GENOMEREPORT - PDF document

GENOMEREPORT WholeGenomeSequenceofTwoWild-DerivedmusculusdomesticusInbredStrains,LEWES/EiJandZALENDE/EiJ,withDifferentDiploidNumbersAndrewP.Morgan,*JohnP.Didion,*AnthonyG.Doran,JamesM.Holt,LeonardMcMillan,ThomasM.Keane,andFernandoPardo-ManueldeVillena**DepartmentofGenetics,LinebergerComprehensiveCancerCenterandDepartmentofComputerScience,UniversityofNorthCarolina,ChapelHill,NorthCarolina27599-7264,WellcomeTrustSangerInstitute,Hinxton,Cambridge,CB101HH,UnitedKingdom Copyright©2016Morganetal.doi:10.1534/g3.116.034751ManuscriptreceivedAugust22,2016;acceptedforpublicationSeptember19, Volume6|December2016| brought to you by CORE View metadata, citation and similar papers at core.ac.uk provided by Carolina Digital Repository Figure1Sequencingcoverage.(A)ProlesofnormalizedreaddepthacrossautosomesandXchromosome.Blueandpurpleregionsshowcoveragebyreadswithmappingquality(MQ)20;darkgrayregionsshowcoveragebyreadswithMQ20.Graydashedlineindicatesexpectedhaploiddepth.Boxesbelowaxisshowpositionsofsegmentalduplications100kbinthemm10referencegenome.NotethattheresultsforZALENDE/EiJareprojectionsontothereferencegenome,sincethisstrainshasonly13chromosomes;chromosomepairsinvolvedinRobertsonianfusionsareindicatedatright.(B)HistogramsofcoveragebyreadswithMQ20acrossthegenome.Graydashedlineindicatesmediancoverageineachsample.(C)Estimatedancestryproportions(dom,M.m.domesticus;mus,M.m.musculus;cas,M.m.castaneus;?,masked)onautosomesandXchromosome.|A.P.Morganetal. Here,wereportthewhole-genomesequencingoftwoM.m.wild-derivedinbredstrains:LEWES/EiJ,whichisderivedfrommicetrappedinLewes,DE,withthestandardM.musculusdiploidchromosomenumberof40;andZALENDE/EiJ,whichisderivedfrommicetrappedinthePoschiavinusValley(Zalende,Switzerland),andhasa26-chromosomekaryotypeduetoxationofsevenRbtranslocations.WesequencedLEWES/EiJandZALENDE/EiJtoenableseveralclinesofinquiry.First,thisefforttriplesthenumberofM.m.domesticusstrainssequenced,andthusprovidesaclearerpictureofintra-cvariation.LEWES/EiJandZALENDE/EiJwereamongthetop10inbredstrainsrecommendedforresequencingbasedontheirpotentialtoincreasethecatalogofknownmousevariants(Kirbyetal.Inaddition,Rbtranslocationshavebeenimplicatedintheevolutionofthemammaliankaryotype,andaresubjecttomeioticdriveduringfemalemeiosisinbothmouseandhumans(Pardo-ManueldeVillenaandSapienza2001b).OurlaboratoryisinterestedinthechromosomalracesofM.m.domesticus(GroppandWinking1981;Qumsiyeh1994;Piáleketal.2005;Garagnaetal.2014)asamodelofnonrandomchromosomesegregation,karyotypeevolution,andthemechanismsunderlyingtherelativelyhighratesofaneuploidyandtrisomyinhu-mans(Pardo-ManueldeVillenaandSapienza2001a).Wewerepar-ticularlyinterestedinwhetherxationofmultipleRbtranslocationse.g.,inZALENDE/EiJ)isassociatedwithlossesorgainsonthecen-tromericendsofthechromosomesinvolved.LEWES/EiJwasselectedbecauseithasbeenusedextensivelyinstudiesofmalesterilityinM.m.domesticusM.m.musculushybrids(Goodetal.2008).KnowledgeofthespecicallelescarriedbyLEWES/EiJatkeyhybridsterilitylociwillguideinterpretationofthosestudies.Finally,werecentlydiscoveredalargecopynumbervariantonChromosome2,,forwhichthehighcopynumberalleleisassoci-atedwithdistortedtransmissionratiosinheterozygousfemalecarriers(Didionetal.2015).Importantly,wefoundthathasdrivenselectivesweepsintheabsenceoftnessgain(selshsweeps)inmultiplein-dependentmousepopulations(Di

dionetal.2016).rstiden-edinWSB/EiJ,aM.m.domesticusstrainderivedfrommicetrappedinCentreville,MD.SNPgenotypingdata(Yangetal.2011;Didionetal.2012;Morganetal.2016a)indicatedthatZALENDE/EiJharborsthehigh-copy(,distortion-associated)allele,whileLEWES/EiJderivedfrommicetrappedonly100kmawayfromCentrevillethelow-copy(i.e.,wild-type)allele.Wehypothesizedthatcompar-isonoftheWSB/EiJgenome,whichwassequencedpreviously(Keaneetal.2011),totheLEWES/EiJandZALENDE/EiJgenomeswouldhelp,andcharacterizeitsevolutionaryhistory(Morganetal.2016b),andcouldbeoffurtheruseinunderstandingtherelation-shipbetweencopynumberandtransmissiondistortionatthislocus.Here,wedescribethebasiccharacteristicsofthesetwogenomes,makethemavailableforpublicuse,anddiscusshowthisresourcemaybenetthecommunity.MATERIALSANDMETHODSMousestrainsLEWES/EiJ(DerivedfromwildmicetrappedinLewes,DE.MiceweresentfromMichaelPotter(NationalCancerInstitute)toEvaM.EicheratTheJacksonLaboratoryin1996.ZALENDE/EiJ(DerivedfrommicetrappedinthePoschiavinusValley(Zalende,Switzerland)byRichardD.Sage.MicefromSagescolonyweretransferredtoMichaelPotterin1981.AsinglepairofmicewassentfromMichaelPottertoEvaM.EicheratTheJacksonLaboratoryin1982.ZALENDE/EiJishomozygousforsevenRbtranslocations(1.3,4.6,5.15,11.13,8.12,9.14,and16.17).HighmolecularweightDNAfromoneZALENDE/EiJmalewasobtainedfromTheJacksonLaboratory.HighmolecularweightDNAfromaLEWES/EiJfemalewaspreparedfromtissuessamplesfromacolonymaintainedinthePardo-ManueldeVillenalaboratoryinthepast(Belletal.2006)LibrarieswerepreparedandsequencedattheUniversityofNorthCarolinaHighThroughputSequencingFacility.GenomicDNAswereshearedbyultrasonicationandtheresultingfragmentsweresize-selectedtotargetsize350bpusingaPippinPrepsystem.Sampleswerebarcoded(LEWES/EiJ,twobarcodes;ZALENDE/EiJ,fourbarcodes),pooled,andsequencedacrossmultiplelanesandmultipleowcellsonanIlluminaHiSeq2000instrument.Afterasmallpilotrunwithsingle-end50-bpreads,andamixtureofsingle-andpaired-end100-bpreadsweregeneratedforeachsample.BasecallinganddemultiplexingwereperformedusingtheCasava1.8pipeline.Weobtained498,668,400readsforLEWES/EiJand573,861,165readsforZALENDE/EiJ.DataprocessingIntegrityofrawsequencingreadswasconrmedusingFastQC(Andrews2010).Readswerealignedtothemm10referencegenomeusingbwamemv0.7.5ar406(Li2013).Coverageandqualitysumma-rieswerecomputedusingthePicardsuite(http://broadinstitute.github.