Plant Functional Genomics. Science

PLANTBIOTECHNOLOGY:FOODANDFEED

PlantFunctionalGenomics

ChrisSomerville*andShaunaSomerville

NucleotidesequencingoftheArabidopsisgenomeisnearingcompletion,sequencingofthericegenomehasbegun,andlargeamountsofexpressedsequencetaginformationarebeingobtainedformanyotherplants.Therearemanyopportunitiestousethiswealthofsequenceinformationtoaccelerateprogresstowardacomprehensiveunderstandingofthegeneticmechanismsthatcontrolplantgrowthanddevelopmentandresponsestotheenvironment.

Therecentcompletionofthegenomese-quencesofanumberofbacterialspeciesandseveraleukaryotes(1)hasdemonstratedthefeasibilityandutilityofsequencinglargege-nomes.Mostbiologistsnowenvisionthedaywhenthecompletegenomesequenceoftheirfavoriteorganisms,oraproxythereof,willbeavailableinpowerfulelectronicdatabases.Accesstothisinformation,andnewtoolsthatexploitit,willprofoundlyalterthewaysweselectandapproachquestionsinbiology.This,inturn,willdirectlyaffecttheapplica-tionofgeneticmethodsforimprovingeco-nomicallyimportantspecies.Althoughfuturedevelopmentsinarapidlyemergingfieldaredifficulttopredict,webelievemanyofthemajordevelopmentsingenomicsthatwillinfluencebasicresearchinplantbiologyandplantimprovementduringthenextdecadecanbeanticipated.Someofthesepossibili-tiesaresummarizedhereaswellasinrecentarticles(2,3).

nomesequenceofArabidopsiswillbeavail-ablebytheendoftheyear2000.

BecauseArabidopsisisonlydistantlyre-latedtothecerealcropsthatprovidethebulkoftheworld’sfoodsupply,thegenomeofricewillalsobesequencedduringthenextdecade(6).Ricewaschosenbecause,inad-ditiontoitsimportanceasafoodsourceforaboutone-quarterofthehumanpopulation,ithasoneofthemostcompactgenomesamongthecereals.Itcontainsabout3.5timesasmuchDNAasArabidopsisbutonlyabout20%asmuchDNAasmaizeandabout3%asmuchDNAaswheat(7).However,thege-nomeorganizationofthecerealsappearstobeveryhighlyconserved;rice,wheat,maize,sorghum,millet,andothercerealsexhibitahighdegreeofsynteny(8).Thedifferencesingenomesizeareprimarilyduetoamplifica-tionofinterspersedrepetitivesequences(9);thereisnoevidencethatangiospermswithlargeamountsofDNApercellhavesubstan-tiallygreaternumbersoffunctionalgenesthan

angiospermswithrelativelysmallamountsofDNA.Becauseofextensivesyntenyamongthecerealgenomes,knowledgeofgeneorderandorganizationinricemaybeusedtoisolateandcharacterizethecorrespondinggenesinothercereals(8,10).Thus,forinstance,ifageneticlocuswhereausefultraitisencodedismappedbetweenapairofcloselylinkedmolecularmarkersinwheat,itmaybepossibletoiden-tifycandidategenesforthericeorthologbyanalyzingthericegenomesequencelocatedbetweenthericeorthologsofthemolecularmarkers.

ThesequencesofArabidopsisandricewillprovidetwofocifromwhichthegenomecontentsofotherhigherplantscanbeextrap-olated.Itappearslikelythat,asthecostsofDNAsequencingcontinuetodecrease,addi-tionalplantgenomesmayeventuallybese-quenced.However,duringthenextdecadeadditionalcompleteplantgenomesequencesprobablywillnotbepubliclyavailablebe-causeofthehighcostofsequencingthewholegenomeofanyofthemajorcrops.Forinstance,thecostofsequencingthemaizegenomeisexpectedtobeaboutthesameasthecostofsequencingthehumangenome.However,extensivepartialcDNAsequenceinformationwillbepubliclyavailableformostofthegenesfrommanyimportantplantspecies(11).Therearecurrentlymorethan

