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breeding desigigns for recombinant

CopyrightÓ2008bytheGeneticsSocietyofAmericaDOI:10.1534/genetics.107.083873

BreedingDesignsforRecombinantInbredAdvancedIntercrossLines

MatthewV.Rockman1andLeonidKruglyak

Lewis-SiglerInstituteforIntegrativeGenomicsandDepartmentofEcologyandEvolutionaryBiology,PrincetonUniversity,Princeton,NewJersey08544

ManuscriptreceivedOctober27,2007AcceptedforpublicationMarch31,2008

ABSTRACT

Recombinantinbredlinesderivedfromanadvancedintercross,inwhichmultiplegenerationsofmatinghaveincreasedthedensityofrecombinationbreakpoints,arepowerfultoolsformappingthelociunderlyingcomplextraits.Weinvestigatedtheeffectsofintercrossbreedingdesignsontheutilityofsuchlinesformapping.Thesimplestdesign,randompairmatingwitheachpaircontributingexactlytwooffspringtothenextgeneration,performedaswellasthemostextremeinbreedingavoidanceschemeatexpandingthegeneticmap,increasing ne-mappingresolution,andcontrollinggeneticdrift.Circularmatingdesignsoffernegligibleadvantagesforcontrollingdriftandexhibitgreatlyreducedmapexpansion.Random-matingdesignswithvarianceinoffspringnumberarealsopooratincreasingmappingresolution.Givenequalcontributionsofeachparenttothenextgeneration,theconstraintofmonogamyhasnoimpactonthequalitiesofthe nalpopulationofinbredlines.We ndthattheeasiestcrossestoperformarewellsuitedtothetaskofgeneratingpopulationsofhighlyrecombinantinbredlines.

D

ESPITEdecadesofeffort,themolecularvariantsthatunderliecomplextraitvariationhavelargelyeludeddetection.Quantitativegeneticshasmappedthesefundamentalunitsofthegenotype–phenotypere-lationshiptobroadchromosomalregionsandquanti-tativetraitloci(QTL),butdissectingQTLintotheirconstituentquantitativetraitnucleotides(QTNs)hasbeenchallenging.Historically,amajorimpedimenttoQTLmappingwasthedevelopmentofmolecularmarkers,butasthetimeandcostofmarkerdevelopmentandgenotypinghavedeclined,thebottleneckinQTNdiscoveryhasshiftedtothemappingresolutionpermit-tedbya nitenumberofmeioticrecombinationevents.Simple,practicalmethodsforincreasingmappingresolutionwillhelpbreaktheQTNlogjam.Wein-vestigatedaspectsofinbredlinecrossdesignstoidentifysuchsimple,practicalmethods.

Manytechniquesincreasethenumberofinformativemeiosescontributingtoamappingpopulationderivedfromacrossbetweeninbredstrains.Thesimplesttech-niqueismerelytoincreasethenumberofindividualssampledinanF2orbackcross(BC)population.Amoreappealingapproachistoincreasethenumberofmeiosesperindividual,whichincreasesthemappingresolutionwithoutincreasingthenumberofindividualstobephenotypedandgenotypedandpermitstheseparationoflinkedQTL.Theproductionofrecombinantinbredlines(RILs),derivedfromanF2populationbygener-1

Correspondingauthor:110CarlIcahnLaboratory,PrincetonUniversity,Princeton,NJ08544.E-mail:mrockman@princeton.edu

Genetics179:1069–1078(June2008)

ationsofsibmatingorsel ng(Bailey1971;SollerandBeckman1990),allowsfortheaccumulationofre-combinationbreakpointsduringtheinbreedingphase,increasingtheirnumberbytwofoldinthecaseofsel ngandfourfoldinthecaseofsibmating(HaldaneandWaddington1931).

TheaccumulationofbreakpointsinRILsislimitedbythefactthateachgenerationofinbreedingmakestherecombiningchromosomesmoresimilartoonean-other,sothatmeiosisceasestogeneratenewrecom-binanthaplotypes.AsanalternativetoRILs,DarvasiandSoller(1995)proposedrandomlymatingtheF2progenyofacrossbetweeninbredfoundersandusingsuccessivegenerationsofrandommating(RM)topromotetheaccumulationofrecombinationbreak-pointsintheresultingadvancedintercrosslines(AILs).Linkagedisequilibriumdecayseachgenerationassexdoestheworkofproducingnewhaplotypes.AtrivialextensionoftheAILdesignpreservesthediversityintheintercrosspopulationbyinbreedingtoyieldhighlyre-combinantinbredlines,asDarvasiandSoller(1995)noted.SuchadesignhadpreviouslybeenemployedbyEbertetal.(1993).ThisrecombinantinbredadvancedintercrosslinedesignhasobviousappealinitsunionoftheadvantagesofbothAILsandRILsandhasbeenemployedintheproductionofmappingpopulationsinseveralspecies(Ebertetal.1993;Liuetal.1996;Leeetal.2002;Peirceetal.2004).

Theinbredlinesderivedbyinbreedingfromanadvancedintercrosspopulationhavemanynamesintheliterature,includingintermatedrecombinantin-

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