org/picardSNVandshortindelvariantswerecalledusingtheSangerMouseGenomesProjectpipeline,thecurrentversionofwhichisdescribedindetailelsewhere(Doranetal.2016).Briey,samtoolsmpileupv1.1andbcftoolscallv1.1wereusedtogenerateaninitialcallsetforthenucleargenomeandmitochondrialgenome.Candidatevariantswerelteredonthebasisofreaddepth(100fornucleargenome;350formitochondrialgenome),mappingquality(20),numberofreadssupportingthealternateallele(5),proximitytoanindel(2bp;SNVsonly)andhomozygosity.Variantsweredeclaredprivatetoastrainifthealternateallelewasabsentfromall30otherstrainsintheMouseGenomesProjectcatalog.Analysespresentedinthismanuscriptwereperformedonlyonvariantspassingalllters.Burrows-WheelertransformsThemulti-stringBurrows-Wheelertransform(BWT)foreachwholegenomedatasetwasindividuallyconstructedin-memoryusingtheropebwt2program(Li2014).Afterconstruction,eachBWTwasencodedusingtherun-lengthencodingformatofthemsbwtprogram(HoltandMcMillan2014)fordiskstorage.TheBWTsforL

EWES/EiJandZALENDE/EiJare9.6and10.1GBinsize,respectively.Instruc-tionsforbuildingBWTsarepubliclyavailableathttps://github.com/holtjma/msbwt/wiki/Converting-to-msbwts-RLE-format Table1Variant-callingstatistics LEWES/EiJZALENDE/EiJShared PrivateSNVs403,770612,721102,561Coding36190.90%55250.90%6720.66%Damaging390.01%670.01%30.00%Privateindels92,082157,36619,684Coding510.06%860.05%90.05%Damaging490.05%770.05%70.04% Volume6December2016|GenomesofWild-DerivedMouseStrains| DataavailabilityRawreadshavebeendepositedintheEuropeanNucleotideArchive(accession#PRJEB15190).Allprocesseddataareavail-ablefromtheSangerMouseGenomesProject(http://www.sanger.ac.uk/science/data/mouse-genomes-project).Alignedreads(inBAMformat):.ac.uk/current_bamswebinterfaceforqueryingvariants:sanger/Mouse_SnpViewer/rel-1505;bulkdownloadofvariants(VCFformat):.ac.uk/current_snpsBWTsareavailablefordownloadathttp://csbio.unc.edu/RESULTSANDDISCUSSIONWesequencedonefemaleLEWES/EiJindividualtomedian14cov-erage(overallalignmentrate99.5%),andonemaleZALENDE/EiJin-dividualtomedian18coverage(alignmentrate99.4%).GeneticsexwasconrmedbycomparingrelativereaddepthontheXchromosometotheautosomes.Coverageprolesacrossthenucleargenomeare Table2Deletionsofprotein-codinggenes StrainEnsemblGeneIDGeneSymbolChromosome LEWES/EiJENSMUSG00000070868ENSMUSG00000055960ZALENDE/EiJENSMUSG00000073609ENSMUSG00000094651ENSMUSG00000093805ENSMUSG00000089951ENSMUSG00000070868ENSMUSG00000055960ENSMUSG00000049972ENSMUSG000000555945530400C23RikENSMUSG00000067599ENSMUSG00000091620ENSMUSG00000094298ENSMUSG00000094981ENSMUSG00000093941ENSMUSG00000091195ENSMUSG00000091275ENSMUSG00000096345ENSMUSG00000079342ENSMUSG00000079387 Figure2PhylogenetictreeofMouseGenomesProjectstrains.Treewasconstructedfromgeno-typesat30,000ancestry-informativeSNPsfromtheMouseDiversityArrayidentiedinYangetal.(2011).Filleddots,inbredstrainssequencedbySangerMGP;opendots,wild-caughtmicefrometal.