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