REVIEW

ADNASequenceTransect

OneofthefirsteukaryoticorganismsthatwillbecompletelysequencedisthesmallmustardspeciesArabidopsisthaliana(4)(Fig.1).Duringthepastdecade,Arabidopsishasemergedasoneofthemostwidelyusedmodelorganismsforstudyingthebiologyofhigherplants.Asamemberofthemustardfamily,itiscloselyrelatedtomanyfoodplantssuchascanola,cabbage,cauliflower,broccoli,turnip,rutabaga,kale,brusselssprouts,kohlrabi,andradish.Itwaschosenforsequencingbecauseithasahighlycom-pactgenomeofabout130MbwithlittleinterspersedrepetitiveDNA.SixresearchgroupsinJapan,Europe,andtheUnitedStatesarecollaboratingonthesequencing.About59%ofthegenomesequenceiscur-rentlyavailableinpublicdatabasesandalargeproportionofthegenesarealsorepre-sentedbypartialcDNAsequences(4,5).Itiscurrentlyanticipatedthatthecompletege-CarnegieInstitutionofWashington,DepartmentofPlantBiology,260PanamaStreet,StanfordCA94305,USA.

*Towhomcorrespondenceshouldbeaddressed.E-mail:crs@andrew2.stanford.edu

Fig.1.StatusoftheArabidopsisgenomesequencingproject.The vechromosomesarerepresentedbyrectangles;lengthisapproximatelytoscale.GreenregionsrepresentannotatedsequencesavailableinGenBank;yellowrepresentsregionscompletedandlargelyavailableinvariousdatabases;orangeindicatesregionsthatarecurrentlybeingsequenced;grayindicatesregionsinpreparationforsequenc-ing.FromtheArabidopsisdatabaseAtDB(http://genome-www3.stanford.edu/cgi-bin/AtDB/Schrom)withpermission.

PLANTBIOTECHNOLOGY:FOODANDFEED

127,000expressedsequencetag(EST)se-quencesfrom19plantspeciesinpublicda-tabasesandthenumberisexpectedtogrowrapidlyduringthenextseveralyears.Thesesequenceswillprovideisomorphismsbe-tweenthemodelgenomesandotherspecies,formingakindoftransectthroughgenomediversityinhigherplantsthatisanchoredincomprehensiveknowledgeofthetworepre-sentativespecies.Thus,asgenesassociatedwithfunctionsortraitsinoneplantarecloned,itusuallywillbepossibletoidentifytheorthologsresponsibleforthetraitinotherplantspeciesbyadatabasesearchorbyusingthesequenceinformationtoclonethecorre-spondinggenefromthespeciesofinterest.

ofprobablegenefunction,ifitisknown,inanyhigherplant.Thisisillustratedbyacomparisonofsequenceidentityofaran-domsampleofputativelyorthologousriceandArabidopsisproteins(Fig.2).Becauseoftherelativelyrecentradiationoftheangiosperms,weconsideritlikelythattherewillbeveryfewprotein-encodingangiospermgenesthatdonothaveor-thologsorparalogsinArabidopsisorrice.Therefore,understandingthegeneticbasisfordiversitymaydevolvetoidentifyingtherelevantdifferencesinthecontrolofex-pressionorthefunctionofessentiallythesamesetofgenes.Indeed,ithasbeenhypothesizedthatthedevelopmentaldiver-sityofhigherplantsmaybelargelyduetochangesinthecis-regulatorysequencesoftranscriptionalregulators(12).

Amajorchallengetounderstandingthegeneticbasisofinterspeciesdiversityisthat,inatleastsomecases,minorchangesinthestructureorexpressionofagenemayleadtomajorchangesinphenotype.Thiswasrecentlyillustratedforthegenesthatcontrolmodificationsoffattyacidsinplants(13).Higherplantscollectivelypro-ducemorethan200fattyacids,whichac-cumulateasstorageoilsinseeds.Thesefattyacidsdifferprimarilybecauseofthepresenceofdoublebonds,hydroxyls,ep-oxygroups,triplebonds,orsecondarymodificationsofthesefunctionalgroupsatvariouscarbonsalongthefattyacylchains.Ithasrecentlybecomeapparentthatthesefunctionalgroupsareproducedbyafamilyofcloselyrelatedfattyacyldesaturase-likeenzymes(14).Theobservationthatasfewasfouraminoacidsubstitutionscancon-vertadesaturasetoahydroxylaseillus-trateshownewchemicalconstituentscanaccumulatewithouttheevolutionofanob-viouslydistinctenzyme(13).Largegenefamilieshavealsobeenobservedforcyto-chromeP450s,enzymesinvolvedinpoly-saccharidebiosynthesis,disease-relatedgenes,transcriptionfactors,proteinkinases,andphos-phatasestonameafew.Thus,amajorchal-lengeassociatedwithexploitingtheexplosionofgenomeinformationwillbeindeducingrulesthatcanpredicttheprecisefunctionofmembersofgenefamilies.

