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VoT. ?5. pp. 1~I-I974. Mach 1998 ,. .. . Colloqulum Lisper ` ~r ~` ~ ~/ ~ ~~f~7z art <~ ~, ^~d ant: 7~ 6~ ~ oaf G~ , ~ ~ ?~! ~& ~ ~ a. ^~, A~ Ha./ 2-{ 799! ~ 0) Comparative genetics in the grasses REHEEL C. CALL* ADD CREW ~ DEVOS Jobs Incas 3~. No~kb R~so~=h Park Ulna. ~or~!~b ~R4 7UH. Unfed K}n~ ABS~ ~ ~~ of ~( ma~ ad rim find other press species ~11b common DIVA probes teas re- ve~led remarkable conscr~don of Bang content and gene order over the ~ million Mars of ~dist10n of ~ Abe linear organization of penes in some nine different penomes dishrag in basic chromosome number ram 3 to 12 and curter Day amount tom 40010 6~000 gab. can be described intermsofonly25~rlceUnFugeblocks/~{beextentto~bicb 1hisintergenomiccoli~earit>iscon~undedattbemiCrol~el nedupUcabon~ndm~ro-~ar~n~en~tsissUHanopen qUest10~.Neverthciess,itiscleartbatib~elucidatiOnoftbe organization ofthe economically important Trusses w1Ib largergenomes,such~sm~be(2n =10~4~300 ~bD\At~', to ~ ~reaterorlesserextent.be predicted Mom sequence anal}sisofsmall~rgenomessu~b~srice~w~hon}~400 gab. h~hinturnm~ ~ Emu aide ~ kneed oftbe Atom seq~enceof]~.~hichma~be:~ab~leassoo~as1~he turnoftbecentury.Comp~r~lIvege~etics~Blpro~ld~thek~ to ~nlock~be penomic secrets nfcrop plants ~11b biter genomes1~an~ lntbc midI930s~henresthcLor b~mcnllen~iLpolymor~ . . . ^ .~.. .^ ~ ,- . . pnlsm (~3 1cchnoIogy was Brat applied to plants the o~ec~ves ofthe earn c~p~rim~nl&--inlom~to. ~>ZZ2~1, lay Steve l~a~n~ksicyTo Maw ~exic<~.~in m~l}/~.Z<~:z amp, by Tim H~[cngarb iD Ltab, and ourselves in bread ~l]~'t,73777~>z'~: ~.S)T+~?, [1] ~[lllltTrid~c>-~OrC ~110 more al]l- bL[ous Wan 10 produc~an~w gen~rab~noYmarkers ~rUseLv breeder~Inthcracetobuildtbe Crs1denseg~n~tic m~ps,tb) early report of Valery across ~rom~si~ I988 - between 10maloand p~lalotD ad D\A sequences. Lasso numbers of ch~racl~rked C\^ probes acre still not av~i~l~b~lo. filed 1-~se~lrcllcrs Off flue do. t~heFe~Forc. used RFLP probes Ratable in onc species 10 chase phonetic maps in related gnomes. Pxamplas are Do use o~m~Iz~ probes 10 map sorghum. #~~ >~r (3\ and Shoal prams 10 map rye >~ rr~2 (4), and both studies revealed vat more colireari0. ~ev~rlhel~s, it Was rot clear al the hmc liar irtergenomic synergy chards only 10 1be panes lhemscIvos. Since 1ha garb }990s alternative maker systems based on PER have complemented RFLPs. however. ~ross-~CnorlC signals are on} Tn~qu~nlly observed by using s~q~e~-t~gc~)es or m~rosatchi1c primers because the soquc~ces mug mslcb tbe template DN) precisely. Is act. had POR been discovered years parlor we ma PHI ha been ignorant at the conservation of gent order amok plant species. a) !~)!~8 tat 1`1~< ~:~1~1 ^~1e~l~ of Sews gaff \~/~8,~5.1~1^~.~./~} Con~ensusG~ss Map Soon alder comparisons 1)el~een Irlbes were reported Hahn and T~nksTcy ~ ~. and maize enomaslob~clos~>rcIat~d:Kurat~l~/.~6)sho~od Wand heattobecolincar;Devos~ ~7)sho~ej mai/eand bobcat toh~vc ~1~in~dcobne~rky;Van D ~nze~8jexiend~dth~ ace, m~ze,and ~h~tcomp~rRon 10 incIudean 3~- )~ x ~.~rdiploTd oJ1 map; Devon (9)compared Satan mUlet.6e~h) )~,snd rice:the complex pobploid susarcane~sm~pp~dalon~side malzeandsor~hu~ by Gravel 7 ~< (10) and dcc by augur of ~< (11~. more Fork, as vet un.r~por1cd, Will dOll]O[lsl~l81C tale petrol. mi~]le1~,.~'l~z>~ >~~ (~.\i.~.,T.S.Du~d~l^~.Couchma~.and hi.D.C.. unpu~3b~d dot #,Qn~er COWL (~ of (\i. .D.~.,and K.~4.D.,unp ~ ~heddala~and Bra. ~\i. H:~y~rd.1.P.~Kin~.l~. arid [ll~nl:~s,J. Kelly. [. Armsl~:ld. J. Forsler, ~.~ll~umphri~s. clod ~ hiorg~l(. unpublished delay ago have genomos that are closely reclad to the other economic grass species. The first consensus Mass map Knin the gems of seven dint grass species was shown bv M5ore ~< ~S (T2~. and an attended and more delayed verge is shin in t1~. I. gals map descants tho d1^rert grass Gnomes in farms of ' ace (nk~g~ blocks' Fig. 1 she the {vcr~1 areas of uncertain"\ (shown ~ hatched re<10ns) notwithstanding, that now nin) dirt ~enome~diploid oath a #~ AL burly consen- sus, the 1~0 renames of mazy. sorghum. the two Becomes ~ ~ and ~ #~^ of su~rcsn~. ~a] miDe6 and rico-can be described by oily ~ rice linkage blocks. ~nd~ubted~ this estimate wig ~ as mare doled ~ added. Hoover, already 1b~ consensus can be used 1O rapidly con- str~ maps of 01her grass species ~ using a set Of anchor probes And Raced around the circles. Ad to predict the locations of key bangs far adaptation from one crop species to . ~ ~ ~ =~.~1 . Dear Gene Syn{eny ALbough most oftbe m~ppedlocithat~nchor1hecons~nsus map~red~tcctedby RFLPprohesofunkno~n Duncan some dear rclabonships between ~ ~ genes of economy and adapts importance are abeam apparent. An und~r~i~ assumption to 1be consensus shown in Fib. 1 is Chat it presents summed i~. ~crc~1 Gnomes carry about 2i.000 genes, then alla should be able ~ dram 23.0do radii around ah circles to pass 1hrou~b homoeoloci in the d>Dren1 gO I1 m as. These relationsb[ps can clearly be scan among 1bo many bo~ymo loci that ha been mapped in the different species. ~bbrevi~do~s: Ram. ~s~ichon hangman! length poJvmo~h~m: OII. qtt~lj~ltit:~tliv~ plait loci. auto whom rcprinl r~q~es1~ should be addressed. ~-msi) ~1~) . . . . ~ . .... .. ~sr.AC.~< 'I {)?'! . .. ~ ~

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I972 Colloquium Paper: Gale and Devos GRASS Gum Cp~ ^~ .,,,,, ~ ~ .~ ~ I", `^ ^ V }~!~ "me Cures add a~rl]1 {sbne or 1~p/bot10m) designs are as descried ~ ~ Donoughuc ~< <31) ha+ oath Parka ~r ~< (S2) far sorghum, [u~ur (11) far lh; 6u~a;can) Venoms Wang ~ ~! (33) in ago miJeL and Sing Of ~! (34) in Ice. Other examples include ~ (~) genes in ad of the species in rice ankle block 6a; the Unless (~) loci in burly. maize. and ~ in Ramp Ones corolla {bb~r~Diu insenshiv~y and plant heat in Opal -# and magic ~ )~) in R=3b; and red grain colorTn abed 0R)and rye pR))in RLBlb.In otb~r cases. genes controlling major mulanlphenolypescanbe allied Bulb Anemic Actors with lesser Uncle, Bach hoe [seen m~ast~re<1 as qua~nti1~1~ve trait loci (OTL) ill fisher genomes. An example h the ~Esnmenl of the major maize , i. . . .. Sarong lock ~ ~7. ~ Adam Ash Of ~r plant heat in Cream (I3). Similar ~ major ~CDC Or sbatterin~, a keg component of domestication of crop plank ~ banned exacts web Of tar sh~ttorin~ in ace and made (143. Tbus maw .. . . Pollee major gODC mutants mappedin badey, m'Lc.and dcc may go used as poinlerslo ho moos wilb more subtle exploitable eD>clslntbes~me orothor~enom~s. Plaint tb~ro ~ a need 1~ continue the mewing oftbe old classical maps~ithlben~er'(molccular~ maps.Ther~cenl explosion ofexpressed s~qu~nc~tag (ES1] detain rice and maim and their localization on angelic or pLyslcal maps combined witb~herapid}expanding~cnes~quencedatabases All makes po~erfulye~De-~[lliIlin~l~l. ~orEvolu110naryCbromosomalRearrangtments In~r~nccscan~lsobc mad~fromibe m~orgenomicrear- ra~cmcntslhath~et^cnpL~ during ^~utiona~d~crc ^~calcdtbro~h ~ecomp~al\ran~i~In~,consctv~ Jonof~encordcrkso mucb~bcruletbattb~di~trencesin Labonb~t~cn~enomescanb~used Or ma 1=onomlc a~alysis[see K>Hogg (Ti)Tn tbisissuc oftbe 2~e~f~z~]. Wi~re~re^ctoFig.I.tb~inserbonof~colink'~ black 10intoidescribestheprcs~nt~d~ Tri~ccac~roupIchromo so~cs and oats chromosome ~ and ~ arcs to bat common lo JO Pocidcae. Similar>, phenols of the P~[oideae species arc ~1 defined ~ the Sermons of rice linkage block 9 into 7 and 10 into 3. AD of these rearrangements are holy 10 date back 60-100 minions of Mars to 1be early r~diadon of the I. ~ to which a~an~emcn~ ~ am of those emend today. ~ the . . . . #1 ~ dam argue that the ~C1 1ba1 dcc [okay block jO, freestanding in ace. ~ today guild in 1 OCR for page 1

