquesappliedonmango 198
12.6 ApplicationofRAAmethodonmango 204
12.7 Problemsinmangoimprovementusingbiotechnology 205
12.8 Conclusionanddirectionoffutureresearch 206
References 207
13 Cottongenomicsandbiotechnology 213
HaoJuanandSunYuqiang
13.1 Introduction 213
13.2 Cottongenomics 214
viii Contents
13.3 Cottonfibrefunctiongenomics 216
13.4 Cottonbiotechnology 222
Listofabbreviations 223
References 224
14 Virustechnologyforfunctionalgenomicsinplants 229
ChengQin,QiZhang,MeilingHe,JunhuaKong,BinLi,
AtefMohamed,WeiweiChen,PengchengZhang,XianZhang,
ZhimingYu,TongfeiLai,NongnongShi,TobaOsmanandYiguoHong
Acronyms 229
14.1 Introduction 229
14.2 VRMA(cid:1)virus-basedRNAmobilityassay 234
14.3 Conclusion 234
References 235
15 PARPproteins,NAD,epigenetics,antioxidativeresponse
toabioticstress 237
PalmiroPoltronieriandMasanaoMiwa
15.1 Introduction 237
15.2 Conclusion 247
Acknowledgement 247
References 247
16 Appliedoilseedrapemarkertechnologyandgenomics 253
ChristianObermeierandWolfgangFriedt
16.1 Globalimportanceofoilseedrape 253
16.2 Rapeseedyieldandqualityandpotentialimprovements 256
16.3 FuturepotentialsofOSRvarietyandcropimprovement 258
16.4 Conclusion 285
References 285
Index 297
List of figures
Figure1.1 Schematicrepresentationoftargetedgenomemodificationsusing 4
site-specificnucleases.
Figure3.1 Flowchartofthecriticalsteps,fromgenestopatient’ssymptoms, 36
involvedinappleallergy.Ontherightsideareshownsomeofthe
environmental/endogenousfactorsandontheleftsidetheseveral
disciplinesinvolvedinthestudyofthedeterminantsofapplefruit
allergy.
Figure3.2 Rankingofdifferentapplecultivarsafterstandardizationand 38
accordingtopulp(a)andpeel(b)allergenicity.Theallergenicitywas
measuredbySPTandprick-to-prick-test(PTP),employingboth
commerciallyavailableappleextractsandseparatedpeelandpulp
directly.Thedarkdotsrepresenttheoutliers.(a)Inpulp,Jonathan,
Jonagold,GoldenDeliciousandFiestaappearedtobethemost
allergeniccultivars.(b)Inpeel,Gala,FiestaandGoldenDelicious
apparentlycausedthelargerwheals.
Figure3.3 Mald1genefamilyalignment(a)andstructure(b).(a)Neighbour- 40
joiningtreebasedonthecodingsequenceofthe31Mald1genes
retrievedfromthe‘GoldenDelicious’Malusxdomesticav1.0genome
sequence(Velascoetal.,2010).Eachgeneisdescribedwiththe
genomereferenceaccessionnumber(MDP);verticallinesandroman
numerals(I(cid:1)V)delineatethesub-families.(b)Thecorrespondinggene
structureofeachsub-familyisshowninscale;thelinerepresentsthe
intron,whilethegreyandwhiterectanglesrepresentthefirstand
secondexons,respectively.
Figure3.4 EffectoflightgrowthconditionsontheexpressionprofileofthreeMald4 44
genesinGoldenDeliciousfruits.Plantsweregrownundernormallight
(NL)orshadowing(SH);fruitsweredividedintocortex(Ctx)and
epidermis(Epi)tissues.Expressionvalueswerereportedasarbitraryunits
(A.U.)afternormalizationtoubiquitingene.WiththeexceptionofMald
4.02incortex,shadowinghasanirrelevantorup-regulationeffect.
Figure3.5 Effectofstoragetimeandcultivar(CoxandJonagored)onMald1 46
levels(μg/gpulp)inapplesstoredunder(a)ambientconditions
(AMB,20(cid:3)C),(b)coldwithnocontrolledatmosphere(CS,2(cid:3)C)or
(c)controlledatmosphereconditions(CA,,0.5%CO and
2
1.25%O at3.8(cid:3)C)forupto5months.
2
Figure5.1 Electronmicrographsofplant-producedHPV-16L1(L1ΔC22)and 76
chimericconstruct(ChiM2e h4)(Matic´ etal.,2011).Black
2-24
arrows555-nmT7VLPs;greyarrows530-nmT1VLPs;white
arrows5capsomers.AssembledL1structuresforeachconstructare
enlargedontherightside.Bar550nm.