gwas qtl tutorial - triticeae · the qtl report page provides details on the individual qtl, such...
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GrainGenes Tutorial:ViewingGWASQTLsinCMap
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GrainGenes containsanincreasingamountofdatafrompeer-reviewedpublicationsofgenome-wideassociationstudies(GWAS).ManyoftheQTLsfoundinthesestudiesforvariousimportanttraitscanbeviewingintheCMap Viewerwithrelativemappositionsonconsensusmaps.ToviewasummaryofsomeofthemapsheldinGrainGenes,gototheMapssectionunderQueryDataTypes.
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TheMapsShortlistshowsthemajormapsetsavailableinGrainGenes sortedbyspecies.Foracompletelistofmapsets,clickthelinkforTheCompleteList.
Forthistutorial,wewilllookatanoatmapset.ClickOatMapstonavigatedownthepagetothelistofoatmaps.
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TheMapsShortlistprovidesabriefsummaryofeachmapset,includingtheyearitwaspublished,thenumberandtypesofmarkers,andthelinkagegroupsforwhichtherearemaps.ThereisalsoalinkprovidedtotheMapDataReportPageforthatmapset.Asanexample,wewilllookatamapsetfroma2016GWASofbarleyyellowdwarfvirusresistanceinhexaploidoat,Oat-2016-CORE-BYDV.ClickLinktogothetheMapDataReportPage
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TheMapDataReportPageprovidesinformationonthemapset,includingtheincludedmaps,thepublicationitisfrom,lociinthemap,andanyQTLSthatareinsidethemap.ForthisparticularGWASdata,thereisphenotypedataavailableinT3:TheTriticeae Toolbox.ByclickingonthelinksnexttoExternalDatabases,wearebroughttothelocationofthethisdataontheT3/Oatwebsite.
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AtT3/OatwecanfindinformationonthegermplasmusedinGWASandobtainphenotypescoresforindividuallines.Thisdataisavailablefordownloadandfurtheranalysis.
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FormoreinformationontheQTLfoundinthisGWAS,wecanclickonthelinkstonavigatetotheQTLReportpagefortheindividualQTL.Thereweretwofoundinthisstudy.Inthistutorial,wewilllookatQBydv.CORE.17,whichwaslocatedonlinkagegroupMrg17fromtheHexaploid OatConsensusMap.**ItisimportanttonotethatthemappositionslistedinthismapsetarerelativeandwerebasedoffoftheOatConsensusMap(Chaffinetal.2016).**
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TheQTLReportPageprovidesdetailsontheindividualQTL,suchaswhichtraitisaffected,itsLODscoreandphenotypicR-squared,aswellasmarkerscontainedwithintheQTL.InordertoviewtheQTLinCMap,clickthelinknexttoMap,labelledOat-2016-CORE-BYDV-Mrg17.
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ThemapthatisinitiallyshowncontainsonlythesignificantmarkerscontainedinQBydv.CORE.17,aswellastwoframingmarkers.Byitself,thismapisnotparticularlyuseful.Asmentionedbefore,mappositionswereobtainedfromtheOatConsensusMap,sowemustalignthetwomapstogetasenseofthisQTL’slocationonthelinkagegroup.Todothis,scrolldownthepagetoanareawithalightbluebox.ThenclickAddMapsRight.(FormoreinformationonhowtouseCMap,seetheCMap Tutorial.)
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Fromthedropdownthatappears,selecttheoptionfortheOat—2016-Consensusmap,thenselectOat-2016-Consensus-17.ThenclickAddMaps.
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TheresultingmapshowsthecorrespondencesbetweenthesignificantmarkerscontainedwithintheQTLtothefullconsensusmapforlinkagegroupMrg17.Theareahighlightedinyellow,theQTLitself,nowcanbepositionedrelativetoothermarkersinthemap,andcomparedtodatafromotherstudiesthatusesharedmarkers.