Estimation of (co)variances for genomic regions of flexible sizes application to complex infectious udder diseases in dairy cattle.docVIP

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Estimation of (co)variances for genomic regions of flexible sizes application to complex infectious udder diseases in dairy cattle.doc

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Estimation of (co)variances for genomic regions of flexible sizes application to complex infectious udder diseases in dairy cattle

S?rensenetal.GeneticsSelectionEvolution2012,44:18 /content/44/1/18 G enetics Selection Evolution RESEARCH OpenAccess Estimationof(co)variancesforgenomicregionsof flexiblesizes:applicationtocomplexinfectious udderdiseasesindairycattle LarsPS?rensen1*,LucJanss1,PerMadsen1,ThomasMark2andMogensSLund1 Abstract Background:Multi-traitgenomicmodelsinaBayesiancontextcanbeusedtoestimategenomic(co)variances, eitherforacompletegenomeorforgenomicregions(e.g.perchromosome)forthepurposeofmulti-traitgenomic selectionortogainfurtherinsightintothegenomicarchitectureofrelatedtraitssuchasmammarydiseasetraitsin dairycattle. Methods:Dataonprogenymeansofsixtraitsrelatedtomastitisresistanceindairycattle(generalmastitis resistanceandfivepathogen-specificmastitisresistancetraits)wereanalyzedusingabivariateBayesianSNP-based genomicmodelwithacommonpriordistributionforthemarkerallelesubstitutioneffectsandestimationofthe hyperparametersinthispriordistributionfromtheprogenymeansdata.FromtheMarkovchainMonteCarlo samplesoftheallelesubstitutioneffects,genomic(co)varianceswerecalculatedonawhole-genomelevel,per chromosome,andinregionsof100SNPonachromosome. Results:Genomicproportionsofthetotalvariancedifferedbetweentraits.Genomiccorrelationswerelowerthan pedigree-basedgeneticcorrelationsandtheywerehighestbetweengeneralmastitisandpathogen-specifictraits becauseofthepart-wholerelationshipbetweenthesetraits.Thechromosome-wisegenomicproportionsofthe totalvariancedifferedbetweentraits,withsomechromosomesexplaininghigherorlowervaluesthanexpectedin relationtochromosomesize.Fewchromosomesshowedpleiotropiceffectsandonlychromosome19hadaclear effectonalltraits,indicatingthepresenceofQTLwithageneraleffectonmastitisresistance.Theregion-wise patternsofgenomicvariancesdifferedbetweentraits.PeaksindicatingQTLwereidentifiedbutwerenotvery distinctivebecauseacommonpriorforthemarkereffectswasused.Therewasacleardifferenceintheregion-wise patternsofgenomiccorrelationamongcombinationsoftraits,withdistinctivepeaksindicating