(2011),identiedbytwo-lettercoun-trycode.Samplesarecoloredaccordingtosubspeciesoforigin:blue,M.m.domesticusM.m.musculus;maroon,M.m.molossinus(MOLF/EiJ);green,M.m.castaneus.ThetreewasrootedusingSPRET/EiJ(M.spretus)asthe|A.P.Morganetal. showninFigure1A;correspondinghistogramsappearinFigure1B.Afterlteringreadswithambiguousalignmentsorpoorbase-callqual-ity,coverageofatleast10wasachievedover77.2and84.7%ofthegenomeineachsample,respectively.Thisrepresentsthefractionofthegenomeaccessibleforidenticationofsequencevariants.Theremain-ingfractionofthegenomeliesalmostentirelyinrepetitiveelementsandclustersofpolymorphicsegmentalduplications(e.g.,theproximalregionsofchromosomes7and14)whereunambiguousalignmentofshortreadsisnotpossible.Sequencevariants(SNVsandshortindels10bpinsize)wereascertainedusingtheSangerMouseGenomesProjectpipeline(Doranetal.2016).Weidentied1,119,052SNVsthathavenotbeenpreviouslyreportedinanyothermouseinbredstrain(Keaneetal.2011;Doranetal.2016).Ofthosevariants,102,561aresharedexclusivelybythetwostrains,while403,770and612,721SNVsareprivatetoLEWES/EiJandZALENDE/EiJ,respectively(Table1),withatransition:transversionratioof2.14.Comparisonofthesetotalswiththenumberofuniquevariantsdiscoveredinotherinbredstrainsrevealsthatsequencingofwild-derivedinbredstrainsofM.m.domesticusoriginidentiesatleastoneorderofmagnitudemorevariantsthatsequencingclassicallabo-ratorystrains(Table2)(Keaneetal.2011;Dorane

tal.2016).Ofthe1.1Mnewvariants,0.88%fallwithincodingsequencesandthree(shared),39(privatetoLEWES/EiJ),and67(privatetoZALENDE/EiJ)arepredictedtodisruptgenefunction.Weobserveasimilarpictureforsmallindels(Table1).Asexpected,thenumberofsmallindelsthatfallwithcodingexonsissmallerbuttheproportionofpredicteddamagingmutationsishigher.Wealsoidentiedlargedeletionsthatarepredictedtoencompassmultipleexonsofatleast20genes(Table2).Thesedeletionscanbeascribedto11events,andrepresentnaturalknockoutsthatarecom-patiblewithlifeinalaboratorysetting.Mostofthemaffectmembersoflargeandhighlypolymorphicgenefamilies.Thosethataffectsingle-copygenesofwell-denedfunctionsuchasD2hgdhandGal3st2,arealsopresentinothersequencedstrains(Keaneetal.2011,Doranetal.2016).Interestingly,boththenumberofdeletionevents,andgenesdeleted,appearstobehigherinZALEDE/EiJthaninLEWES/EiJ.WespeculatethatdifferencesbetweenthetwostrainsinboththeirphylogeneticproximitytotheC57BL/6Jreferencesequence,andtheeffectivepopulationsizesoftheirwildprogenitors,mayexplainthesedifferences.BothLEWES/EiJandZALENDE/EiJwerereportedtohaveessentiallypureM.m.domesticusancestrybasedongenotypesfromthe600KSNPMouseDiversityArray(Yangetal.2011;Figure2).Wesoughttoconrmthisresultusingdensegenotypesfromwhole-genomesequencing.Weusedthreewild-derivedstrainsalreadysequencedbytheMouseGenomesProjectWSB/EiJ(M.m.domesticus),PWK/PhJM.m.musculus)andCAST/EiJ(M.m.castaneusasrepresentativesfortheirsubspecies,andSPRET/EiJ(Musspretus)asanoutgroup.Weclassiedallelesasancestralorderivedbasedonthepatternofsharingwiththeoutgroup.Aftermaskingthe19%ofthegenomewithknownintersubspecicintrogressionorcontaminationinthesestrains(Yangetal.2011),wecalculated(in25-kbwindows)theproportionofderivedallelessharedbetweenLEWES/EiJandexactlyoneofWSB/EiJ,PWK/PhJ,orCAST/EiJ,andrepeatedthisanalysiswithZALENDE/EiJ.BothstrainsshareamajorityofderivedalleleswithWSB/EiJ(M.m.domesticus)over92and94%ofthegenome,respec-tively(Figure1C).Theremaining8and6%ofwindowsrepresenteitherintrogressionfromM.m.musculusM.m.castaneusinthetwowild-derivedinbredstrainssequencedhere;smallM.m.domesticusgressionsintoPWK/PhJandCAST/EiJ(Wangetal.2012);regionsofincompletesortingofancestralpolymorphismamongthethreesubspecies(Keaneetal.2011);homoplasy(recurrentmutation);orsomecombinationofthethese.Finally,weinvestigatedwhethertheRobertsoniantranslocationsinZALENDE/EiJareassociatedwithlargedeletionsorduplicationsnearthecentromeresoftheaffectedchromosomes(1,3,4,5,6,8,9,11,12,13,14,15,16,and17).WefoundnoevidenceforprivateCNVsinanyofthesecentromere-proximalregions(Figure1A).BasedontheresultsobtainedinZALENDE/EiJ,itwouldappearthattheemergenceofRbracesisnotassociatedwithlarge-scalechangesinsequencecontent,atleastintheregionsofthegenomeincludedinthereferenceassembly.NovelallelespresentedherehavealreadybeenusedtoincreasetheutilityofSNParraysforgenotypingofwildmice(Morganetal.2016a).Weprovidetoolstobrowsethevariants,theunderlyingreadalign-ments,andtherawreads(seeDataAvailabilityMaterialsandMeth-ods).Inparticular,weprovideaccesstotheBWTofthesequencingreadsgeneratedfromeachofthesestrains.ABWTisacompactandlosslessdatastructurethatallowsrapidinterrogationofthereadsintheabsenceofalignment.IntegrationofthesetwonovelgenomesequenceswiththegrowingcatalogofknownM.musculusgeneticvariationwillprovideavaluableresourcetoresearchersusingmousemod

elstostudyawidevarietyofbiologicalprocesses,includingkaryotypeevolution(Chmátaletal.2014),speciation(PayseurandPlace2007),proteinevolution(Karnetal.2008;Stempeletal.2016),geneduplications(Laukaitisetal.2008;Morganetal.2016b),X-chromosomeinactivation(Calawayetal.2013),anddisease-associatedquantitativetraits(Cervinoetal.2005;Perezetal.2013;Nicodetal.2016).WewishtothankTimothyA.BellforhelppreparingtheDNA.ThisworkwassupportedinpartbyNationalInstitutesofHealth(NIH)grantsF30MH103925(A.P.M.),T32GM067553(A.P.M.andJ.P.D.),P50GM076468,andU19AI100625(F.P.