Searching for phenotypic causal networks involving complex traits an application to European quail 英文参考文献.docVIP

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Searching for phenotypic causal networks involving complex traits an application to European quail 英文参考文献.doc

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Searching for phenotypic causal networks involving complex traits an application to European quail 英文参考文献

Valenteetal.GeneticsSelectionEvolution2011,43:37 /content/43/1/37 G enetics Selection Evolution RESEARCH OpenAccess Searchingforphenotypiccausalnetworks involvingcomplextraits:anapplicationto Europeanquail BrunoDValente1,2*,GuilhermeJMRosa2,3,MartinhoASilva1,RafaelBTeixeira4andRobledoATorres4 Abstract Background:Structuralequationmodels(SEM)areusedtomodelmultipletraitsandthecasuallinksamongthem. ThenumberofdifferentcausalstructuresthatcanbeusedtofitaSEMistypicallyverylarge,evenwhenonlya fewtraitsarestudied.InrecentapplicationsofSEMinquantitativegeneticsmixedmodelsettings,causalstructures werepre-selectedbasedonpriorbeliefsalone.Alternatively,therearealgorithmsthatsearchforstructuresthatare compatiblewiththejointdistributionofthedata.However,suchasearchcannotbeperformeddirectlyonthe jointdistributionofthephenotypessincecausalrelationshipsarepossiblymaskedbygeneticcovariances.Inthis context,theapplicationoftheInductiveCausation(IC)algorithmtothejointdistributionofphenotypes conditionaltounobservablegeneticeffectshasbeenproposed. Methods:Here,weappliedthisapproachtofivetraitsinEuropeanquail:birthweight(BW),weightat35daysof age(W35),ageatfirstegg(AFE),averageeggweightfrom77to110daysofage(AEW),andnumberofeggslaid inthesameperiod(NE).Wehavefocusedthediscussiononthechallengesanddifficultiesresultingfromapplying thismethodtofielddata.StatisticaldecisionsregardingpartialcorrelationswerebasedondifferentHighest PosteriorDensity(HPD)intervalcontentsandmodelsbasedontheselectedcausalstructureswerecompared usingtheDevianceInformationCriterion(DIC).Inaddition,weusedtemporalinformationtoperformadditional edgeorienting,overridingthealgorithmoutputwhennecessary. Results:Asaresult,thefinalcausalstructureconsistedoftwoseparatedsubstructures:BW?AEWand W35?AFE?NE,whereanarrowrepresentsadirecteffect.ComparisonbetweenaSEMwiththeselectedstructure andaMultipleTraitAnimalModelusingDICindicatedthattheSEMismoreplausible. Conclusions:CouplingpriorknowledgewiththeoutputprovidedbytheICalgorithmal