Using the Pareto principle in genome-wide breeding value estimation 英文参考文献.docVIP

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Using the Pareto principle in genome-wide breeding value estimation 英文参考文献.doc

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Using the Pareto principle in genome-wide breeding value estimation 英文参考文献

YuandMeuwissenGeneticsSelectionEvolution2011,43:35 /content/43/1/35 G enetics Selection Evolution RESEARCH OpenAccess UsingtheParetoprincipleingenome-wide breedingvalueestimation XijiangYu*andTheoHEMeuwissen Abstract Genome-widebreedingvalue(GWEBV)estimationmethodscanbeclassifiedbasedonthepriordistribution assumptionsofmarkereffects.Genome-wideBLUPmethodsassumeanormalpriordistributionforallmarkerswith aconstantvariance,andarecomputationallyfast.InBayesianmethods,moreflexiblepriordistributionsofSNP effectsareappliedthatallowforverylargeSNPeffectsalthoughmostaresmallorevenzero,buttheseprior distributionsareoftenalsocomputationallydemandingastheyrelyonMonteCarloMarkovchainsampling.Inthis study,weadoptedtheParetoprincipletoweightavailablemarkerloci,i.e.,weconsiderthatx%ofthelociexplain (100-x)%ofthetotalgeneticvariance.Assumingthisprinciple,itisalsopossibletodefinethevariancesofthe priordistributionofthe‘big’and‘small’SNP.TherelativelyfewlargeSNPexplainalargeproportionofthegenetic varianceandthemajorityoftheSNPshowsmalleffectsandexplainaminorproportionofthegeneticvariance. WenamethismethodMixP,wherethepriordistributionisamixtureoftwonormaldistributions,i.e.onewitha bigvarianceandonewithasmallvariance.Simulationresults,usingarealNorwegianRedcattlepedigree,show thatMixPisatleastasaccurateastheothermethodsinallstudiedcases.Thismethodalsoreducesthehyper- parametersofthepriordistributionfrom2(proportionandvarianceofSNPwithbigeffects)to1(proportionof SNPwithbigeffects),assumingtheoverallgeneticvarianceisknown.Themixtureofnormaldistributionprior madeitpossibletosolvetheequationsiteratively,whichgreatlyreducedcomputationloadsbytwoordersof magnitude.Intheeraofmarkerdensityreachingmillion(s)andwhole-genomesequencedata,MixPprovidesa computationallyfeasibleBayesianmethodofanalysis. Introduction (MCMC) algorithms which make them computation- Genomic selection (GS) is currently being adopted by allydemanding. the dairy cattle breeding industries around the world Meuwissenetal.[2]p