rationalimprovementinotherspecies.

Incontrasttomicroarrays,whicharepro-ducedbydirectlyspottingDNAonamatrix,genechipsareproducedbysynthesizingoligo-nucleotidesonasolidsupportbyphotolithog-raphyorothermethods(32).Thismethodhasthepotentialtoproducearraysthatcontainsev-eralhundredthousandoligonucleotides.Thus,assumingfurtherimprovementsofthetechnol-ogy,itispossibletoenvisiongenechipswithsufficientcomplexitytorepresentanentireplantgenome.Genechipshavebeenusedtomeasuretheexpressionofallgenesintheyeastgenomewithminimalconcernaboutcrosshy-bridizationofstructurallyrelatedgenes(33).ByhybridizingyeastgenomicDNAtosuchchips,3714single-nucleotidepolymorphismsbe-tweentwogenotypescouldbeidentifiedinasinglehybridization(34).Althoughthechipsarecurrentlytoocostlyforroutineuseinmanybreedingprograms,itseemslikelythattechni-calinnovationsandtheefficienciesassociatedwithexpandedusewilldrivethecostsdown.Theapplicationofsuchchipsorotheroligonu-cleotidearraytechnologiestogenotypingindi-vidualsinsegregatingpopulationswillrevolu-tionizegeneticmappingandmarker-assistedbreeding.

explorethegeneticbasisofcomplextraits.Inprinciple,itmaybepossibletoidentifythegenesforusefulpathwaysortraitsbyfragmentingadonorgenomeintolargepieces—say50genesegments—andthenintroducingthemintoarecipientplantsuchasArabidopsisandtestingforcomponentsofthephenotypeofinterest.Thiswillbeusefulonlyifthepresenceoftheintro-ducedgeneconfersadominantorsemi-dominantphenotypesuchasthepresenceofanewenzymeactivity,analtereddiseasereaction,ormodificationofadevelopmen-talprocess.Byintroducing50genesatatimeintoArabidopsis,onlyabout500transgenicplantswouldneedtobeassayedinordertoexploretheentiregenomeofatypicaldiploidangiospermat1Xcoverage.Itseemslikelythatthistypeofanalysiswillbeaccomplishedbymakingplantarti-ficialchromosome(PLAC)librariesofanumberofplantspecieswithdivergentpropertiesandsmallgenomes.Thecentro-meresinArabidopsishavebeenmapped(35)andcurrentgenomesequencingeffortswillsoonextendthroughtheseregions,facilitatingidentificationandmanipulationofcentromere-containingregionsofchro-mosomes.Althoughthereissubstantialun-certaintyaboutwhatfactorsotherthanDNAsequencemayberequiredtorecon-stituteafunctionalplantcentromere,itmaybepossibletodevelopnewvectorsthatcontainbothyeastandArabidopsiscentro-meres.BecauseArabidopsistelomeresareverysimilartothoseinyeast(36)itmaybepossibletouseahybridsequenceofalter-natingplantandyeastsequencesthatfunc-tioninbothtypesoforganisms.Thus,itmaybepossibletodevelopyeastartificialchromosome–PLAClibrariesofmanyplantsinyeastandthenintroducethemintoasuitableplanthosttoevaluatethepheno-typicconsequences.Byprovidingadefinedchromosomalenvironmentforclonedgenes,theuseofPLACsmayalsoenhanceourabilitytoreproduciblyproducetrans-genicplantswithdefinedlevelsofgeneexpression.

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ReferencesandNotes

Arti cialPlantChromosomes

AsthegenomicsofArabidopsisandriceprogress,oneoftheprincipalchallengeswillbetodevelopthemethodsbywhichad-vancedknowledgeabouttheseorganismsistranslatedintousefulinsightsaboutthehun-dredormoreplantspeciesofeconomicim-portance.Atthesinglegenelevel,excellenttoolsarebeingdevelopedforcomparingthefunctionsofplantgenes.ItiseasytoproducelargenumbersofstabletransgenicplantsofArabidopsis.Thus,totestthefunctionofaclonedgenefromahigherplant,afacilemethodistodeterminewhetheritcomple-mentsamutationinthecorrespondingAra-bidopsisgeneorinanotherhost.Althoughtheresultsmaysometimesbedifficulttointerpretwhenthetraitcontrolledbythegeneishighlydivergentbetweenthehostandthegenedonor,thisshouldbeabroadlyusefulmethod.Itseemslikelythat,whentheanal-ysisofthericegenomeismorefullydevel-oped,acomprehensivecollectionofricemu-tationsmayprovideasimilarlyusefulalter-nativehostforanalyzinggenefunction.Inadditiontothegene-by-geneap-proach,itwouldbeusefultotransferlargenumbersofgenesamongplantspecies.Forinstance,becauseofthelargenumbersofgenesthattypicallyencodeseedstorageproteinsinplants,itmaybenecessarytomanipulatedozensofmodifiedseedstorageproteingenesinordertobeabletotailortheaminoacidcontentofseeds.Itmayalsobeusefultobeabletosimultaneouslyin-troducelargenumbersofgenesinorderto

RationalPlantImprovement

Theimplicationsofgenomicswithrespecttofood,feed,andfiberproductioncanbeenvi-sionedonmanyfronts.Atthemostfunda-mentallevel,theadvancesingenomicswillgreatlyacceleratetheacquisitionofknowl-edgeandthat,inturn,willdirectlyaffectmanyaspectsoftheprocessesassociatedwithplantimprovement.Knowledgeofthefunc-tionofallplantgenes,inconjunctionwithfurtherdevelopmentoftoolsformodifyingandinterrogatinggenomes,willleadtode-velopmentofarobustgeneticengineeringdisciplineinwhichrationalchangescanbedesignedandmodeledfromfirstprinciples.

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