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.