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1974 Col~logtlium Paper: Gala and Devos has also r^cakd genes or small 11nk^c segments ironed ~ duplications. ~ S{)O-kb sepllle~nt on rice chooses 9 is duplic~10d ~ ~ m~ units bel~ the ~~(cal rc~ion on ~he~t chromosomc iB (23~. #~ ~ore perplexin~ ~ {bc discovcry, in th~ Iatler cxpcriment, of ~ smaH regio~ ~ilh sy~tc~v correspondin~ to rice chromosome 11 inte~olat~d in recion ~)h app~rcnt 10taI coIi~e~rT~ ~)h ri~ 9 , . . Thr ~ro~iny ~ppreci~1Ton of thr cxien1 of cnnsorvation of ~enes ~d yene ord~r is ~reat ~gn i~c~nt~ ~^chn~ ~e ~< in wElLb ~c think ~bout th~ g~nctics of tbe m~or cereal~ ^s yet tllo lTnkin~ T~n~rm~t~iol1 bel~een difitre~t (ell~mes ~is stil~1 100 sparsc 10 accurato~ pinpcinl candidat~ bomoco~encs exc~pt i~n tlle fe~ cases ~h~re tbe si~m:il~ritias in p~b~notY-p;s ~ra obviolls. Ho~ever, t~his limitation ~T1I lift as ~6rc co~r:~t~ive da1~ arc addod ~ the m~ps ~nd 1he unde~inning koin~r~ mad~ is derIoped. Tbe time ~ Usl approachin~ ~hen thc ~r~sses,)~luding aD ofthe m {orccreal~ can be~onsidcr~d s~ ~ ~ ~ ~ ~ ~ ~ ~ ~~ ~ructurc,geneacLon,mctabobsm.phy~olo~y,andphenotYpe ~ccumul~tcd ovorthepastcenturyInlh~di~ re~tsp~cies/in bopooled. ~D im mediatepr~chcalimpUcationislbJ/brc~deFs necdDoIongerbcrestrict~dtolheirow~spccicsinthelTsearch ~rexploRabl~v~i~Con.Homoco~enesand ~lofthciralleIes in ah specTos ~iH bc av~iIable lo ~ ccre~ bFeeder/~enelic cnyineorofthe eady 2Istcentury. Tbee~entto which ~ teny w~ beause~Itool ~Fou~bout aD crop speci~ hasv~tto be delermined;ho~avcr,evi~ence ~rsimiT~r consorv>) ~enome relationships are a~eady ~ell d~v~loped in legumes (24.2i) and cruci~rs(26.27~. (hich includ~ th~ m,1n br~ssica cr~ specics and the mod31 plan1 a~ . ~ po~b~ t~ r~ ~r thc monocosdkot divide. ~bich m~ re~rcsc~ I30-200 miL l~n ye~ ~ ~depcnd~nt e~hon (28. ~; ~ sdD open. lnthguin~ p~mpses of conscr~cd re~106s are. howev~F~ boin~ no1cd ~om prcbmin~rv an~l~is of the #'bidopsk ~enomic . . , , ~ sequ~nces ~ts~lt~is ploduced (\V.~R.~ct30~mb:i3, L. ~arllel~l. R. Win<,and R.\iar~cncssen.unpub~sh~d da1~} Th~ impac1 ofth~ discov~ry otconserv~d sY2~nv ~ also mostimport~ntintheconsid~rahonof~enomi~ pro~ams ~r tbc m~orcerc~l~ ~b~atand m~Le.Both of~eses16Tccrops h~e~enomesl~r~erlhan th~ human ~enome:h~ev~p ~r dcc.atonly ~urtimesthcsizaofthiar~bidopsispen~mo, m~ors~quercinginRialKesa~ aI~advund~rdi~us~onin China]#pan.Lurope.andtbeL.S.Itis~erypossiblethalthe ~enomesot maTz~ and whestc~n both he dcEnedcompleteR byap/~ ~. ~e~7 ~ ~,~ CambrTdg~ LaboratoFy, C~mbrid~e). pp. 493~498. 3. ~-Berh~n ^.. Nulb~. S. H~ Builer, L G. ~ Benn~n~ ~ L. (1993) #~r #S #~< 86, 398~. 4. Devurt. R. I..` Ko~bncr. R. ~. ~., ~LTu, C. j., ~tS<L~lluc. 1. S. Ab~. S. N Skipoon~i~a1. ~H'^i~g10n. S. E. ~Tesias~ E S~ b-~. D. P~cCoucb S. R. ~ So=~Us, ~. E. (199i} ~ ~. ~. 249, 349-336. 9. Ocvr~s. K. ~., ~llg. Z. Y. ~B~aIos. J.^ Su:, ~P.. ll~mll^ P.. Rqucs. I). G~nn, ~ C. (1994) ~, i~08. 1 j. Du~ur. P. (1996) Pb.D. tb~sL (Ln~er~1E de Parh Sud. Fr~nce~ ~12. ~ooro, G.. Devs. K. M.. W~1~. Z. ~. ~ G:llo. Y. D. (~1995) [z~r'< ~ , ~ ~ . , . )~. ~ /~/-/~. I3. FcrciF/, ~. G. ~ Lee. Y. (1995) ~r ~! 6~< 9D, 380~88. 14. P~tcrson. A. 1I.. 1~TT1^ \.-R. I.T. Z.. Sch~rt; K. F . DoeblcY, j. ~F.. Fin~. S. R. ~.. Lu S -C.. Sla~s~l. J. ~. ~ lrv~e j. E. t19~j i~ 269, 1714~1 7T8. ~15. Kellog~. ~E. ^. (1998} ~< ^~/. .~. S~f. ~4 93. 2003-2()-T(~}. (;~'z~. ~ pre~s. .~# ~ ~R.. ~ {u. S.-C.. Bur<~. ~. D ~ Ko~a~Iski. S. P.. K~tl;~tr~ C. S.` DeI~ontc. T. ^.. Feldmann. K. ~ ~ Scher~, K. F. ~ W~nd~t j F~ (1996) ^< ~^ 14. 380-382. N~amura, Y~ lnou~. T., An10ni0 B. ^~ Shima~o. T.` # ~^ ~ . ~ /~. Chen ~.. S>tn~;guel. P. de OlTveir~I. ^. C.. W~o. S. S.. Zb~llg O~ ~in~, R. ~ ~ Benn~1z~n, J. L. (1998) #~. #< ~ (< {~4, in press. 6~le. T. Robods. ~ <^ta, N., S~kt T. ~ Yoorc O. (1997) ~e'rr'2~ ~147, 801-807. Wecd~n, \. F~ ~uchlb~r F. J. ~ L~d~n^. G. (19~) . 83, 123-129 ~eD=cio-Haule~. D.. ~loku~. C. ^.. ~ar L, Dan~sh. D. Youn~. N. D. (1993) ~^ ~. 86, }9~8TO. L~g~rcrsntz, [. ~ ~di~t~. O. J. (199~) ~144, 1903-1910. .agel^c~rantz. [., PuttelilT, j.. ColIpla:nd. ~. ~ l.~te. D. (~1996) #~r~ ~ 13-20 ~ol~` ~. ~11~.. ~)tl7~ ~., \~Ilg. \.-W., STlarp. [. ~. ~ 1..~. W.-1~. (1989) ~. \:~/. J~~. \~. ~} 86. 62()~1-6203. Cr~ne. P. R~ Fr~s. E. ~ ~ Peders~n. ~. R. (199i) # (~j 374. 2~3. 30. V~ D~i: a, ~. G.. I.~ ~.. ~Br~ll\~l-Cox. <.. ~oodrnarl. ~. DoebjoY. J. ~ Wl]itktls R. (1994) (;~ 37. 236-243. S3. Wan~. Z. ~.. Devos~ K. ~.. Liu. C. J. ~ C~le ~. D. (1997) # .~/. 6~:~., in press 34. Si~~[rc~. ^.. Iluan~. ~., Br:}~. D. S. ~ Khtls~ll. G. S. {1996) #r #? J~. (7 ~ ~, 6163-61~8.

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Van. 9~. pp. 1.975-1.978. ~rcb ~1998 Colloquium Paper ^~& ~r ~, pa ~' ~ ~~~ C~ (~ 0~r ^~2 Ala: ^f '~C ~/ GB~E ~ ,, ~ ~ ~ ~- ~d ^~ [. ^~ Ae~ ^~8 ~i. 7996 ~- ~ ~o ^~' ~ ~ ~ Of ~ Jr~ o~ ^~ ~~ ~- i~ 6~ Ha. Grass genocides (cbromosoma1 glutton /gene di sc~ry/genome ~ar~~gemen1/~netic maps/ microcolhnearity) REFRY L BENT PHILIP S^~1~EL~# J1~HENG C^~# ^~N~PR TI~ONOV? REHEEL FRA\CK~, ~D ZOY~ ^Vk^~OV^~ SD~mCO1 Of BiOIO~ SCORN ~] YOCn01^ PLOT ^~UC UCT~r~t~ Act L8#e1~ IN 479073392 ABE Or He mom park studio ~ grass Came structure have bee" Ilmited lo 1be peneralion of ~bole~genome genedc maps or the One structure and sequence analysis of single genes or gene fluster. ~ brave investi~1ed large Wondrous segments of He Gnomes of Malay sorghum, and rice, primarHy focusing on lntergenic spaces. Our data indI- cate Hat murb (>50~) of the maIze genome ~ composed of interspersed repetitive Dada, primar1~ nested Trots posonsthatinsertbeD~eengenes.These ~1roelementsa~less ubundantin smaller genome plants>~nc[uding rice and sor- ibum.~Rboupb5-to200-kbblocksofmethylated~presumab~ beterochromatic, ~trotransposons flank most maize genes, rice end sorghum genes are often a~cent.Similarge~nesure cam money ~undintbe same rela1ivecbromosom~1 locations and orien1~1ionsin each oflbesetb~especies,~11houXbtbere are numerouse:~ce~ptionsfotbiscolll~nearl1y(~.e.!rearrange~ ments){bat can be detected at Elevens ofDotb the recom- binat~1 map and Toned ORAL E~oludonarBy conserved sequences a~ large" conOnedlo penes end fLeirrequla~ry elements. Our results indicate lbu1 ~ kuo~4edge of grass genomestructu~re v~llbea use~ilool Air gene discovery end isolation, but the general cures end biological signiOcance of grass genome organiza1ion remain to be determined. Morel oven the name And Quench of e~ephons to the general pa1ternsoT grass penome St~C1U~ aud coHinear~v a~ stat gun and ~ll~qui~ ~ensh~ Hers tan. \~ryli1Uc~kno~n about thc~uctureoT1b~nuclcar~nomes of bigger plenty ~Ithou~h compr~bens~e in~csh~abons arc now underwayin10 the sequence compos~ionof the unusualb sm ~l[aboullIO-mcg~basepak~mbpTl~enomeof~ ~D ~ . Most pivot nuclei contain mare than five limes as much D NA as tat of ~ Craning up to 1bc over 110,000 mbEo~f~'z~'z~l).P~>t6:~1bisgenomesize variationisc~usedbydif~renc~sinploidv,but the msiorilvis caused by dibtrencesTn the amours of~epeUtivc D\^ At. Some of tbesc rcpe1~\c sequ~nccs are Fund in tandems repeated satellites. lee the chromosome kegs of maize <3), but most are represented ~ interspersed repeats that vary in copy number Mom t~nslo bundredsto thousands per haplold nuclcus(4j.Tben~turo and or~'n~ahonof these {peals and thok ~nct~nal~rstruc~ralr~abonshiplo gODCS. are Novell understood. Lo~densRypencl~ m~ps^1ncludinythosc ~rseveralcereaT species I. bave abort that conserved Dig A markers (primsci~ ~enes~ohen ~= Pundit the same ~ncarorderin different plant species. This discovery of the colhncarLy of ortbolo~ous~ genes 6.~ 1boso with a direct evoIotionari~ 1~8 ~ T>C #~ Loamy Of ITS O<-~/~#i~-4~.~/O P\/\S IS 5~11Gt)12 To: a!: l::tp://~.l>~l~.~:~rg. relationship) in cereals has filmed ~ whole new persp~cdve on ha Ices and information can be used ~htk~l~ in the sag and improvement of U1 grasses (8-10). Although maw except~ionsto collinearity cx:isl~in these comparative ~e~netic tool far botb gene discovery and gene isolation. Or. colhnead~ providrs~nopportunit<10d~coverbow evolution has premed new morpbologies, physiologies. patb~ay~ and speclcstrom thesam~setofstartin~ genetic m'1erist Rec~nl ~dv~ncesin ah tccbnolopies needed 10 ~enerale near~saU~tedr~combinatlon~lmaps.indudin~hnaslfuctuFa m~psof~en~ dust~rsandla~e(>100kb)donedsegmenlsof cbromos ~ es. Yield our Fat delayed insights into Abe evolved structures of compIcx plant genomes~In addibon, DbL\sequ~ncingtechnologieshaveimprovedfoalev~lwh~re ondguous venoms sequenced covering multiple genes and ntergenlcspaccs.can bc ~ener~tedrapidIysnd atrcasonablc COSL Webavc decidcd 10 usethesetechnoIo~ies 10 invesUg~lc 1hecomp[ex~e~om~sotmalze.sor~hum.~nUdce.Thesethrec . ~ rassspeclesw~rechosenpart} b~causcofth~ir~gronomic import~nceandgenetich~lorY but mains b~causeoftheir d~if~rences in Broome size (4~0 map Air {ice, 75{) mbp far sorghum and 2500 1~bp ~, adz) (~11) and tbe~ir Lean p~lo~cnetlc relatedness (I2j. Our dale indicate thst ~ coma . . . ^ payee analog of arms Venoms wO1 be tremendous used. but that conclusion: regarding tbc most e~cienl rout to ibis sy~llcr~islic knowledge acqu~is11:ion now require ~ddilion~l c~- . . . .. perlm~nts on local yenome structure and evolution. MATERIALS ADD METHODS blaterials.The nature and sources ofYe~slard~ci~IcbTo~ , . . mosome clones from maize and bacterial ~rtiEci~1 chromed some {BAC) clones from sorghum alla rice have bean de- s=~ed (1~15~. ~didon~I as containing J~) . a, . , ~ genomlc1~^ acre obtained Mom the J ~~6 Biological Resource Center at Ohio State [nDers~v. Gel Blot ~#bridizatioa, Restriclion \~,pplng, and Data Sequencing. G~nonlic and cloned D\A isolation. go blot anat~i~ndbybAdizabon~rc ~lasdescrib~dprevious\~14. 16~. Restriction enzymes were used accordin/10 the Annul Actuary recom mendabons.S~quenUng and~equence anaL ysis Hera asdrscribed~j6 TV. RESELTS lbeStru~u~ ofa )1~^ Chromo~om ~ Sp~.\Vebavc used D NA sequencing~ndrctroelementstru~ralana~shto ~br~via1~ns: ~C. b~1eh~1 Cal chromosome: gap, m~sbase psl.r. TO ~huld be t~ddl-essed. -mails male bib. bl.pu.rcI<~e.~dl~ ~ ., ., ~ ~ .. . ....

