Gene-based systems approach to simulate soybean growth and development and application to ideotype design in target environments

157 Pages·2003·6.3 MB·English

by  Messina, Carlos Daniel

GENE-BASEDSYSTEMSAPPROACHTOSIMULATESOYBEANGROWTHAND
DEVELOPMENTANDAPPLICATIONTOIDEOTYPEDESIGNINTARGET
ENVIRONMENTS
By
CARLOSDANIELMESSINA
ADISSERTATIONPRESENTEDTOTHEGRADUATESCHOOL
OFTHEUNIVERSITYOFFLORIDAINPARTIALFULFILLMENT
OFTHEREQUIREMENTSFORTHEDEGREEOF
DOCTOROFPHILOSOPHY
UNIVERSITYOFFLORIDA
2003
Copyright2003
by
CarlosDanielMessina
..tomygrandmotherAngelaC.Untermannandtothememoryofmygrandparents
ACKNOWLEDGMENTS
Iwishtoextendheartfeltthankstomycommitteemembersandtotheprofessors,
graduatestudentsandtechnicianswhohavecontributedtothisdissertation.Itwasa
privilegeandhonortoworkwiththemat,andfor,theUniversityofFlorida.
Specialthanksgotomyadvisorandmentor,Dr.JamesW.Jones.Hegaveme
absolutefreedomandindependenceofthoughttogetherwithguidanceandintellectual
andeconomicsupport.Hiswisdomandexpertisehelpedmefocusandkeptmyresearch
ontherighttrack.Healwayshadtimetodiscussresearchproblems,tocommenton
manuscriptsandtogivemeadviceaboutmyprofessionalcareer.Icouldnothaveasked
forabetteradvisor.
IwouldliketothankDr.W.Graham,Dr.B.HauserandDr.J.T.Ritchiefortheir
valuableadviceasmembersofmycommittee.IwishtothankDr.Booteforhisvaluable
guidanceduringtheconceptionoftheresearchproject,forreviewingdraftdocuments,
andforthepleasantandstimulatingdiscussionswehadaboutcropphysiologyand
modeling.Healsogavemetheopportunitytoteachplantphysiology,forwhichIam
verythankful.
ThisdissertationwouldnothavebeencompletewithoutthehelpofDr.C.E.
Vallejos.Hehadacriticalrolebyteachingmegenetics,molecularbiologyandlaboratory
techniquesthatallowedmetosignificantlyimprovethisresearch.Iamspeciallythankful
forhisthought-provokingquestionsanddiscussions,forhisadviceongrantsmanship,
andforlettingmeparticipateinhisresearchonbeans.
iv
Iwouldliketoacknowledgecontributionofmanypeoplewhoprovidedvaluable
technicalsupport,especiallytoValerieJones,JeanThomas,WayneWilliamsandCheryl
Porter.Dr.L.BernardfromtheUniversityofIllinois,providedthenear-isogenicsoybean
linesIusedtodevelopmymodel.Dr.R.Nelson,curatoroftheUSDAgermoplasm
collection,providedsoybeancultivarsthatIusedtoevaluatethemodelinperformance
varietytrials.Dr.G.PodestafromtheUniversityofMiamiprovidedmewithhighquality
weatherseriesforArgentinelocations.JulioDardanelli,Graciela.Magrin,Santiago.
MeiraandMariaTravassokindlymadeavailablesoilparametersandinitialconditions,
whichIusedtorunthesimulationsinArgentina.Dr.TheodorosMavromatismade
availableavarietytrialdatabasealongwithsoilparametersandgeneticcoefficientsfora
setofvarietiesIusedtotestthemodel.
IwishtothankDr.RogerBoermaandDr.JamesSpechtfortheirvaluable
commentswhileIformulatedmydissertationproject.
MyexperienceattheUniversityofFloridawouldhavenotbeencompletewithout
themomentssharedwithAndresFerreyraandFredRoyce,andtheinteractionswithDr.
CurtisHannah,Dr.CharlesGuyandDr.JaneLuzar.AmongthemanythingsIhaveto
acknowledge,Iwouldliketothankthemforhelpingmegrow.Dr.Luzar,withhernever-
endingenthusiasm,helpedAndresandmestarttheTownHallandamentoringand
undergraduateresearchprogramattheGraduateStudentCouncil.
Tomyfamily,Iwouldliketoexpressmygratitudefortheirdedication,supportand
love.Iwouldliketoexpressmydearestappreciationtomywife.Herendlesslove,
friendship,encouragementandpatiencecontributedgreatlytothisachievement.
v
81
TABLEOFCONTENTS
Page
ACKNOWLEDGMENTS iv
LISTOFTABLES ix
LISTOFFIGURES xi
ABSTRACT xiii
CHAPTER
1 Generalintroduction 1
StatementoftheProblem 1
TheBottomUpApproach 2
TheTopDownApproach 5
OverallObjectiveandOrganizationofthisDissertation 8
2 Geneticcontrolofreproductivedevelopmentandresponsestophotoperiodin
soybean[GlycinemaxL.] 11
Introduction 1
MaterialsandMethods 15
FieldExperiments 1
StatisticalAnalyses 20
Results 22
PodAdditionDuration 23
DurationofTimeBetweenFloweringandFirstPod(Rl-OPA) 27
DurationbetweenOPAandR5 29
FinalPodNumberandPodAdditionDuration 32
DurationbetweenR5andR7 34
DiscussionandConclusions 35
3 Agene-basedapproachtosimulatesoybeandevelopmentandyieldresponsestothe
environment 42
Introduction 42
MaterialsandMethods 45