Onepromisingavenue,termedphylo-genomics,exploitstheuseofevolutionaryinformationtofacilitateassignmentofgenefunction(15).Theapproachisbasedontheideathatfunctionalpredictionscanbegreatlyimprovedbyfocusingonhowgenesbecamesimilarinsequenceduringevolutioninsteadoffocusingonthesequencesimilarityitself.Becausethepoweroftheanalysisincreasesinproportiontothenumberofsequencesthatareavailable,thismethodshouldbecomemoreusefulasthedatabaseofplantsequenc-esexpands.

FloweringPlantsContaintheSameGenes

Althoughfloweringplantshaveevolveddur-ingthepast150millionyearsorsoandthereforemightbeexpectedtobeverysimi-laratthegeneticlevel,substantialdevelop-mentalandmetabolicdiversityexists.Under-standingthebasisforthisdiversityisakeytounderstandinghowtoeffectrationalim-provementsintheproductivityandutilityofcropspecies.Knowledgeofthegeneticbasisforintraspeciesvariationinspecifictraitsshouldbeusefulforselectingorcreatingusefulvariationwithinaspecies.

TheavailabilityofextensiveESTinfor-mationformanyspecies,inconjunctionwiththecompletesequencesofriceandArabidopsis,willallowunambiguousin-sightintothequestionofhowsimilarthegenomesofhigherplantsare.WhentheArabidopsisandricesequencesarecom-plete,itwillbepossibletodirectlycomparealltheESTandotheravailablesequencesfromvariousplantswiththegenomicse-quencesfromthemodelgenomes.Ourpre-liminaryanalysisofavailablesequencessuggeststhatmostgeneproductsfromhigherplantsexhibitadequatesequencesimilaritytodeducedaminoacidsequencesofotherplantgenestopermitassignment

AssigningFunctiontoGenes

Oneofthemajorefficienciesthathasemergedfromplantgenomeresearchtodateisthatabout54%ofhigherplantgenescanbeassignedsomedegreeoffunctionbycomparingthemwiththesequencesofgenesofknownfunction(16)(Fig.3).Ineffect,auniversalbiologyhascoalescedfromthecommonlanguageofgeneandproteinsequences.Unfortunately,knowingthegeneralfunctionfrequentlydoesnotprovideaninsightintothespecificroleintheorganism.Forinstance,onthebasisofsequenceanalysis,about13%ofArabidop-sisgenesareinferredtobeinvolvedintranscriptionorsignaltransduction(16).However,knowingthatageneencodesakinaseortranscriptionfactordoesnotpro-videanyusefulinformationaboutwhatpro-cessesarecontrolledbythesegenes.Thus,completionofthegenomesequencesofAra-bidopsisandricewillbefollowedbyasec-ondphaseoflarge-scalefunctionalgenomicsinwhichallofthe20,000to25,000genesthatmakeupthebasicangiospermgenomewillbeassignedfunctiononthebasisofexperimentalevidence.Consideringthatthecombinedeffortsoftheplantbiologycom-

Fig.2.SequenceidentityofArabi-dopsisandriceproteins.Percentsequenceidentityoverthefulllengthoftheproteinswascalcu-latedfor64randomlyselectedproteinsforwhichtheprobablefunctionwasknownandforwhichfull-lengthornear-full-lengthse-quenceswereavailable.Toavoidcomparingmembersoflargemul-tigenefamilies,wedidnotincludeaproteininthecomparisonifse-quenceswereavailableformorethantwoapparentlyrelatedpro-teinsfromeitherofthespecies.Becauseitisuncertainwhether

other,morecloselyrelatedproteinsareencodedintheunsequencedregionsoftheArabidopsisorricegenome,thisanalysisunderestimatesthedegreeofidentitybetweenthesequencesofArabidopsisandriceproteins.

Fig.3.Functionalclassi cationofpredictedgenesina1.9-MbregionoftheArabidopsisgenome.Proteinrelatedreferstogeneproductsinvolvedinsynthesis,degradation,modi ca-tion,storage,andtargetingofproteinsandinintracellulartraf cking.Analysiswasbasedon389predictedorknowngenes.From(16).