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1978 Colloquium Papyri Benne~en ~ ~< In maim (18~. su~shn~ that equals large blows of act chromatic and met~lated relro~an~osons also ^31 in ~b species. Maize. sorghum. gad rice ma not diner in the nature . ~ , or size of these repel blocks but only in the Squeak ash which they are present between any pair of genes. Wore experimcntaJon ~ needed to ch~rscter~c Gnome organ~a- bon in dcc and sorghum before am comprebensKe conclu . . . Cons can go organ. Grass Genomic CoUinearh, and its Exceptions. ~OS1 in- vestig~tion~ of map colEnearky in the cereals and other plants have used the Hybridization of 1~-co~-number DNA markers Cat am USA In. Bow c~l^~d~ Ad ^ Than observed. appear to be limbed to genes. Akbo~b co~p~ratir maps ~ we grasses sham laF/o fins of c~I~e~i#. ~o~mU a a ~~ untie arms or sc~mcnts of arms are not uncommon (5, ~ 27~. Particulars confusing ~rcomp~rative mapping sludies~ro ~dislant~t~d~m~duplicationsthstpl~ce~es~me makers orUncar~rr~ of markers at 1~0 ~e[~separatadlocationson hOs~mechFomosome~rm(28~.Tb~sel~Fgcrc~rr~n~cmcOts arc no1 n~cessari~ problematic, as chromosome walking 10 done a gone or mapping 1O iden30 ~ Prolog Gould be hindered only if the i~esb~ated area crossed one of the brc~oints of the rc~=gement. However, comparisons of rccombinaJon~1 maps between kiosks related plant species omen viola 20-40~ of the markers . , that do not 611 info am odious coBinearLy, or even gantry. relations (IO) Abase makers are usual 1~5 oF of the comparator maps to simplify the prcsont~don. Reports of colEnearky and orgy between mapped Genes Including ~>L\ markersand morpboIogicaltraits)~lso~rebias~dio~rd tbesuccesses.Failuresaresimplynolreportcd,parlp because ne~ativeresultsrare} recede attention and partly because a laCkofobsc~vedcolUne~kycouIdbecaus~dbytcchnicalerror orto an inappropriate co ~ adson between parlous rather than Portholes. Gloomy CoHineark, as ~ Tool far Crop Improvement genetic m~lpcomp~lrisons m~l~ke~ilclesrlhatge:necom~positio~ and ordeF.oth~rwbekno~n as mspcolEncarhy, ~ com ~ n On plant p~rEcul~rlybet~centb~cer~ls(3~10~.lnsomo cases,tbiscoU1nearhy mayextend oven b~t~co~ monocotyle- donous and dicoty~donous plants (27~. However. many ex- cep~o~s have been ignored and local re~rrsn~cment (.e~ m~ocoDincad#)h~snotb~cne~ensRe~examined. Withal scan Stack otcoUinear1# been m Size and dcc donesin 3~7-homologoosre~ions.~4~rocolDncaFi~ brews ~ ~~> /~p~) and ATE monocotyledonousplanl may borate. A1tb~ ~ ^> a. ~ A_ Ha. .^ ~? . ~Bennc~eD. J. L ~ FreeEng. Y. {1993) #~^ We ~ 2i9-26I. 9. Moore. G. Gale. Y. D.. Manta, A. ~ F1~. R. B. (1993) ~/73~-z~# ~1~1. S84-i89. Bcnnetzen, j. L. ~ FreeEng. ha. (1997) ~ am. ~ 30J<06. #~u,anatb=, K. ~ Earls. E. O. {1991) Adz +< #! 9* 208-218. 12. Doebley, j., Durbin. Y~ Oolc~bc~, E. ad., C1~. Ha. T. ~ As. D. P. (1990) EM Ha. ~1 097-1 108. Spider ~ ~ Ld^~d~ ~ ~ ~ BE ~ L (~2 P~^ \~.~( OCR for page 1
am #~ ~ ~ ~ Yol. 95. pp. 1~79-1982. ~aFcb 1998 oquTu~ Paper ^ ~ ~ ~- of ~ co~~ f~ <~g 0~r ^~ ~ : ~ #~c ~' Em ~, >? ~~d ~ ~ ~- ~d ~ a. ^~\ 4~ ^~ 2) 7996 ~- I/ ~ ~ iC2~ ~' ~r ]~ ~ ^~' ^~ Over /~ If ma. Do~n-regulat1on of I, the ^~F homolog of Are, Pied Eta panicle branch 1nihation JUMBO KYOZUK^~?, STENO KON ISHI')$, KEI~St] KE N ERGO] O~ES1I I ~I/~A'7, ^~1~) KO S{1~1~[ 0~ '~L~bo:ra10~-y of P1~T11 ~ol~cul~r (~Se1i~1ics. N~:~a 1~I1StT1~u1C (~] scieIlce SIllt>~,v~ S)16-5 l`akav~l~l~t. l~k~oma, -1 .~T)~11: Stall. >13~i\'CTSitY ()I l'()kY(~. fly of ^gr:icLIlttlrC~ l -j Royal, ~Bt':n~o-ku, 113 `1~P~J1 ABSTRACT ^~ #~) of ]~~ and #~ ~ ~ the ~rmabon ~ Bong merbtems. To ermine wbetber same me~banisms control floral d~elopmen1 to distantly related species sorb as grasses, ~ isolated ~ )~# homolog of rice, and examined its expression and Anchor. ~ortbern analysis so ~1~ ~ ~p~- Ding ~ ^ panicle but not in mature fiords, Moore leaves, or roots. ~ `^ ~brldization rarefied tbat ~ R\A gas expressed in epiderma1 cells in young leaves at vegelative growth stage. Over the t~nsi110~n to reproduct1ve stage, R) k\A gas detected in all lagers of very young panicle including the api,~1 meristem, but absent in Me incipient primary branches. As development of brunches proceeds, ~ MA ~ccumulat10n lounged in the drooping bunches ~1 far the apica1 mer~1ems of the branches and secondary blob primo~la. impassion pattern of ~ raised ~ possibly that, unlike #O and {^ ~ might be involved in panicle bunching. T~nspenic ~6 ~ plants constRutivel, expressly ~ Mom (be cnul~l~r mosaic virus 3SS promoter Ore pro- duced ~ test whether 35S~ Quad cause ~m11ar pbeno~pe as observed In 35S~F plenty In 33S~ plant` tensor motion of inflorescence meristem 10 flo~1 meristem Is ~~1> observed. instead, development of cotyledons, rosette leaves, pe1~1` and stamens Is stereo affected, demons an fba1~ function is distinct Mom that of [^ Our results surest that m^~nisms controls Do~1 d~iopment In rice might be diverged Mom that of ]~4 ~ and <~- ~. 6~ is a lard and variable Amid. away stores of flower d^clopm~n1 and mature architecture of grass floors and inf}orosccnces arc distinct from those of dicots. Allb~ngb our knowledge on the genetic NetBIOS g^~mi~ inaction and mo~hog~ncsR of Rioters increased signi~cant~ in 1be last s~cr~1 yeses, Iitbe is known about molecular mechanisms conlroUing floral development in grass species. Understanding press Pear d~pm~nt ma oar amoral insights info the genetic and d~velopmcntsl bases of morphological evolution among the plant species. Rice (~ ~~ Lj has several ~dv,nt~g~s 1h'1 make ~ a good candidate as s model species lo stub molecular basis of grass flogger development (1~. Rice ~ ~ discoid species Ash ~ sm~[1 Venoms (430 ~b/h~loid), and analyses of the Ace Rename and cD\As hag rapids pro- pr~ssed (2, 3~. Moreover. tr~ns~enic Ace plants can be rel'- dv~p easily produced -mediated lr~ns~rma- 1ion (4~. Genetic and molecule studies with two tricot plants. J~ ~ and J~~. hoe Ghan tab the Fanatic network . . . . . . PEES iS JV5~1{lb1C (~111~Te {1t 11t1~17:~/ /~ {)I1aS (:>~S conlroDi~< flier d~v~lopmcnl is conserved at Icss1 in the two dicta species (~73. Stag the transition from vegetative to r~productRe deveIopmcnt. floral mer~t~ms are iDid~t~d ~ the Don ofa set offends called floral Moslem ident~v Boned Among them. FILLS (~) of /~{ ends ~~2countc~artLE]~!F~ scemloplayth~ mostimportantrole Earths eslablishmcntofflor~l ~te.ln slrong{S and 0# mut~nlplants.flow~rs~rctr~ns~rmcd i~10 inflorescenceshoots(8,9~.~/~Fencode putativ~lran~ S=iphon Pacers ~ ~ donotsbo~sign~cantbomologytoany knowngenes(8,93. To understand molecular mechanisms controlling floral meristeminiJalionandinflorcscencestruclureotrice~ehave Lolated6F[.tb~/~7h~mologotrice.and~al~cdits oxpressionand Unction. We ~undlhatibe ~nctionof~F! distincttrom that of [~1( Our ~nslysls on ~L expression sbo~cdth~1ilisllnlikclytbat~E ~ absolutes required far floral initiation in bcc instead, the expression pattern of ~FL suggests its possible i~o\cment in panicle bract. Our results shag that Me Endows obtained Tom J~~ and ~ .. ~ my not be amply applied as a general modal to other distant} related Decals such as grasses. ~DERIALS (D METHODS Construcu~n and Screening of cD~ Libeler>. To construct a cC\^ library. 10t~1 Ram was land from young panicles of rice (~4Z67 \~as) . . / , ..