-M.dV.).T.M.K.andA.G.D.aresupportedbytheMedicalResearchCouncil(MR/L007428/1),theBiotechnologyandBiologicalSciencesResearchCouncil(BB/M000281/1),andtheWellcomeTrust.LITERATURECITEDAndrews,S.,2010FastQC:AQualityControlToolforHighThroughputSequenceData.Availableat:http://www.bioinformatics.babraham.ac.uk/projects/fastqc.Accessed:August1,2016.Bell,T.A.,E.delaCasa-Esperón,H.E.Doherty,F.Ideraabdullah,K.Kimetal.,2006ThepaternalgeneoftheDDKsyndromemapstotheSchlafengeneclusteronmousechromosome11.Genetics172:411Calaway,J.D.,A.B.Lenarcic,J.P.Didion,J.R.Wang,J.B.Searleetal.2013GeneticarchitectureofskewedXinactivationinthelaboratorymouse.PLoSGenet.9:e1003853.Cervino,A.C.,G.Li,S.Edwards,J.Zhu,C.Laurieetal.,2005IntegratingQTLandhigh-densitySNPanalysesinmicetoidentifyInsig2asasusceptibilitygeneforplasmacholesterollevels.Genomics86:505Chick,J.M.,S.C.Munger,P.Simecek,E.L.Huttlin,K.Choietal.2016Deningtheconsequencesofgeneticvariationonaproteome-widescale.Nature534:500Chmátal,L.,S.I.Gabriel,G.P.Mitsainas,J.Martínez-Vargas,J.Venturaetal.,2014Centromerestrengthprovidesthecellbiologicalbasisformeioticdriveandkaryotypeevolutioninmice.Curr.Biol.24:CollaborativeCrossConsortium,2012Thegenomearchitectureofthecollaborativecrossmousegeneticreferencepopulation.Genetics190:Didion,J.P.,andF.Pardo-ManueldeVillena,2013Deconstructinggemischus:advancesinunderstandingancestry,structure,andvariationinthegenomeofthelaboratorymouse.Mamm.Genome24:1 Volume6December2016|GenomesofWild-DerivedMouseStrains| Didion,J.P.,H.Yang,K.Sheppard,C.-P.Fu,L.McMillanetal.,2012Discoveryofnovelvariantsingenotypingarraysimprovesgenotyperetentionandreducesascertainmentbias.BMCGenomics13:34Didion,J.P.,A.P.Morgan,A.M.F.Clayshulte,R.C.McMullan,L.Yadgaryetal.,2015Amulti-megabasecopynumbergaincausesmaternaltrans-missionratiodistortiononmousechromosome2.PLoSGenet.11:e1004850.Didion,J.P.,A.P.Morgan,L.Yadgary,T.A.Bell,R.C.McMullanetal.2016R2d2drivesselshsweepsinthehousemouse.Mol.Biol.Evol.33:Doran,A.G.,K.Wong,J.Flint,D.J.Adams,K.W.Hunteretal.2016Deepgenomesequencingandvariationanalysisof13inbredmousestrainsdenescandidatephenotypicalleles,privatevariationandhomozygoustruncatingmutations.GenomeBiol.17:167.Garagna,S.,J.Page,R.Fernandez-Donoso,M.Zuccotti,andJ.B.Searle,2014TheRobertsonianphenomenoninthehousemouse:mutation,meiosisandspeciation.Chromosoma123:529Good,J.M.,M.A.Handel,andM.W.Nachman,2008Asymmetryandpolymorphismofhybridmalesterilityduringtheearlystagesofspecia-tioninhousemice.Evolution62:50Gregorová,S.,P.Divina,R.Storchova,Z.Trachtulec,V.Fotopulosovaetal.2008Mouseconsomicstrains:exploitinggeneticdivergencebetweenMusm.musculusandMusm.domesticussubspecies.GenomeRes.18:509515.Gropp,A.,andH.Winking,1981Robertsoniantranslocations:cytology,meiosis,segregationpatternsandbiologicalconsequences.N

ature405:Guénet,J.L.,andF.Bonhomme,2003Wildmice:anever-increasingcontributiontoapopularmammalianmodel.TrendsGenet.19:24Holt,J.,andL.McMillan,2014Mergingofmulti-stringBWTswithap-plications.Bioinformatics30:3524Ideraabdullah,F.Y.,E.delaCasa-Esperón,T.A.Bell,D.A.Detwiler,T.etal.,2004Geneticandhaplotypediversityamongwild-derivedmouseinbredstrains.GenomeRes.14:1880Karn,R.C.,N.L.Clark,E.D.Nguyen,andW.J.Swanson,2008Adaptiveevolutioninrodentseminalvesiclesecretionproteins.