Prediction of identity by descent probabilities from marker-haplotypes 英文参考文献.docVIP

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Prediction of identity by descent probabilities from marker-haplotypes 英文参考文献.doc

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Prediction of identity by descent probabilities from marker-haplotypes 英文参考文献

Genet. Sel. Evol. 33(2001) 605–634 ?INRA, EDP Sciences, 2001 605 Original article Predictionofidentitybydescent probabilitiesfrommarker-haplotypes TheoH.E.MEUWISSEN a,?,MikeE.GODDARD b aResearchInstituteofAnimalScienceandHealth, Box65,8200ABLelystad,TheNetherlands bInstituteofLandandFoodResources,UniversityofMelbourne,Parkville VictorianInstituteofAnimalScience,Attwood,Victoria,Australia (Received13February2001;accepted11June2001) Abstract– Thepredictionofidentitybydescent(IBD)probabilitiesisessentialforallmethods thatmapquantitativetraitloci(QTL).The IBDprobabilitiesmaybepredictedfrommarker genotypesand/orpedigreeinformation. Here,amethodispresentedthatpredictsIBDprob- abilitiesatagivenchromosomallocationgivendataonahaplotypeofmarkersspanningthat position.Themethodisbasedonasimpli?cationofthecoalescenceprocess,andassumesthat thenumberofgenerationssincethebasepopulationandeffectivepopulationsizeisknown, although effective size may be estimated from the data. The probability that two gametes areIBDataparticularlocusincreasesasthenumberofmarkerssurroundingthelocuswith identicalallelesincreases.Thiseffectismorepronouncedwheneffectivepopulationsizeishigh. Henceaseffectivepopulationsizeincreases,theIBDprobabilitiesbecomemoresensitivetothe markerdatawhichshouldfavour?nerscalemappingoftheQTL.TheIBDprobabilityprediction methodwasdevelopedforthesituationwherethepedigreeoftheanimalswasunknown(i.e.all informationcamefromthemarkergenotypes),andthesituationwhere,sayT,generationsof unknownpedigreearefollowedbysomegenerationswherepedigreeandmarkergenotypesare known. identitybydescent /haplotypeanalysis/coalescence process /linkagedisequilibrium/ QTLmapping 1.INTRODUCTION Often,ageneforadiscreteorquantitativetraitismappedrelativetogenetic markersbut not identi?ed [15]. The mapping and subsequent investigation ofthemappedgenedependsontheabilitytopredictwhethertwoanimalsor gametesarecarryingthesamealleleatthisgenebecausetheyareidenticalby descent(IBD;e.g.[9]). Forinstanc