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~22 Colloquium P~er:~adienssen ~uuicopyandSinple~Copylnsert10~1~utagenesl~Inscr~ Con~mut^cnes6=presentsapower~lw~todel~rmincthe ncdonofplanlg~6esidentibedin ~s10~aEcgenomeand e\pressedsequrnc~tagsequencin~p~jecl~ Essential6,t~o typesof~ppro~cEcanb~considered:~)theuscotpl~ntsw~b higEco~ numbersothighlyac~veLansposonsparyenomc and Abe use otpl~~ limb a singe cow ofa goon ~osonper~enome Ine~chcase.~co~eclislorec~er a1leastonein~rmaliveinserhonpcry~ne.Higb-co~ methods h~otheadvantag~lhalrel~t~elysm~llpopulatIon~otpIants needlobem~ntained~rcomplete~enomec^cr~^SingL- copymelhodsrequiremuchlar~crpopulations~buttbOyhavc anumberofotbera~anla~os.First~ngle-copy~ansposons coo be usediointe~r'1ereporter~cnesin101he Gnome, Howinggene ~pressiontobeobservedaleacbinte~r~tion. uldco~ ~po~ergeneinso~10ns~o~dh~em~cUpa~erns , . of expression. Second, ~le-copy lr~nsposons ago can be used to integrate gcnatic and physical msrkersinlo 1bc gc- nom~, avowing their use in m~p-based penomic strategies. Fi~n~lly,si~D~le-copy transposon i~nscrlio~ns can lee sequenced dRectPlbusreducin~tbe number oYm~nipul~donsrequirOdto isolateinserdonsin ovary gene.Jb~se aspects ofsin~le-~nd muLTcopy systems are explored below with r~spcctto trans- poson Ash main made and ~ a*. Site-Selected Tr~nsposon Mutagenesis in Maize. Trans- posons have been used aided to generate populations of model organisms (Ubrariosj that can be se~rcbed far those individuals web tr~nsposonlnserbonsin anv gLen scquencc <26-32# Scabs arc performed by ampli~ing D\A Mom these popUabonsbyusiggspeci~cpdmer$ Mom ~etransp~- son gad Mom the ~enc.Fos>Rc pools are rescreened by jib selOctiontoidenti~indKidualstbalhave the desiredinseFdon. Tob~vca95~ probe of~ndin~aninscdionintoanYgcnc in If Is, C ~ ~ (wbic~b gave Similar Venoms sags and gene den(1i^) such ~ l~r~v needs to contain ~TOO,OOOinserbons(32~.F~enso,mostin~erhons are into noncodTn~ regions and have no phenotypic entcL SOc .. . . onuary lOserbons or deletions must be generated at rho lows ~ remobilizing the 1r~nsposon to disrupt gene function (28 30~. Swear methods hoe been developed far Lol~dng insertion alleles in maize {30~. For Sample. sac used the Robertsons' boor system of 1r~nspos~ns as inscrbonal mutagens. ~esc ~anspcsons emit in hundreds of copies per genomo, subdi~ aided into six classes that share 200-bp terminal inverted repeals but aft otherwise unrelated Transposition is ~dh~ 1a1Odbytbc)~z~R~u10nomoustransposoutb~tencodes~encs required ~rtbelransposkionoftheoiborRober~o~'sif)~r 1r~nsposon (if~)elements<33,34~. We used i1~ Halo isolate nufl~Leles ofthe maize cane /~#d*~bicbencod~s~ch~rop~slpro~ininvoRedin ~ m- branebiogenesL(35) Thcre~Fencc~Dcle~11heD<~blocus bas ~ il~7 e}ementinsor1cd in the promolcF region, much resullsin a farm ofepig~nct~ instability (36~. We reasoned ~1 deletions and inn ~ions[nto tha Ecus would l~e~ be morcstablelhan1bc ori~inal~hele(33.34j.\Ve used ~ PER strstegy to isolate derivatives Of ~ ~ ad ~ screening t~o- dimcns10n~1poolsofseedlIn~sbyusin~primerstrom they cE mentand Mom Me D~\7 gene <3b~ Ibree new alleles mere id ~ aged. ibis first allele had a 200-bp delc~onthatremovedthe Frst~xon ofthe ~ene.Th~ second ~ndth~daFel~s,bo~ever.hadne~inserbo/> off ~nd~z~R^resp~c~v~Iy,insertedattbes~me~locationintbC [rstintron ofthd -7 and ~ild-type gencs.respec~ Meld The ago derogate whelps mare no longer su~ecito ep~geneticinst~bil~it:y<3o). 1~ method can be u~edto ~ol~telnse~ionsin any Ova\ sequencointh~ m ~ze~enom~.eventbosethatmighlbel~thal ortboseth~tm ~hthsvenoph~nolyp~ consequence.~other ~dva~,g~ ~ that ~er~mi~al excisions arc vary rare in #~, Sac #~ J#{ ~ ~ [nes(33,34),son~waDol~sarc1Ypic~UvstabTeinthlssOnse. ~ m~ordis~dvantagcL1hatma~ (perhaps most~inscrbons w]I~glnintrons and olber~nkin~re~ions.Thcseinserbons ypic~[ycon~r~e~korunde1ccl;blopOcnot~es.Inlhese c~scs~our method can be us~dio pcncra10 deletion and sOcond~ryinsertionallelesin order tostabiL/e~ndenh~ncc am mut~ntpheno1~e(36~ Our resubssho~th,1no~ins~ionsintomak~genes can be , . .. ~ 001aln~d from a very smog sample size {2 insertions into I,JOO potential cbromosomes screened). Pioneer HLBred (Des goings IA) has developed a far) coEcchon of pooled [~es to enable PCR screening of a standard array of ~ Tommies, each corresponding to ~ selEpolEn~t~d parent plant (R. Reels Ad S. Brand personal co~municabon). n~l~od colIecdon is a very useful rosour~. pr~ided screening procedures are used that conserve OF samples and seed stocks after n~oltip~lc~ screens. However. our results shod that a few thousand ~ seedlings cs~ be screened e~cicDt} lo obtain i~inscrGonsinto~cnesidentiC~d by sequence ~ono.[ysel~poUinahng t[C pla~tsaher DbL\ bus been coHected,the D>L\ pools can be scrod repeats we pdmc~ [~m diddrent genes ~ ~ Gus ~ Zinc far indivlduallaboratoricsto perform sLc-selccled mutagenesis on a mana~eabl~scale(30j. Enbancer and Gene Trap hlutagenes~in~n~D One Caps and enb~nccr traps arc reporter Bangs that arc not norm~lvexprassedunl~sstbevareinte~r>cdne~ror~ilbina , . , ~ cbromosom,1 pane. Enb~ncer traps are equipped with minimal promoter tat can respond JO nearby cnb~ncer~ and gone traps ma equipped with a space acceptor ~ that inte- gr~don ~itbin inures leads 10 ~adlb~u~ transcription Ad splicing (37-39~. In each case. the expression of the reporter gene closed mimics that of the chromosomal acne. Large coUcchons of Whiner ~ Ad gene ~~ I-< cacb carrel a unique reporter gone insertion somewhere in the Gnome. ha been est~#sbed in~^ Ad in He mouse. b~ are being used extensively far bate drelopmcntal biology and demonic research (40, 41~. Me hoe devised a System far gene trap and enhancer Cap tr,~sposon mu1~gonosis inapt ~ (12. 42~. We arc using ~nsposons (~) from maize 1bat ~c ham cncL neared to caky a ~^ [~-glucuronidasc (~LS)1 reporter gage and an #7~ kan~in resistance cane. In our WE fens hanccr trap) construct the reporter Fine ~ preceded by 1hc -46 region of the Ca~V 35S promoter, which bus been shown to have no dotect~blc 1ranscription~1 ~ctKEv unless ~ is in tbc v~in~yofsncnhanccr.lrour~enetrap~construc6UlC reporter g~nc~preced~dby atripl~sp~ccaccep10ra~d ~ a shortintronsotb~tinscrbonintochr~mosomalintronsIe~ds lo r~portergelle expression v~ia;~T1:crnate splici~n~in each reedit ~,meti2.423Ad~lion~Ispl~c donor skesin~c end ofZ~me~nsth~1 reporier~eneexpF~s~on aRocanresub~hon be[~clementisinsorted iD10 ~nexon(43~.Thecl~ments . ~ . . . are moUDlzedUycrossestotrans~enlcpIanisc~rryin~r transposase~cne ~)~ansposasedrTvenbv1be333promoter from Cs~iV.Thisresultsin high ~cquenc~sofiransposkion early in developmcIl1~44~4ij. TTansposed clemonts arc sag lamed by using a postage marker ~)hinlhe ~\ elemen1(th~ i, an, . ~ ^~ ~cne)and a neonate marker a~acenttoi1(thc Nancy PosbRe-ne~at~eseL3ion on naphtha Cane ac~t~ide and kana~rin resulisins~cdli~sthat~averetain~d ~c elemen1butlostth~ donor ~tctrom ~henceitcame<42.46~. Because selector depends on r~combinaDon between the anspos~dolemcntand ~edo~orsbc.thotransposcd~I~men1 ~ almost~l~aysunlinkedlothc donoFIocus. We gave Lund tb~t90> of~enetr~p [ne6carry a ~n~l~tr~nspos~d Clement ~tesscrtia~yrandom loca1ionsinlhe~enol~e(423.Th~ other (nOsbavemnbipleelemc~ts{3~)ori~serdonstha1disruptthO n~a1~ marker OCR for page 1
Colloquium lSapcl-:>iarlie~rlssc~ . . retorted 1c Susan ET (enhancerlr~p) or FIT (genetrap~line depending on1be ~ansposon. Tbob~cl~rialgene~4 0~1ha1cncodes ~ LS hasboen the Fcporter Echoic far plantsludics and is used in our system (42.47) Akhou~h there ~ very h1~ background in plant tissues, ~ US is inhThi10d by oxidation c~lsl~sts that . ~ . . , Prc!en1dlflu~l~noftbeind~oreactionproductsb~redimer~ Ha, ~^ ~ ~ s~~ ~ ~~ cision. Nonetb~l~ss.1be hugevaricly of~eryspecIEcpatter~s that we have observ~dindic~testhat ~ USisa~ efiJentaDd reliable markergenc.R~cen16, Hhin~encsf~[owin~i~ rti~ctualT~nsertionsinto selectable marker~on>~.Simi~rlv 4i~ of ~Dbancertr~p unserious age rise ~ reporter Icy . . . . ~ expression in seedlings, but up to 80/ ~ rise to reposer expression some~berein the pla~1.Thes~numborssoem blab. butin Scathed arc notinconshtcntwith~enedens~v~shTn~es . , derived Mom genom~seq~encln~(one 23~kb gene every 45 kb~ori3~ith only ~sh~btbi~s ~rinserhonsintoCencsts bias that b~sbecnobservej far ~nsposoni~serd~sln may c!~anisms~ ~ hsvcr~covcrcd aveFy ~id~r~n~c otc~pre~ Con p~tler~s,lnclodin~ y~ncs~xprcssedinspeci~cc~lblyp~s. e~esexpr~ss~dinceDsnndergoinpcoN dragon arch deslb, .. . . No genes oxprcss~d in prep~t1crnslh~t predict rath~F1ban reflect morphogoD~s~inth~pl~nl.A ~ 3~'mplesare~bo~n .. ... . last. I. Systematic Insertion Site Sequencing: ~uR1~ vs. S1ngle- Co~ Libraries. As d~s~ib~d abbe. [brari~ of plants that bee one or mare transposon i~serhons par plant can be reedit screened tar insertions into genes ~ inleros1 ^ silo . . . . it. sel~clc~ mules lhk approach involves pooling file plants and doing hundreds of PCRs far each When {enc. [low~ver,if most fifths genesis a goon become are to be 1a~ledinthL ~a~,ilisco~siderabF mor~cficientlo obtain . . , 1nse~10n ~l~sequenc~ ~s{oma1Tcal~lnstcad.Each sequence only requires ~ b~ndful of PCRs 10 obtain in tag Rev (see belong. The database ofsequrnc~s can then be scree;ej by computer ~rinscrbonsinlo gencsof interest in principle.both muldcopylr~nsposo~3brarlessnd~inJr- copy Ebrariescan be us~dlo dovelopinser60~ skesequencc d~tab~sesofthls sorL Ther~lativ~ merksofe~ch method are ~xpIord b~lo~,t~kin~tbe i<~ Moslem in mains and the gene 1rap system in ~ ~~G as examples. Ofcoursc.th~ principles apply squall to other mulUc~py and sin~[~copy approachesin each species. Curator insertion Otis in maize can be sequenced Tn a Thematic way.lndividu~1 PER products Mom multiple ele- menls arc obtained by one of a number of anchored PCR appro~cb~sard are displayed byg~lel~ctrophores3.Individ- u~1 bands are excLed and tbc products are purified far s~quencin~.Ih~id~a klobuild up~c~l~lo~ofinser60nsinlo recognizable ~enessoth~l~ctcd ~ m~icsc~n be examined Arabs ph~nolypic consequences ofa gRen inserdoI~ Ho~- ever.