Mol.Biol.Evol.25:Keane,T.M.,L.Goodstadt,P.Danecek,M.A.White,K.Wongetal.2011Mousegenomicvariationanditseffectonphenotypesandgeneregulation.Nature477:289Kirby,A.,H.M.Kang,C.M.Wade,C.Cotsapas,E.Kostemetal.,2010Finemappingin94inbredmousestrainsusingahigh-densityhaplotypere-source.Genetics185:1081Laukaitis,C.M.,A.Heger,T.D.Blakley,P.Munclinger,C.P.Pontingetal.2008Rapidburstsofandrogen-bindingprotein(Abp)geneduplicationoccurredindependentlyindiversemammals.BMCEvol.Biol.8:46.Li,H.,2013Aligningsequencereads,clonesequencesandassemblycontigswithBWA-MEM.arxiv:1303.3997Li,H.,2014FastconstructionofFM-indexforlongsequencereads.Bioinformatics30:3274Morgan,A.P.,C.-P.Fu,C.-Y.Kao,C.E.Welsh,J.P.Didionetal.,2016aThemouseuniversalgenotypingarray:fromsubstrainstosubspecies.G3(Bethesda)6:263279.Morgan,A.P.,J.M.Holt,R.C.McMullan,T.A.Bell,A.M.-F.Clayshulteetal.,2016bTheevolutionaryfatesofalargesegmentalduplicationinmouse.Genetics204:267Nachman,M.W.,andJ.B.Searle,1995Whyisthehousemousekaryotypesovariable?TrendsEcol.Evol.(Amst.)10:397Nicod,J.,R.W.Davies,N.Cai,C.Hassett,L.Goodstadtetal.,2016Genome-wideassociationofmultiplecomplextraitsinoutbredmicebyultra-low-coveragesequencing.Nat.Genet.48:912918.Pardo-ManueldeVillena,F.,andC.Sapienza,2001aFemalemeiosisdriveskaryotypicevolutioninmammals.Genetics159:1179Pardo-ManueldeVillena,F.,andC.Sapienza,2001bTransmissionratiodistortioninoffspringofheterozygousfemalecarriersofRobertsoniantranslocations.Hum.Genet.108:31Payseur,B.A.,andM.Place,2007Searchingthegenomesofinbredmousestrainsforincompatibilitiesthatreproductivelyisolatetheirwildrelatives.J.Hered.98:115Perez,C.J.,A.Dumas,L.Vallières,J.-L.Guénet,andF.Benavides,2013Severalclassicalmouseinbredstrains,includingDBA/2,NOD/Lt,FVB/N,andSJL/J,carryaputativeloss-of-functionalleleofGpr84.J.Hered.104:565571.Phifer-Rixey,M.,andM.W.Nachman,2015InsightsintomammalianbiologyfromthewildhousemouseMusmusculus.eLife4:e05959.Piálek,J.,H.C.Hauffe,andJ.B.Searle,2005Chromosomalvariationinthehousemouse.Biol.J.Linn.Soc.Lond.84:535Qumsiyeh,M.B.,1994Evolutionofnumberandmorphologyofhetero-zygosity.Symp.Zool.Soc.Lond.47:141Stempel,H.,M.Jung,A.Pérez-Gómez,T.Leinders-Zufall,F.Zufalletal.2016Strain-speciclossofformylpeptidereceptor3inthemurinevomeronasalandimmunesystems.J.Biol.Chem.291:9762Svenson,K.L.,D.M.Gatti,W.Valdar,C.E.Welsh,R.Chengetal.2012High-resolutiongeneticmappingusingthemousediversityout-bredpopulation.Genetics190:437Takada,T.,A.Mita,A.Maeno,T.Sakai,H.Shitaraetal.,2008Mouseinter-cconsomicstrainsforgeneticdissectionofquantitativecom-plextraits.GenomeRes.18:500Wang,J.R.,F.Pardo-ManueldeVillena,H.A.Lawson,J.M.Cheverud,G.A.etal.,2012ImputationofSNPsininbredmiceusinglocalphylogeny.Genetics190:449.Yang,H.,J.R.Wang,J.P.Didion,R.J.Buus,T.A.Belletal.,2011coriginandhaplotypediversityinthelaboratorymouse.Nat.Genet.43:648Communicatingeditor:B.J.Andrews|A.P.Morganetal.