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munityhaveresultedindirectfunctionalanalysisofonlyabout1000genestodate(5),thismayseemlikeatallorder.However,itappearslikelythattheefficiencygainedby“reversegenetics”rgecollectionsofinsertionmutantsareavailableforArabidopsis,maize,petunia,andsnapdragon,andcollectionsofinsertionmutantswillprobablybecreatedinseveralotherspeciesincludingrice.Thesecollectionscanbescreenedforaninsertionalinactivationofanygenebyusingthepoly-merasechainreaction(PCR)primedwitholigonucleotidesbasedonthesequencesofthetargetgeneandtheinsertionalmutagen(3,17).ThepresenceofaninsertioninthetargetgeneisindicatedbythepresenceofaPCRproduct.BymultiplexingDNAsam-ples,hundredsofthousandsoflinescanbescreenedandthecorrespondingmutantplantscanbeidentifiedwithrelativelysmalleffort.Inaddition,severalgroupsareembarkingonsequencingthegenomicDNAflankingalargenumberofinsertionssothataninsertioninvirtuallyanygenecanbeidentifiedbyacomputersearch(2,18).Analysisofthephe-notypeandotherpropertiesofthecorre-spondingmutantwillfrequentlyprovideaninsightintothefunctionofthegene.

AmajorlimitationtotheanalysisofgenefunctionbymutationisthatahighdegreeofgeneduplicationisapparentinArabidopsis(16)andis,therefore,probablyacommonfeatureofplantgenomes.BecausemanyofthegeneduplicationsinArabidopsisareverytightlylinked,itusuallywillnotbefeasibletoproducedoublemutantsbygeneticrecom-bination.Apossiblesolutionmaybetousehomologousrecombinationtoeliminatetan-demgenessimultaneouslybygenereplace-ment(19).Alternatively,amethodforpro-ducingpointmutationsbyusingRNA-DNAhybridsmaybeuseful(20).Bytargetingmutagenicsequencesthatintroducestopco-donstoregionsthatareconservedamongallduplicatesitmaybepossibletogenerateallcombinationsofnullmutationsinallmem-bersofamultigenefamilyfromoneexperi-ment.Althoughthesemethodsareamenabletoagene-by-geneapproach,theyarenotwellsuitedtoahighthroughputapproachbecauseoflowefficiencyorbecauseofthenecessityofregeneratingplantsfromsingleculturedcells.BecauseoftheeasewithwhichlargenumbersoftransgenicArabidopsisplantscanbegeneratedbyinfectingflowerswithAgrobacteriumtumefacienscontaininganin-sertionalmutagen(21),amethodofgenesilencingbasedonproducingdouble-strand-edRNAfrombidirectionaltranscriptionofgenesintransgenicplantsmaybebroadlyusefulforhigh-throughputgeneinactivation(22).Thismethodcould,inprinciple,bede-signedtousepromotersthatareexpressedinonlyafewcelltypesorataparticulardevel-opmentalstageorinresponsetoanexternalstimulus.Thiscouldsignificantlyobviateproblemsassociatedwiththelethalityofsomemutations.Althoughthemechanismisnotyetunderstood,itbearssomeresem-blancetodouble-strandedRNA–mediatedgenesilencinginnematodes(23).

Formanyapplications,particularlyinspe-ciesotherthanArabidopsiswhereproductionoftensofthousandsoftransformantsisslowandtime-consuming,virus-inducedgenesi-lencingmaybethemostfacilemethodforsuppressinggenefunction(24).Thismethodexploitsthefactthatsomeorallplantshaveasurveillancesystemthatcanspecificallyrecognizeviralnucleicacidsandmountasequence-specificsuppressionofviralRNAaccumulation.Byinoculatingplantswitharecombinantviruscontainingpartofaplantgene,itispossibletorapidlysilencetheendogenousplantgene(25).

Itisexpectedthatapplicationoftheseandrelatedmethodswillleadtotheassignmentofsomedegreeofgenefunctiontoallgenesinthebasicangiospermgenomewithinthenextdecade.Inaddition,parallelstudiesofthefunctionofgenesinother,nonplant,organ-ismswillcontributeagreatdealtounder-standinggenefunction.Thiscomprehensiveapproachtounderstandinggenefunctionwillgreatlyfacilitatethecreationofplantim-provementsthatarebasedonknowledgeoftheentiresysteminsteadofonagene-by-genebasis.

rolesofthegeneaffectedbythemutation(27).