~umb~rotproblemsmigh1beanbcipa1~d.FirsCsom~lk lr~nspos)ionsthat~ro~ttraDsm~t~d~ermin~l}~lso/)llC~d lo7CR produce These w~lnolb~re{cse~ted ~ tb~pro~e~y ofscl~ct~d Tactics. Sec~d.eachpl~tc~rriesse~rsT hundred fang )~? /~ Act 63< Hi #~( 2023 insertions and typic~#yabandf;Iofv~ible mutalions.SorLn~ tbrou~bth~ mutaUonst~determine~bichphenolypcis cause) by~hichinserdontak~ssevcr~lp~neration~nd {uLiplc[CR reschons. Final6. manyinscrU~ns ~reintointrons and nor- codinGregionstbataredificulftoreco~nizeinthc~bsenceof ~tem~dc~bole-~cnom~sequencin~.Ampli~cabonotcD^~\ by rapid ~mpE[c~tion of cD\~ and and PCR mill be pre~rableinlhi6 ease. . ... .. , LDC ~uJ~co~ appro~cb ma bo necessary in gage becomes 1lke maize when plaudit ~o~tl1 space is limiting l~ec~usc a sm lit bbrsty of plants can barbor a large number of elements. .. -, . ., ~ow~!q Ha. ~ 2. sin~-c~pyappro~chesha of sl1 ~illsc~rl~in SilCS by ~l[~inc ~ hierarchica} tiered procedure by Isle a minima~number FCRs.TI~s~ productsaresequenced dkecdy without Ocher resolution on gate The aced Tom each plots stored and c~l~logucd.~ndthes~qu~nce ~ ~nter~dinlo ~ the gene trap datab~s~c~n be used 10 in~rlh~ .. . .. . uncllon ~~ 1n maw cases tab pallors of and expression associated with mosf of the genes in the ~> Venoms. A metal- all in labs ftllure-~ill be in o be addressed dirty. That a. combination~ciins~r~onsi~d>~rcntm~ber ofa m~ld~ne Amid can be made bycr~ssi~dividu~llinesto~lber.>b~ approach can be ~herreLned by ~ombi~i~ser~o~sin

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2024 Colloquium Paper: ~articnssen ~S nit 1! Ilk FG. 1. IN of =~hcr steno e~rcs~on ~e) ~ Adds Sac Cap and enhancer ~ hen Gus cell ~po-~Ec ~pr~sion. exp~i~ in ~epa1~s, Ad Or gene ~ loc~iz~hon. Sacking Hera ~ ~ continua Hilt far 7 jag, ~d far GES acting, geared in 70> ~tbanol, and mounted far dl~rential inter~rcncc contrast micr~sco~ in 25~ ~IyceroT (i2. 42~. Pi Nuclear gaining (arrow) roots Mom bcie~zy~0us~/ + plants (~) ~crL1em s1~i~in~ in the shoot. ha) CLS c~prcs~on at 1hL basal bound~dos of Jag primord!~. <~) GES Preside in coJumella inks in tbc root. JO GUS ~press10n in root cap cells. ha) OLS expression in immure 1richo~es. (~) COS expression 1~ 1rlchIne accessory calls. g~ncsthat~~ expressed ~ (mbarbssues and might tberc~re be expected to have overlapping roles. For example. an ~nhanccrtr~pinsert~in the ~(DLS (agsmousqlkc) hi~dDS box Manse lotion [~torgene ~ cypresscd early duringinflo- rescence development and late during dc~elopmeIl1 o~fthe UiL in agreement ~1tb RNA expression studios (50) Ho- mozygous ~ ~ )-7 mulantplantsbavesnul1 mut~lionlnthe J(LP? acne and only have ~ fruit pbc~otype (O. Cu. C. Fcrrandiz, At. Yano~ky, and R..{.. u[lpub~lisbed Works. However, when combined with mutadonsin rclalcd ~i) OS box genes expressed in the earIyinfloresccnce.~ r~durds~t rolc ~rtbis geneill ~cri~slem ~idcIllity is uncovered (C. Brandy. O. Ou. R.~.~.,and at. Y~o[~,unpubEs~d observations). LetbalInsertions.Transmission studies using deficiencies indTcaletbatat1oastlgene ~oryI00 ~ isessonlialtothc baploid ~2 gamatophyle and/or the garb diploid embryo til).ThL me~nstb~t~k~2 b~s1,0003 000 essentialgenes.compuredw~b2000inb~ploldy~ast(3.43. EssentiaIgencs arc ragoi~d ~rccH~ro~1hanUdivi~on,so ~T~ostaU'rcexp~ctediobavca ~nctionelsewbcreinibe diploid plant bot(I23.Ho~err,~^lt~nctionsof essential genes cannot tee assessed ithomoz~ous mutants do not survivoto malurhy.Oeneir~psand~nhanccrlr~pscan~ive somcindTcadon of these adult Mentions because ofTepo~or gene Impassion in viable hetcroz~otes. Somatic mosaics and secondary screens then can be performed lo confirm those roles. be ability to idonti~ essential pcncs with colas in later d~elopmenl bus prawn 10 be one of ah most lmportan1 applications of onh~nccr traps in ~ developmental biology (40, 52~. Lethal insertions in /~6 can be letbal abhor to the diploid embryo or to the baploid gametop~te. They arc id~nl~icd ~ opening selLpol(~ated Piques Tom h~tcrozy gous ~ansposants under ~ dRsecdon scope and looking bitetratberth~n ~reen~seed orun~Hized ovul^,respec- 1Re\~12) One apropo~ion ofl~th~I mutations recovered ourscreen~r~c~u~cdbythotransposontunpubILbedresull$> These exhibit s~grogationdls10rtion ~rthek~namycinresis- tance gene contend Bin the Zig clemenl(12~. Letb~1 mut~honsca~sed ~tb~ansposoncanbeconbrmedreadi~ bytr~nsposon~mediatedrevcrsion.Each1r~nsposantwithre~ ducOdsoedsetistest-crossedioplantscscryi6~r.FIplanls arelbooexamined ~rthepresenc~ofoccasionalbranchcs w:ithfu~llSeedsOt<12~.T~hism~s~icTs~mro:f~l~ctssomalic~x~c~ision oftbeZ~elomentandLavery~ron~indica1~0nib~ltbolethal phc~ot~6causedby~inscrdo/~12~.Tbe~genc, and01h~r~nesinrK~dinceDd\Lioncy~econtrotare~od HIus~aGons ofessen1Tal ~neslhalhave roIesthrou~bou d~vclop~en1~12~.~ ~ncodesabomolog ~ the CDC?~7)DNAreplicationEcensing~c10r~omyeas and m~mm~i~nceDs.I1~'sldentib~das~lethaImutatio~ caused Babe insertion ofZ~inlolhe}ast intron ofthe~en~. I~viablehe10ro~01es.1boresulUrgrcporlergone Adonis }oc~lCdinthenuc}eus~sexpecled~raO~^r~plic~1ion~clor (Fi~.T~)'ndisexpressedwidelyindividin~cclls(T2). RemobiCzat10n: ~osal~sand Local ~u1~penesis. Unlike T-DNA andotberlypesofinserUon~lmu1~en transp~sons canbe ~mobEized ~ rc~nt~du~ionof~e BIB -l~ns- posasc.TheresuIh~rerFsionofthamulationcanbeusOd 10 con~rmlba1il~caused ~lbetrsnsposon.R~m~ilb~honof tr~sposons~socanbeusedlogeneratcpbenotypicmosa~s. Thati~homozy~ousmutanlslhatcarry8cwRlh~v~somatic sectorstbatb~elostlb~Z61ran~oson ~dsoh^ OCR for page 1
Colloquium Paper: Ya~ienss~n #^ Venoms. In cases in which ~ transposon bus integrated near, but not Cabin, ~ dusked acne. it can then be use as Launch pad' ~r local mutag~esL. This ~ because Jr) tr~nsposons, in common gab most eukaryotic inver~rape~t ansposons.havos pronounced pre~renc~to integrate Bobbin s ~ ce~timor~ans of their sturdy location afar transpose don (33, 54~. We demonstrated the tcchnTq~e inducing new #~ lr~ns- poshions around tab ~~ gene on the short arm of chromosome 4 (C. Yordan. J. ~onl<~ D. Busb. P. Spr1~cr. and R.... unpublished Wok ad rag 467 Simon ~eque~- dcs am so high (44; ~) Cal local 1~sposidons cay be rechewed ~ selecting far the 1r~nsposon {kanamycin) and against ~r (napthal~ne acetamide). #~proxim~l~ly ones quarter of the selected plants hoe We or more transposed cJemcnt~ and the remainder retain tbc p~rcn1~1 elc~onl. Pooling strategies similar to those described far maize (30) ado the recovery of trsnsposons into nearby regions ~ v21uc of PCR-medi~ted silc~sel~clion.Tbisr~mobUizstion strategy ~Ho~slaunch padsto b~usedfo d~ruptgeneslb~tbavebecn mapped ~enc~c~l~ to any h~enomicandexpressedsequence tag databases wig agog thelocalion of evil insertion to be determined gab nu~eotidc pr~ci~on, aDo\\ng tbeir use as tools in poslbon~1 cloning as Deli as in aide scale gene dlsr~tio~ ~ examining reporter gene expression palter~s in Viable beleroz~otes, the role of Essential bangs can he assessed in later deveIopmen1 cvcn if insertions are homo/v~ous or baploid lethal. ~ combining insertions in homologous genes, the anchor of rcd~dan1 gongs can be assessed also. Iacknow}edgeth~ pBS1 andpresc~tmemb~rsothislaborat~ho h~econldbut~d10thL ~o~.pa~iculady P.Springer. O. du. c. Yo~an.J.~onts~u.J.STmorowsktR.Benlon.andL.D~ F~lw~s assembled ~ P.Sprin~cr.Th~ d~v~lopmentofth~ gcn~c;apta~ da1'baseisacoJ~toraJon~ith W.Richard ~cCombi~ndm~mbe) ofLisTabor~lory.Tbe Chid Sp~n~Ila~or Laboratory ~enetr~p Alum wssderiop~d ~ R. ad V.Su~dar~an.Jh3\o~ ~# Supported ~ ~sh~nalFcicnc~Fou~dado~Gr~nts~CB~9408042~nd IB\-9723671~nd mailed St~1CS ~ep~rtme~cof)~ricull~rc Or~n 9i~37300-1778toR.~and ~.~.~.Tbedevelopmcn10flhe~one~ap Datum Would not h~beenposs~l~w~b~ut~egcne~ussuppo~of es~aco,lnc~DavidL Luke.IU.andlheR-crt~nRese~rb Fund. lapoloBb~tothose~hosework~ss not ciledinthEr~ie~bec~use ofsp~cc FCq-Llir~ment Goodm~n.H. ~,Ecker.J.R.~ Dean.C.~1995)~^ ^ ~ ~ ~< ~) ~,I083I-10835. 2. Cooke. R.. Raying. Hi.. Laudic, at. GreJlo1,F..DeTscn<, at.. ~orris,P.C. Cuerrie.T.D. Giraud~t.j.,Oui~Tey,F..Cl~auTt. G~(1996)~/ 9,IOT-T24. 3. OT\~S.G.(1996)~(~j379,iS#600. 4. K~mpin.S.A.,I,iIjegren,S.j..Bjock,l. M..Rounsley.S.D., Y~no6~,~.E ~ Lam.E.~~ 7~j389, 803803. i. Baulcomb~.D.C.3996~! ~32, 79-88. 6. Fedora \.V.~ Sm~h.D.L.(j\93)~/ 3,273-289. 7. Eeldm~n K.~.(199I)~f! i.7J~82. 8. T6ppin~.J.F~y~ma~,F..Ile~dc~l.B.\ Lads ~f1994) p~ ~ . ~ ~ o0c ^~? . ~ . 9 . . . . . . ^~< ~ 5, 89i#03. Sundown V. (1996) ~ #~: ~ ~ 184-191. 10. Wilson. K., Long. D.. ~i~burnc, J. ~ Coupland. G. (I?96) ^ #~ ~ 6i9-671. 