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

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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.