Applied Plant Genomics and Biotechnology Related titles Fromplantgenomicstoplantbiotechnology (ISBN:978-1-907568-29-9) Anintroductiontobiotechnology (ISBN:978-1-907568-28-2) MATLABsinbioscienceandbiotechnology (ISBN:978-1-907568-04-6) Woodhead Publishing Series in Biomedicine: Number 72 Applied Plant Genomics and Biotechnology Edited by Palmiro Poltronieri Yiguo Hong AMSTERDAM(cid:129)BOSTON(cid:129)HEIDELBERG(cid:129)LONDON NEWYORK(cid:129)OXFORD(cid:129)PARIS(cid:129)SANDIEGO SANFRANCISCO(cid:129)SINGAPORE(cid:129)SYDNEY(cid:129)TOKYO WoodheadPublishingisanimprintofElsevier WoodheadPublishingLimitedisanimprintofElsevier 80HighStreet,Sawston,Cambridge,CB223HJ,UK 225WymanStreet,Waltham,MA02451,USA LangfordLane,Kidlington,OX51GB,UK Copyright©2015P.PoltronieriandY.Hong.Allrightsreserved. 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Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgeinevaluating andusinganyinformation,methods,compounds,orexperimentsdescribedherein.Inusingsuch informationormethodstheyshouldbemindfuloftheirownsafetyandthesafetyofothers,including partiesforwhomtheyhaveaprofessionalresponsibility. Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors, assumeanyliabilityforanyinjuryand/ordamagetopersonsorpropertyasamatterofproducts liability,negligenceorotherwise,orfromanyuseoroperationofanymethods,products, instructions,orideascontainedinthematerialherein. ISBN:978-0-08-100068-7(print) ISBN:978-0-08-100071-7(online) BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress LibraryofCongressControlNumber:2014948687 ForInformationonallWoodheadPublishingpublications visitourwebsiteathttp://store.elsevier.com/ TypesetbyMPSLimited,Chennai,India www.adi-mps.com PrintedandboundintheUnitedKingdom 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.