1~1. ~cClin10ck. SUB. (~I950) I'm. Ago. a. Ad. ~ 36 344-3ii. T2. Spri~er. Pa be, W., Su~dar~s~n. V. ~ ~dienssen, R. A. (199i) ~ 268, 877-880. 13 ~U~kt R. ~ Furrow \. (T996) #~r ~ 10, 479-489. 14. ~cTe~Qads, T. (1~) #~ (? >~2 Ad. ~ 90. 3303-SS09. ]i. flu, X.. lJsia, A. P.. Ahab. L., ~ikol~u, B. j. ~ Schll~blc. UP. (1996) >~7 #~ 7, 21iI~I61. 16. Chin. ~= Sane P. de Ottawa, A. Cal Woo, S. S.. /ban~^ H., Winy, OR. A. ~ ~Ben~e1zen. j. L.. (~1997) am!` \~/,,]~, an, ~ 94, 3431~433. :17. Avranlva^ a.. TTkbonoY. A.. San~iguel, P.. jig, \. K., L1t~^ C.. Woo, S. So Wing. R. A. ~ Bennetzen. J. a. (1996) ^~7 ~ 10, 116~1168. 18. Sprin~er.P.S~Pdw~rds.~.J.~ Ben~etzon,J.L.(I994~c \~77.4c~.~.~491.863-867. 19. Sb~phe~.N.S~Sc SommerZ~(enand.~. ~,H.` DeumEn~,B~Peterson.P.^ ~ SacdleF.H.(I982}~l 6~. G>~.18S,266-271. 20. WI~itc.S.E..lTabera.L.F.~ ~essler,S.R.(~1994)~.~. ~ 6~< 63/ 91~1~79#J1796. 2~1. San~iquel`~P.. fiLhnv, A..Jin. Y.-~.. ~ichoulskaia. a., Zakh~rov,D..~el~ke-B~rh~n,^.. ipriTlgOr. P.S..Ed~ards.K.j.. Lce,~ramov~.Z..~(1996) ^~274,763-768. 22. F=~E,R.B.,O Dead ~.~ ~ulcbi~son .191 \ ~/ O'er ~ ~! ~,3013 ad. 23. Hards \.~1987)Ph.~.dL6~adon(C~mbh~e U~..C~m~ brid~e,t)-.~.j. 24. Abble.T.~..R~ader.S.~..Elav~lT, R.B.~ ~oorc.G.~199i)~ ~ 3,5-Ii. 25. 8ellIletzen~ J L. Scbrick,K..Sprin~cr.P.S..Br~n. W.E. San~i~uctP.(1994)63~37.563-i76. Bal~lin~er.~.G.i Be~z~r`S.(1989)~.~. .~73. am. 6~4 86.9402-9406. /~l.R.R.^Broeks.A..~ln ~eurs,J.. ~roeII~< j.l'. ~.~ Pl~s1crk,R.~.^.(~1993)~.~/~:~. #~.~49Q.743]- 7433. No{#in,j..PlastedgR.H.~ Waterslon.~.H..(1395)~c~ 270,410-414. 29. Plasterk.R.~(1~)~^ Cad ~48`i9-80. 3Q. Das,L.~ #arJens~en,R.(1905)~' ~ 7,283294. 3~1. ~cKinll~y,E.C..Ali`N. Tr~ttlt.A..Feld~laTIn,~.~..B~ios- ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ US ~/ \61~622. S2. Kaiser.. Goode al. 3. in. (i990~)~c.~(~..~.~187, I686-1690. 33. Ch~ndler`V.L.&H~rdeman,~(I992)~330.73122. 34. Benn~tz~n.J.L.(1996) ^^ !~.~! ^~3204, ~195~229. 3i. SOttles,^.~..Yonetani.A..Ba~^():~,A..Busll.D.,CliIlc K. ~rbenss~n,R.^.~1998j~278.1467-1470. 36. ~arCc~sse~.~..Bark~n.~..Taylor ~.C.~ Freely. (I990~4.331-343. 37. U^Ksne,C.\ Oehr#~.~.j.~1987~ #~/ ma. S4.~123-9127. ~ .. . ~7 ~ .

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2()26 Co~lloq-L'iu:lll Paper: arts Wilson C Bc11~:~1. ~}~1. J. &: Cehrin~. W. ]. ~ 1990) 3~1~. Rr1. Am. 46. ( ~ 679-714. Sk~rnes, W. C. (1~93j ^> Amp. ~c4~< 4, 684-689. Sp~adli~l~. A. C. Stern. D. Hi.. Kiss 1.. Roots j.. ~Lavcrty. J. ~ RuhTn. G. Hi. (1995) mar. #? J~ #< ~ 92, I08~-I0330. mans, Hi. an C~10n. #. B. L. ~ Ruse A. P. t 1997) 73^ #~< 13. 370-37i St~ndarcs~. V., Springer. F. -V-~>lpe T.. Canard. S.. Dean. (a!.. Jones. Jo ~a. ha. ~ ~Iie~ssen. R. ^. (1995j ~^ ~ 9. 179318IO. 43. Ntlss~uIlle. L. Harrison. K.. gal auk. V., ELI tienssen R.$ Sundown. V. ~ Jonas. j. D. (j395) ^< ma. 0~. 249. 91-lQ1 . . . ...... Swirburnc. J., Balms. L.. Scald. S. R.. j()T1CS. j. By. 6. ~- Coupl~nd. 0. (1992) {~f ~ 4, i83-i9i. Lying, D., S~inburne. j., Martin. Y.. Wilson, K.. St~Ildberg. P., 6~ E. ~ Coupland, 0. (199i) ~ ma. ma. ~F 62~636. arbe~s~n, R. ~ Sprints P. {1998) ~ 2 3~:z<~/ /. ~d. Coupla~nd. G. <~Ac~Llemic. Oxford), in press. , ~ Up 6* 3901~907. Haselo~ j. ~ Amos. B. (1993) #~^ ~< 11, 328-329. 4S ,.. . 49. Lila Y. G.^ ~ilsLlk'w:I. A., OslllllT, T. & Wllitl~iel, R. ~ ~199i~} ^~7 ~ ~ 437-463. go. Handed Y. A. ~ Snot. Y. F. (J99i) #~< 3~ ~ 1763-1771. A. Viz~r^ I. Y., Anderson, Age. L.. Wilson. /. A. ~ Lit B. j. (19~) 6~137, l I l l-T I 19. lodzT~k. Ha.. }lit:: Y.. amber (.! 5. #. (1990) ^) 6D, 211-224. i3. B~c~~. ~ ~ Dean, C. (1993) #~2 134, 122j-T229. 54. Janus. ha. Ha., jr. Ibis, E.. Keller j.. Play. 1~.. Ralston, E. Dooncr H. K. (199i) #~ #~ 7, 309-319. . Goodman. C. S. ~ Rubies

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Vol. 9i, pp. 2023028. at I998 ColIoquTu~ Paper ^~` ages ~> ~~ ~! ~ aft ~~ <~ 0~r ^~ I: 74~ ~ ~ gaze ~ ~ ~ ~ ~ ~ ~ ~ 4~#C #! 7-! ~ ~ ~2 ^~' ~- ~ ~ of ~E ]~ ~ -~' ~~ ~r /~ a, ~ The age genome priest In J-~n T/~tIj1 SASAKI ~ Dice (ewe R~str~ll. Pro, National IllStitt.ltC llg:ica.1 R~sot~s. ~1.-: ABSTRACT Since 199I. the Rice Genome Research Prom Ram in Japan teas charred nut Rae gnomes, curb as lo scale cD\A analysis, construc110n of ~ Sne~sc~le restriction Unguent length polymorphism map, and pbysica1 mapping of the rice penome with yeast ariinc1~1 cbromosome clones. These studies have made ~ goat Impact on resear~b into grass genomes and made rice ~ model plant far other cent crop research. Starting i~ 1998, the Rice Genome Re~ea~b Fro. gum ~1 step In10 ~ nag stage of ~enom~s-th~t of genome sequencing. This project eenlu~> should reveal ~D of tbe genomic sequence information in the rice plun1 Aid be nn indispensable Ad in unders1andinp Abe genomics of odor press species. Rae ~ ~ ample Rod far sbou1 bait of the worlds people and manna harried and consumed in Asia and Ida. Horn rho population ~ expected to double during the next 50 yearn Hang 1Dcr~asing rice production ~ becoming more di~- cull because of diocese. draught. Aid sahni/atIon. We need lo develop improved rice petals that Are tolerant to such stresses. To achieve this tolerance. innate tools are needed to idenli~ Abe ~ene~c Tr~rmabon hidden in ace D) Bob controls aD of the char~ct~risll~ of dcc plants. So art plant becomes ~ not su~Jenl~ advanced to man underhand the molecular gee me~b~nisms re~ons~Ie far the ~ mous phenomena observed by Tremor biondeL E~ory- body learns ~erdcEs 1~ of i~ber)~nce iD their bigh school days, but aver about Rio Wars after ha csl~Ushme~t of modern genetics. no delayed in~rm~1ion is available about #.. . ctorssucb ~s~hatc0~1roL1h~ h~i~htof~'rden beans.But. her\Valson end Cr~k(17 webaveagre~1de~10fin~rmaSon about DNA and are onp now cnteri~th~ Ace of~enom2~-- the aye ofund~r~t~ndi~tbe assembled Length in~rm~lio~ darned Tom the Venoms W ah regard to the understanding of rice. the Japan~sc ovornmcntsl~rt~dits7>earRicc Become Res~rchPro~r~m (RGP) in 1991. Although the program ultimately mans to dab~theent>~r~o~enome sequence, ~Ci~ta1C achievement ofibis~oal,andincreaselb~~\ ana}~.g~n~6c mapping. phrasal mapping, andin~rmatics(23. Tbestrale~yotcONA a~alys~inthe RGPTsr~ndom cloning andparUals~quencin<.This mood ~ ~q~ickandr~ Maya Cone many ront~ro~iD#stages; and #~)toc~ploreth~ ~nc1ionsofy~n~pr~ductsbyscarchin~ public databases ~rsimD~rities. an) ~}998 T:>y 1ITC Nl~tl .~\ctlde~#y 1:~f Scit~tcts (j(~)37 8424'V8/9~2{~27-2$2.(~{~),'{} ['\.\S fig ~lv~lilttI:>l~ :/~/~$.pi:~s <~' nods 2shom~kub~. ~S 3~ Japan So far ~c m ~> b~vesequenced400-3005'4crminalbascs ofsbout36000 cape Bodes Mom 15 main cOX ~ libraries such as~rec~,ndotiolatedseedlinys,yo~n~ro~l~ particles al the flowering same, and calluses cultured pith 2.4- dichIoropbc~oxyacelicacid<3) By using thoF^ST~ sl~orkhm. ~mWah} se~rcha~sinst the ProtcinId~ntiEcation Resources dat~b~sefound <yoflinka~e~n~}sesbasedon RFLPishi~ber thanthose based onsucb methodsasrandom~ ~mpIiEed poRmorphicDN>.0urlat~stRFLPlinkagem~,cc~slrncled by using 136 F2 pleats darned Mom thej~ponic~vari~ty NippoDbar~,ndibeindicav~riolv Fasal,1h bcomposedof ~bou12.3~ O\~ma~ers~)h~t3~g~nchcdistsnceofI.i50 cat ~r12~nk^~ If. r~ri~i~n Ant Tomb pro. ] o whom reprint requests should be addressed. -no: sasaki-~.~r jp. 'a 'tam stir ~

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2028 Col~quTum Peer Sash ~ ~e#~# a Talc ~cndehan factor far ~din) time have been cs1~b- Usbed by an accurate g~nolyping of candidate progenies (63. ~ ~ _ ^ . . . Because Ht~ ~ not convenient far 5urveving many plants in a abort lime, PCR primers using 1be sequence Non of . . ~ ~ . . COrrCSpO~Ol~ KL) markers should bc eslabl~hod. The most important uses of RFLP markers on a linkage map arc as probes far screening a Y^C library to covert genetic phenomena 10 Pascal architecture. Our SAC [brarv Dog one of the parents far links an~Ivsis, N~ip-ponba<. gas composed of about 7,000 cloaca with a) Scrape inscr1 ~z~ of TO ~ (7~. The total insert ~z~ of this library ~ 3.5 equivalents of the rice penomc (430 Am. Colon {ridizalion of YACs gas palmed ~ Ram ma~e~ on a eta dotted Dim 1 536 YA C cJonesover~boutjOOcm2.Th~ positions ofibe positive \ACsonthclinkage map were con~rmcUbYfortb~FS)uthern bybridiz~tion using the same restriction on~vmeto deteclthe , . . . . . polymo~lsm In Nippcnb~rc as was used for the tinkle Nisi Scquence-t~ed Me m~rkcrscouldldenli~ postage \~\C~ by atbree-d1 ~ nsionalpooT ~ mclhod.B~ using both method 3600 ~dependen1~\C\havebc~niderilEed ~ ha, awl about MOO marked ~ ~ ed along the linkage map (bale). On the bags of g~ncdc di~snc3, we Tim Ted tab covcra~c of each chromosome by Sacs to be about 30~. Increasing the markers on lbc latest map for screening and bv using ARC and clones as moorers to i~stig~1e ov~rl~ping Cons Y^Cs 1bc c~erage could be increased 10 about 70% in the case of chromosome 6. For 1bc remaining cbromosom~s, the same sprites is expected lo yield lbc same increase in ~ . ... covera~c. in Don, mapping ESTsto YACs can chtct~e~ identify overlapping YACs wilboull~inkaq~ a~a~lvsis. For this purpose,nuclcotide sequences ofthc 37-[ntr~n~ated region, bicb ~ specific for cacb ~eno,islo be used 10 design PCR primers. Atpresont,tbis third method of ~ ^C assi~;rnent ~ boing ~idelypromotod not only for physical mappin~,but~Iso 10 Hat information on abets w~binlhe genome oach speoiEc . ~ ~ . . . . . :h 1S uerlve~. The