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AComparativeGenomicMappingResourceforGrainsGrameneisacurated,open-source,Web-accessibledataresourceforcomparativegenomeanalysisinthegrasses.Asaninformationresource,Gramene'spurposeistoprovideaddedvaluetodatasetsavailablewithinthepublicsectortofacilitateresearchers'abilitytoleveragethericegenomicsequencetoidentifyandunderstandcorrespondinggenes,pathwaysandphenotypesinthecropgrasses.Thisisachievedbybuildingautomatedandcuratedrelationshipsbetweenriceandothercerealsforbothsequenceandbiology.Extensiveworkoverthepasttwodecadeshasshownremarkablyconsistentconservationofgeneorderwithinlargesegmentsoflinkagegroupsinrice,maize,sorghum,barley,wheat,rye,sugarcaneandotheragriculturallyimportantgrasses.Asubstantialbodyofdatasupportsthenotionthatthericegenomeissignificantlycolinearatbothlargeandshortscaleswithothercropgrasses,openingthepossibilityofusingricesyntenyrelationshipstorapidlyisolateandcharacterizehomologuesinmaize,wheat,barleyandsorghum.GrameneModulesThebestplacetobeginasearchatGrameneisofteninthemoduleofwhatyouwant.Ifyouwantinformationonamarker,lookinthemarkersmodule,ifyouwanttolearnaboutaprotein,gototheproteinsmodule.AnothergoodplacetostartiswiththeQuickSearchonthehomepage,alsofoundatthetoprightofallotherpages.Eventually,youwillfindthatmostofthemodulesareinterconnected,andyoumaymovebetweenmodulesasyoursearchprogresses.–Thepresentationofthemodulesisorganizedaccordingtotheirlocationonthenavigationbar.Thisdoesnotindicatethatyoushouldbeginwiththefirstmodulepresented,norendwiththelastone.TogetherthemodulescomplementeachotherbyformingtheGrameneDatabase.Genomebrowserisadynamicgraphicaldisplayusedtobrowsegenomes.Useitto:•SearchforgenesandotherfeaturesidentifiedfromtheRice-Japonica,MaizeandArabidopsisgenomes,aswellasfeaturesfrommaize,sorghum,barleyandwheatthatweremappedonthericegenome.•Viewthelocationofaparticularfeatureonthericegenome•Examineneighboringgenesandmarkers.•Viewthegenemodelofacandidategeneofinterestinordertodesignprimers.•Identifythegenomicsequencetowhichaparticulargeneismapped.•Lookforsynteny.Comparethepositionoffeaturesfromotherspecieswiththelocationofgenesinthericegenome,suchassequencedgeneticmarkers,ESTs,cDNAs,CDSs,genes,insertionandrepeatelements.GrameneGenomeBrowserAugust2005Linktomapsandontologiesfromthegenomebrowser.Uploadyourdatatoviewinakaryotypeideogram.DownloadgeneticinformationCustomizeyourresultsspecificallyfortheinformationyouneed.GenomeBrowserBrowseaChromosomeorViewaSyntenyMapCustomizeoptionsforContigViewIdentifythelocationofaparticulargene,trait,QTLormarker-andthegrassspeciestheyhavebeenmappedto-ongenetic,QTL,physical,sequence,anddeletionmaps.UsetheCMapviewertoexaminetheco-linearityofaparticularregioninonechromosomeorspeciestoanother;orinferwhichlinkagegroupinonespeciesismostconservedwithalinkagegroupinanotherspecies..Determinewhichmapsarethebestformakingcomparisons.MapsandCMapCompareMapsandCustomizeOptionsThetwoimagesherereflectthesamemapcomparisonwithdifferentoptionsselectedfordisplay.Locateaspecificmarkerbaseduponname,typeorspecies.Viewmarkerinformation,includingID,germplasmandgenomepositioning.Getmarker-typespecificinformation.LinktotheMaps,LiteratureandOntologiesDatabases.MarkersDatabaseMarkerSearchMapMarkersMarkerNameSynonymsSpeciesMarkerTypeGR_TaxOntologiesLiteratureOtherDBMapsSearchMarkerIDMarkerNameSynonymsMarkerTypeSpeciesGermplasmLibraryDescriptionMappingsCorrespondencesCloneRepeatMotifForwardPrimerReversePrimerAnnealTemperatureExpectedPCRProductSizeRemarksSequenceSourceGenomePositionsDBcross-referencesImagesOntologiesSearchOntologyAccessionAspect(Ontology)SynonymsDefinitionOntologyTermAspectDefinitionExternalReferencesDerivationAnnotationsOntologyTermNameObjectObjectAccessionObjectSymbolObjectNameObjectSynonymObjectSpeciesEvidenceLiteratureDBGenomesDBMapsDBProteinsDBGenesDBQTLDBMarkerDBOntologiesMapSearchProteinaccessionNames/Symbols/SynonymsOrganism(Cultivar)EvidenceCodesProteinNameSymbolSynonymEC#GeneNameLinktoBLASTGenBankAccessionTremblAccessionSpecies&CultivarPhenotypeCommentOntologyAssociationsReferencesEvidenceCodesProteinSimilaritiesProteinFeaturesFASTAsequenceGrameneBLASTBrowseOntologyDBAssociatedProteinsOntologiesDBNCBI,ExPaSy,GRINIRIS,PFam,.PROSITE,ProtomapLiteratureDBGenesDBDetailedInformationfromProteinsDatabaseQTLDatabaseQTL(QuantitativeTraitLoci)areastatisticalcreationthatidentifiesaparticularregionofthegenomeascontainingagene(orgenes)thatisassociatedwiththetraitbeingassayedormeasured.LearnwhichtraitisassociatedwithaQTL,findwhereitislocatedonamap,andconstructcomparisonswithothermaps.DeterminewhichmarkersdelimitaQTLDeterminewhatgenesarelocatedinthesameregionasothergenesTraitCategoriesTraitsatGramenearecategorizedaccordingto:Abioticstress:Traitsrelatedtostressesfromabioticenvironment,e.g.,water,light,temperature,orchemical.Anatomy:Traitsdirectlymeasuringplantpartssuchasroot,stemorleaf.Biochemical:Biochemicalandphysiologicaltraits,e.g.,enzymeactivity.Bioticstress:Tra