Thesedatabasesofgeneexpressioninfor-mationwillprovideinsightsintothe“path-ways”ofgenesthatcontrolcomplexresponsesandwillbeafirststeptowardanecologyofthegenomeinwhichthegenomeisviewedasawholeandtherelationshipsofgeneproductstoeachotherwillbeconsideredfromatleastoneperspective(relativelevelofexpression).Per-hapsthetypesofmodelsthatecologistscurrent-lyuseforunderstandingtheinteractionsineco-systemswillproveuseful(28).Indeed,becausemicroarrayscanbemadeforanyorganismforwhichcomplementaryDNAscanbeisolateditseemslikelythatecologicalapplicationswillbefound.ItisnotnecessarytoknowthesequenceofthegenesonaDNAmicroarraybefore-hand—thiscanbedeterminedafterthearrayshavebeenusedtoidentifygenesthatmaybeofinterestbysomecriterion.

TheaccumulationofDNAmicroarrayorgenechipdatafrommanydifferentexperi-mentswillcreateapotentiallyverypowerfulopportunitytoassignfunctionalinformationtogenesofotherwiseunknownfunction.Thecon-ceptualbasisoftheapproachisthatgenesthatcontributetothesamebiologicalprocesswillexhibitsimilarpatternsofexpression.Thus,byclusteringgenesbasedonthesimilarityoftheirrelativelevelsofexpressioninresponsetodi-versestimuliordevelopmentalorenvironmen-talconditions,itshouldbepossibletoassignhypotheticalfunctionstomanygenesbasedontheknownfunctionofothergenesinthecluster(29).Workwithplantmicroarraysisjustbegin-ningbutthereiseveryreasontobelievethatthisapproachwillsoonbeastandardcomponentoftherepertoireofplantbiologists(30).Theprin-cipalchallenge,atpresent,istodevelopmeth-odsfordatabasingandinterrogatingthemas-siveamountsofdatathatresultfromthistypeofexperiment.

Oneofthemostimportantadvancesinplantimprovementwasthediscoveryofhybridvigorandtheexploitationofthisphenomenoninmodernbreedingprograms.Inspiteofexten-sivespeculationaboutthemechanisticbasisforhybridvigor,itispoorlyunderstood(31).Itwillbeveryinterestingtocomparewholegenomemicroarraysofinbredparentallineswiththeheterotichybrids.Wespeculatethatthehybridswillexhibitsignificantdifferencesintheex-pressionofclustersoffunctionallyrelatedgenesandthatdifferenthybridswillhavedif-ferentpatternsofexpression.Ifthisprovestobethecase,itmaybepossibletoprogresstowardmorepredictivedevelopmentofheterotichy-bridsbybreedingforcertainpatternsofgeneexpression.Itmayalsoprovideamuchneededlinkagebetweenthebreedingofdifferentplants—thatis,ifitisfoundthatvariationintheexpressionofcertainpathwaysorprocessesisassociatedwithenhancedyieldorqualityinonespecies,thismayprovidetestabletargetsfor

ImpactofGeneChipsandMicroarrays

Oneofthemostimportantexperimentalapproachesfordiscoveringthefunctionofgenespromisestobegenechipsandmi-croarrays.Inprinciple,DNAsequencesrepresentingallthegenesinanorganismcanbeplacedonminiaturesolidsupportsandusedashybridizationsubstratestoquantitatetheexpressionofallthegenesrepresentedinacomplexmRNAsample(26).Thus,wemayexpecttohaveexten-sivedatabasesofquantitativeinformationaboutthedegreetowhicheachgenere-spondstopathogens,pests,drought,cold,salt,photoperiod,andotherenvironmentalvariation.Similarly,wewillhaveextensiveinformationaboutwhichgenesrespondtochangesindevelopmentalprocessessuchasgerminationandflowering.Inaddition,wewillsoonknowwhichgenesrespondtothephytohormones,growthregulators,safeners,herbicides,andrelatedagrichemi-cals.Perhapslessobviously,wemayex-pecttohavesimilarinformationformanymutantsornaturalaccessionsthatdifferinsomewaythatcannotbereadilyassignedtogeneticvariationbyothercriteria.Knowl-edgeofwhichgenesexhibitchangesinexpressionofamutantofinterestwillbeusefulforformulatinghypothesesaboutthe

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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