latterinfo~rmalion ~111 be important lo iden6~ the exact position oftbc ~ Used Fencing region Ban we begin tbc ace ~cnomc sequencing. For map~bas~d cloning of gene~co~es~ nding lo ~ era), both D NA markers and YACs arc required. as well as a segrc~in~ population for the ta~etl~d~ \(e applied our map-b~scd cloning 1001S 10 isolate ~ rice blight disease- r~s~lance gene )~7 Outer obtaining s \~\C Dana by Dada matLersta~ging ~Z7~1bls \~\C gas used to screen a cad\ library constructed by usill<~vcs of~lresis1~ntvarietYtba1: bad beeninoculat~d w~bibe p~lhogen.Posh~ccD>PA; were uscdfor RFLP markcrsfJr~dUbionalEne m~ppin~,~nd one oftbe cosegregatin~cD Nab showed sequence cha7~cter~t~s ofotberdiscase-res~l~nccg~ncsinpI~nts Ttiscandidatec~ne asconE~mcUto bathe ~ctual)~7 gear bYtransformin Mica pIantssusceptibl~tolhe ~cebEghidisease~ausedbvracelof )~ ~ pa ~ 10 resistance, gab s cosmid oncc~rr~ngtb~geoe.Tbe)~7geneTsr~v~alod~sa member ofa resistance gene ~ mild with nucleotlde binding ~1cs and lcucine-ricb regions<16~. Although map-based cloning ~ undoubt~dl~avervstratc~ic lay 10 isolate a Ecu, many ESTs mav be used far quT/k Gongs by scorching ELF rice bomologues among known genes in orb) specks, such as At. Once an EST wig a sequence bomol~us 10 a know gone is Fund it needs an be mapped and as loci comp~rcd Ash tba1 known to convev ~ pben6+(pic trait. *liar. the conven17~on~T rice map doe)noicorrj~te wel~l~ith DENS marEcrs.andth~isclo~ning~isolllvv~irtual.I~n addidon,thechtcrionotbomoJo~yis~mbi~ous~d.insomC . ~ ~ #. , Instance an ~51 once 1hou~b1to be True bomologue bus turned out to be only ~ member off ~ mite ofthe Sue gene. Nevertheless, virtual cloning is onIv av~i~ble be using the many ES1\ and fine RIlJP maps Produced bv become re- se~rcb. Betbre conjuring virtual cloning 10 roof cloning. a senetical~ csl~bl~hed segregating population c~rrviny Me targettraitis needed.To DcHitatetbe cloning otbi~o~icallv and ~gronomL~Dyimpor1~nl~eno~ RFLP m Sand convey Tonal maps needio be inlc~raled. The next step of gnome analysis is cenome s~quen~ng. Rae ~ thpughtlo be a modeIpl~31for~) often ccrealcrops bocauseofilssmalIgenomes~c~ndsyntenv~ithotherRrass ~cci^.~mr~doned~ ^^thcbasklooRcJation (TR^j. 5. 7 1. Watson. ~ D ~ Wick. F. H. C. (1953) #~ /~) 171, 737-738. Sasaki. T., Yant>. at.. ~OlmOKtI~{l. J. .. ~tll Urn. a., MU. j.. t.7mehara, Y.. ~shika~ 1. & Sssa~ki. T. (~1996) ~< .. 3, 4{)1-406. T3. Koike. K., Yoshino. R. Sue, A.. Umchara, Ye Hike. In (r~1~ N. ~ SasakS T. (1997) ~ Ha. 4. 223. 14. Lmeb~r~^ \Drily. Nabs, 1. ~ Sanka T. (1997} ~# ~ ~ 12LI31. ., -,~ .13. l.{t~OUC. U~ li~l(>~ll, iWET, jSue. atl~e}>ar, Y. Haiku' L, ~rata. N. ~ Masai T. (i99 OCR for page 1

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2030 Colloquium Paper: Cog improved yields by 3-4> add resistance 10 divcrso nYironmcnlalcondibons~such es drought a 20) increase in production etOciency Cabin 10 years~ddi~tless1$4 begonia added Cam value per veal laying the ~ro~n~ork far (miIar '#'nags Or otb~r cereal crops. NC) REOPEN FOR ~\ (a Em) Congross should sc1 aside $10 minion in agricultural Research Serv~e Funds Or the Nations Corn Genome Inidst~e. (FY98 ~ Appropriations) Congress should est~blis~l~ ~ ages grooms mapping away Within He compendia Bawd Nominal Research lnid~tive and appropriate not less than $10 million. (~FY98 Ag ~ppropl i~lll~ons) Con~rcs6sbould~nsurc that notlesstb~n ore-half of 1be research ~ndsin the Fund far Rural America be set-aside far basic research pr~ccls~nd that priority tee Can to plant and animal penome mapping preach (Far m fill Ream ~ lade ~uIbod~(on) Ctlrrente~e~tsandact~lvit~lesofl1]c NCO A,:incJudin~il]~t\]~r~ motion onrcsponscsin C~rcssandtb~ Adminis1r~tion,~ro descr~edintbe Web documc~L The routeto ~istl~sbed-ouiplan basi~voR~dtbrceye~ otcom munic~tion,discussion {b~r~dlbinking.,nd comprise mPe~moo~scient~tssnd m~na~ersinthepublics~c10r~ndir biotechnology and seed trade industries. Ned scientists and :~edindustry,~raIn producers, and grain m~rk~tersa~d pFO- cessor~ {V~h(~lh~basicscicnc~dc~n~swbatcan be done.th~ ctth~t m~zeisacom moJ)y ofsurb economy importance dens the breadth oflhestak~boJders Martha NCG1. ~asm~lgroup meedn& ~ 1~94,Bob~iust~#oftbo NCCL\ st~lcd~'Tb~ m~stimport~ntlhine~ccouIddo ~ ~pth~cor~ . ~ Venom. ~ small group of scientists mot soon Offer, lo consid~FscicntiEcpriorbics~ndlo plan howto procecd.lhe . . perspectives developed by tbal group of scientists gave changed only to tbc extant that tochnolo~ics have opened ~bc~n~tive or more efEcientctoices buttheo~crtives andibe framework othighest-priorLy goals have notund~rgonc sign niEcant ~odi~c~Jon. An aoUon and planning group mat & number of~m~ssubs~qucntly ~ndthrou~h 1995,developin~ 1~0 workshops Cat mare beldin 1996 invo~inescient~tsin .. ~ genomics, breeding, in:~rmalics biochemistry, physiology Hod processing, and nutrition; and involving int~rasts in production marketing, and pus. The No-show outs comas are presented in the Web. and the 1997 document ~ constructed Tom those inputs bc Facula Summary ~ the document drones the minion. o~ect~e. goat management arid opportull~.ty: . . , The mission ~ to provide ~ national resource which wH1 support and simulate sustainable economic ad- vanc~sin ~ pproducd~n.>ith the major ~cusb~ingon corn ash key dr\~roflLc U.S.~gricultur~lsector. The o~cc~v~is 10 ~encr~lcac~r~genomc map which can be upload bythccor~ and otbercropindusthesi~ ala [.S. 10 enhance the amount and tbc quality of produce perspire. The ~o,1 is to implement a directed Add coordinated program to gongs sequence and map the appr~lm~te} iQ.OOO gangs which control Rob, development, yield and qua in corn. Mare would also be associated work related to gene expression information. ~sintaining Pascal stocks. and thc d^clopmen1 of a computers based i~2rm~tics system to slurs. utilize and retrieve us~bIe data. ~ m~ctive ap proa~b~slo belaken 1~qLrest~td>~vic~ coIIlpel~itive 1a,~p~! {~;!lI:i(~>IlS >~c #~? /~7 i~( L\] )~79~) coordinate the comply Wading 10 ensure appro- pri~e coverage ~)houtduJ!caJo~ manage in~rma1ion inputs from par~cipatingIabo- ra10ri~s obtain inIeDectual property protection on behalf of ~ Charm maw nlan~c access to the rcsultsin ~ccord~cc web the agreed procedures provide advio~ to other Ending bodies on the key leverage points far ~pp~cation serve Lisa source otr~rcDcetoI~veraye the results into o1hc, major crops Tteopportunityistbatth~,enes~fcom cabby more precise~Iocat~dtha~ispo~sibletoday,tbatth~func~o~ of many panes can be determined and tracked to a location, and that ah use of this in~rmalion MU transform corn breeding into ~ pipeline which can de~v~rlheproduclsn~ed~d ~rthe~lobslcuslomersof the 2Istcentury.In 01her~rds.tb~vi~onislhat~Lb such a corn denote map. the AS. can maintain a lcad~rshippos~ionin ~orldagriculluralproducdo~and in environments sl~ardship^ ~ Law qu~s~ons deserve considerations relevant 10 the prospects far mcetingthe needs of multiple cropsthrou~h . . . . . gaze l[lltlat~l~vc: (f) Fortlle NC0l,Si43 ~il~lionisrequest~d byLl]c ~. lstbissuficientfor~cb[~vementofth~ Koala sp~ciEc,Uy far maize? as ~ sufficient far extensions 10 Char species? A~c mul~plesp~cies~ecessityloaninih~tivegroundcdi~ maize an extension oraluxury? (~)lsth~ available popuI~tion otpotentislscient~tp~rtic~ in suticicnt far an gristle on this scale? Some ofthe most consuming lash ~(llikeR be done in sb~pstha1 arc , , d~si~nedand geared up ~rcompar~ble bodkin bitmaps OF iG 01herspecicsand ah notrequire crop~speciEc participation; otEcrsar~vcrybiologydep~ndentaDd ~DlrequTrcspedaTis1< the numberof~h ~ Clonic. <~) Wb~t~re the opportuni6rs ~rrese~rcb 1O be under- taken in various crops consonant Pith ~ maize insisted? Because each species has uniquely accessible components of , . . the puzzle Par Sample. rapidly drolopln~ physical maps in certain species and ~11 developed 1ralt analyses in otb~rs), muldplc roles Ed mutual barest wit contribute most e~c- tive~ly. (~)\Vb~ Aid be done with 1bc kno~d~d~c and took? Of high pote~ti~lis the prospect far in~cas~ oar ability 10 utter emoting. unexploited germ plasm 10 contribute lo productRby. Preparation far that, h~vor, requires tray ev~luationsofdRcrsc m~tcrials~ndcll~cteri/alionsoftboir enomic v~riabihty Un~rtun~t~Ty~1ecb~010gy far me~sur~- ellt a~nd:idellti~ficat~ioll~j~]esirc~li:raitsis costly and title li~D]iti~ng~lftlle~p~cCiS:[Oll 1Tccess~lryl/>r g~ncl:ic ~\lysis- will parapet development of oficienI plant, paid. and product me~surc~nt1ccb~iqueshc Hooded? (~) \3llsufOcicrt knowledge develop in peridot for met- ~bolic p~.bToch~m~aIconsh~ent~ and rc~ulabon of genes, 10 allow Abe most adv~nta~lo beta of1be know Cd?Cresource?Pathways and con$[tuc~tstbatarci~common among decide ~long-r~co~nized and Id bed po- ency.are~s~hentp~r~di~m Ron end zenomlc!~cLo~s . . ~ ~ #, in common, and r~uIado~ ~ nag bc~innin~ to be recognized 10 be ~ part of ~r ortholo~y of Stems among species. Expansion of such cross~sp~cies intimation is i~to~r~t and vast to an iniDa1\e. (~0 WH1 concord Among researchers in distant crop coma modifies be suds to drag national SUppOf1 far a mutual pl~nDcd amp? Coursed. Air the plan affect prospects far concord? While sol responding ontLely to the abed questers. cola federations Tom 1b~ NCG1 planning oroc~ss^ and some drawn . ..... . .