SimulationofSoybeanDevelopmentandPodAddition 46
Data 49
vi
ParameterizationofCROPGRO-SoybeantoIncludeGeneticInformation 50
ParameterEstimation,ModelVerificationandEvaluation 52
MolecularMarkerLengthPolymorphismsLinkedtoELociandCultivar
Genotyping 54
DNAExtraction 55
PolymeraseChainReaction(PCR)andPCRProductSeparation 55
PredictingTimetoMaturityofPublicCultivarsofSoybeanGrowninVariety
Trials 56
ResultsandDiscussion 57
CalibrationandEvaluationofCROPGRO-Soybean 58
Soybeandevelopmentduring2001season 58
Simulationofpodadditiondurationandpodnumberin2001 60
Simulationofplantdevelopmenteffectsonthedynamicsofbiomass
accumulation,yieldandharvestindex 64
EstimatingGeneticCoefficientsfromGenotypes 64
EvaluationofCROPGRO-SoybeanwithGeneticCoefficientsEstimatedfromE
Loci.Datacollectedduring2001season 66
ModelEvaluationwithIndependentDatafrom2002 67
SSRLengthPolymorphismsLinkedtoELociandCultivarGenotyping 68
PredictingSoybeanYieldandMaturityinVarietyTrials 71
Conclusions 74
4 Linkingoptimizationalgorithmsandgene-basedmodelsforcropengineeringin
targetenvironments 77
Introduction 77
MaterialsandMethods 80
LinkingCropModelsandOptimizationAlgorithmstoAssistPlantBreeding...80
OptimizationwithAdaptiveSimulatedAnnealing 81
APlantBreedingMetaphorforSA 86
SimulationofCropGrowthandDevelopment 87
LinkagebetweenSAandCROPGRO-Soybean 88
IdentificationofTraitsContributingtoYieldMaximizationinTarget
Environments 89
GeneticBaseBreadthandSelectionPressureEffectsonYieldGains 91
RisksofIgnoringEpistaticandPleiotropicEffectsforIdeotypeDesign 92
Results 93
ConvergenceTowardsaGlobalMaximum 93
PhysiologicalAnalysisofParameterDynamics 94
IdentificationofTraitsContributingtoYieldMaximizationinTarget
Environments T. 97
Ideotypesacrossalatitudinalrange 97
Ideotypesacrossawaterstressgradient 100
GeneticBaseBreadthandSelectionPressureEffectsonYieldGains 102
RisksofIgnoringEpistaticandPleiotropicEffectsforIdeotypeDesign 105
DiscussionandConclusions 107
LinkingSAandCROPGRO-SoybeanforIdeotypeDesign 108
vii
OptimalPlantTraitsforTargetEnvironments 110
GeneticBaseBreadthandCropYields 114
Gene-basedModelsforIdeotypeDesign 115
5 SUMMARYANDCONCLUSIONS 118
LISTOFREFERENCES 123
BIOGRAPHICALSKETCH 141
viii
1
LISTOFTABLES
Table page
2-1.ClarkandHarosoynear-isogeniclinesusedinthisstudy 19
2-2.Analysisofvarianceforfactorsaffectingsoybeanreproductivedevelopment,node
number,andrateanddurationofpodaddition 25
2-3.Eloci,growthhabitandgeneticbackgroundeffectsonpodadditionduration(days)
ondifferentplantingdates 26
2-4.Elocianddtcontroloftheduration(days)betweentheonsetofpodadditionandR5
(beginningseedgrowth)ondifferentplantingdates 30
2-5.EffectsofElociandDtonseedfilldurationfordifferentyears,plantingdatesand
geneticbackground 35
3-1.Listofsoybeannear-isogeniclinesusedformodeldevelopmentandformolecular
markersevaluation 49
3-2.SelectedgeneticcoefficientsinCROPGRO-Soybeancontrollingplantdevelopment
insoybean,potentialassociationswithEanddtloci,andvariablesusedfor
parameterestimation 5
3-3.ComparativeevaluationbetweenCROPGRO-SoybeanandCROPGRO-Soybean
parameterizedusingElociinformationusingdatacollectedduring2001 58
3-4.AssociationsbetweenElociandgeneticcoefficientsinCROPGRO-Soybean 65
3-5.ConfirmationofCROPGRO-SoybeanandCROPGRO-£locitopredictindependent
observations(2002)ofsoybeandevelopment 68
3-6.Predictionerrorsintimetomaturityandyieldforsoybeanpublicvarietiesgrownin
eightlocationsinIllinois(1995-99) 72
4-1.Geneticcoefficients,rangesofvariation,andexamplesforfourmaturitygroups....82
4-2.Associationsbetweenmarkerloci,soybeantraitsandgeneticcoefficients 83
4-3.SoilparametersandsoybeanmanagementforfourlocationsinthePampas 87
ix
4-4.Simulatedsoybeangrowthanddevelopmentforasetofgenotypesacrossa
latitudinalgradient 98
4-5Initialandoptimizedgeneticcoefficients,yieldandyieldcomponentsforPilar,
PergaminoandBalcarce 99
4-6.Simulatedsoybeanphenologyforasetofgenotypesundercontrastingwaterstress
environmentsinSantaRosa."Dry"1945-55."Wet"1985-95 102
4-7.Initialandoptimizedgeneticcoefficients,yieldandyieldcomponentsforSantaRosa
undertwocontrastingenvironments:1945-55and1985-95 103
4-8.Maximum-yieldsensitivitytovariationsinparameters<t>and 104
x