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from discussionsinlbiscoIToqulum,ca~b~distUledtothe ~Jo~ingrese~=hnc~ds ELF the RIFT. tomakerapidprog~ss . . 1~acompFc~ens~c m~nner.B~c~nsethesuccessof~yenomics cD3~ d~pc~ds more onflexiblo~uidancebyaslooring~roup than on sbsolut~s.lhese brick represent nc~dstbal appear todsytobelhe ~ghestpriorbL~,snd may~eUberophork~ed asch~nyes~Fescento be n~cdcd. One Slow ~sn1~enomepro~r~m ma ukimate~ beg completesequenceofacere~l~e~omeandofotb~rsel~cted crop geno~s.achiev~dthroughint~rn~tionalcoopor~tion. ThOCrs~priorLy~eeds,ho~er,aretod~r\cplanningand priork~atiorproc~dures,andtoinlhatetboseessenti~ef~rts . . that notary wig enable serious Cons otgenom~ in~rmationand1oolsbula~o~T~s~t1hcstayc~rsequ~ncing and~sdeEnllKeimp~cton ~opgenomi^. Sev~n~Crst~priorLy~ss~ntiaG ~ra~>ct\~plantgenomc program a~eas~llows: . #. #~Ala~e~mberotcD~Asegmentstc.g-30,000~30~) seotab0n. representing expressed genes should be isolated, in part Mom maize and in part from other cereals sequenced Id ass~m blcd {Le., distinguished as unique vs. overlappings; located to postman ~ Tenets or paws m<; and ~ncd ~ ~p~~ Cords to tissues. cell jest d~lop~nt~1 sties, and targeted response condidons. ... ~ndp~Needshou}db~anticipalcdby scaling upoires~aTchin tbe~re~sotme1abolicp~1b~s1~ps,~n~mics,andflux,~r substaDtiala~anc~me~tsinknowledge~imul~t~d~tbapl= eenom~pro~rsm ()TosClccl~elys~quence~enesofintercstirom any species without having to sequencelarge amounts of noncodiny . . . . . re~onstoundl~Iar~e gnome new mcans~re necded.This tec~olo~ would ~ciJ1~1etb~scquencing ofortbol0~us gone Amid members from di~>renlspecies.and from gene ~ri~nts~und~bbin~erm plasm collections. (~)E~cic~lmelhods~eneed~d~rstu~ ofbi6trencesa6 sm'D~ssingle-b~sc pairs. 10 b~appliedin more-direct~p- pTC8c[Cs 10 gangs that a~>ctmeasur~letr~ts(quanl~a1~ . . . trskloci,OlI~. (~)Hi~>e~tct~capproachcs are needed ~ which~onc expression can be c~1e~0r~ed and defied explicate. These include comprch~ns~\e methods to. arrays); molbod~tha1 display ~nctio~inpl~c~in~ssues;m~tb~ds ~rd~ri~i~clon~s ,t~eled 6~ctio~sorl~r~t~d traits: and 1OS1S of # ~.. alla reliability of ~pplic~1~i0ns of transE]r~stion Pinto bacterial yeas6 and other species. 0~) Ore-precise 1cchniqucs and tools, nondestructive whenever possible. are much needed far measurement of traps relevant to productivity. {~) Programming sad consensus Arc nr~cntly needed on map rcprcsent~tion intersp~cies comparisons, and metabolic rep- rescstaIion. Case arc far Be most part in~rmatics dopen- dentandsbouldintecralecloselv with th~biolo~icaladvancc~ #.. , ~ meats . .. . JO A ~eodn~ group should be fished to Wide a ~ #. a. ,. muTha~cncY{c~mpetb~e cram peer rriowcdj program ~ , .. .. ~ .. ~ iBidal~tod~elop procedures bywbichplsnning and priory b/ationar~do~c,toinibaletb~pro~ram,andtose!continuity and roproscnlationprocednr~sinmolion.M~mDc~bipsbOuld . >. have scientists Limb strong experience in g~nomics resosrcb and should include pFivate~sector and ol~niz~11onalr~pre 00 Worki~groups can b~drolopedby~eslced~g group. 10 Ad in planning and to provide Spud. and 10 be ironed in communic~don within and outride the program; membership should be fluid. cross-commodity, and cross~discipllne. iffy Banking and distribution of materials: Beam access should be Even to Abet ~ available. Oh prompt response. Precision and accuracy would be expected to meet biph standards far the research and utilization community. Qua Database Unctions and continuity (see bolow). (~) ~lopmen1 of pros catchy is needed. posh coUiLons Aim industry and Caters. far e~cic~t ~ccom^ fit ~ Am. #)PosldocloFaTtrainingmusibecnbancedinbiolo~yoicrop species: ingenomics;andinin~rmalics,to~etherdesiGnedto interlacelr~1nirgine~cb~rc~. Ff)Public and stak~holdersr~quircin~rm~don and muslbe cnlLtedinthc~reasoiconcerns.nc~ds.andvaluc. (~0ExisEn~pro~rams(Nshon~ Science Fou~dsdor Ed . , ucation~should be cmploy~d,throu~h intercommunication. ~is1lng resources commuted to plant science research in the public sector arc modest considering the value of crops ~ commodides, fit am pr~cct~d Ending rages Misdoes about what DO be their source. Predicated on that Tcvcls of Ending appropriate to make rapid progress in a comprehensive man- nursed be developed Bailout assumptions as 10 Mar source. Redistribution ofoxistln~ plans research ~ndsls ncilhOrdeskable nor su~gesIed.Thel~velof:~ndin~proposUd fortlleNCOlisI~odest.vetis~re~listic.andu~nquesliOllablY~il~l .. . . . cOD1ribUtC 10 ~#ancesin other cerc~l~Tar~eted work only othOrccre~l~orondicotcrops,wiLbemsdelessUcmandinG ofrOsouTc~sbyv>1ueoftbekno~ledgesndl001soim~izc.In some cases, ~ndin~from commodily-speciEcintc~csts may b~come~ OCR for page 1
2032 Colloquium Paper: go parcel connectivity may be expected to ah now data and new packages, cns~riny immediate cur~cnlness of dale. (~) Databases should bc coupled as closely as possible to research, cats collection. and resource distribution. guided by b1010~ists, and organized around species or closely related ~ . .~ groups of speclos. Funding needs to be at approximated 13-20~ ofth~program,atalo~clsuf~cientto support guabty cur~1ion,service,oulrcach~documcn1~lion~systom~ support end spociahzcdsoftw~re ~heren~ccssary.Thepro~ram must cncouTag~inlersction and mutualdevelop~entof the dated b~sesbythcspecioscurators.cspccial~ 10waFd harmonizing rcpresent~1ion ofbiologicaIin~rmation and1be exploitation of Watery and olherpower~lrclationships. (~) Dat~basecover'gcof:iorphaned'"crops#.~ones~bb no ~s1cm~1ization ofin~rm~tion current\) should be serb ouslyconsid~red.tbroughinl~raction~nd mucus dcv~lopmen aborts with speciahstsin these craps. Cron'~nerT~rtn the d~eIop~odd about be induced. ~, ~. . , a, -a-- -- -~_ _~ gFj ralaDssC programs should De revl~weu and evaluated regulars, web continued Ending dependent upon p~r~r- m~nce. (v) Inlcractlons and linkages sbould be promoted. with databases ~rnonpl~ntspcciesthuman.froTtily.worm~ye~s6 bac1cris~domesUc animals) and with datab~sesth~t~re not speci~c,T~ ~enedc (metaboUsm and biocbemh~v: commodity groups; Harm plasm; borax; filch. P~ed ~ the age plan. oncompas~n~ ah css~nti~. cchnologies, infrastructure. and in~rmatics, otb~r CFOpS, Age. go/. I. ala. ~^ ad (COPE) whethe~rmonocotsordicots,~il~lb~positiol]ed 10 ad~sllccwilb cosl-eO>cb~e p~r'D~l~ csp~ci~l~ far ESTs. markers. and physical mapping. Uncoil ~imulabon and e~ou~oment ~ BE Resell Ed the NC~ ~ VERY much ~r~c~1cd ~ ~scE personal\. as it is bv the , . . .. . maize research and biotechnology community. Jim McLarcn s efforts in developing the plea and documenlahon. and in leading the com . . . . . munlc~non and excn~n~es In ~orksbops ham bean centraL I am ~tc~l far hemps agog and insights award the present papa Tom jell Between. Sag C,~inhou~ Rag ~adi~ns~n. Susan ~cCou~, ~ ~ ~ an ~6 Taco. D \ ~ ~ ~ ( 246-232. Hotbed, S. at., Raffler T. Ed Malt j. ~ ~ Benin. ~ L. (1990) #~ #? Jaw. ^/ ~ 87, 4251-4255. Devos. K. at., Moore. G. ~ Gag, at. (1995) 6~ S5. a,- ~ go /-: ~ a. Yor~, G.. Foote, T., Hel~ngaris, T., Devils. K., Curate, a. & Ogle, Y. (1995) ^~^ 6~< 11, 81-82. 5. V8IT D~y-nze, ^.. Nelson. J., YgIesias, E . 11arrin~>n. S . Brake. On ~cCoucb. S. ~ SorreDs, at. (1993) # 248, /~-/~- 6. B~nnetz~n, J. L. ~ FreeEn~. ~. (1993) 7~ ~< ~ 259-261. 7. Benncizen. j. L. ~ EreeEng. ~ (1997) he 6~ 7, 301~06. 8. Benson, R. 1~ John, O. So Ovine. V. C.. Tossed, J. T.. Schnook. P. So Shelby. R. B. ~ Briggs, S. P. (1995) >~r #~ 7, 73-84. 9. Ah, L. ~ ~a~icnssen. R. (1993) Oaf ~ 7, 28394.