Proc. Natl. Acad. Sci. USAVol. 92, pp. 10831-10835, November 1995

Review

The genome of Arabidopsis thalianaHoward M. Goodman*1t, Joseph R. Ecker§, and Caroline Deanl/*Department of Genetics, Harvard Medical School, and tDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; §Departmentof Biology, University of Pennsylvania, Philadelphia, PA 19104; and llDepartment of Molecular Genetics, Biotechnology and Biological Sciences ResearchCouncil, John Innes Centre, Colney Lane, Norwich, NR4 7UJ, United Kingdom

ABSTRACT Arabidopsis thaliana is asmall flowering plant that is a member ofthe family cruciferae. It has many char-acteristics-diploid genetics, rapidgrowth cycle, relatively low repetitiveDNA content, and small genome size-that recommend it as the model for aplant genome project. The current statusof the genetic and physical maps, as wellas efforts to sequence the genome, arepresented. Examples are given of genesisolated by using map-based cloning. Theimportance of the Arabidopsis project forplant biology in general is discussed.

Our understanding of basic plant biologyand our ability to genetically manipulateplants for agronomic improvement willdepend to a large extent on our under-standing of developmental, genetic, andmetabolic processes which are fundamen-tal to plants. One of the major challengesin plant molecular biology is the isolationof genes in which the biochemical functionof the gene product is unknown. In anumber of plant species, genes controllinga wide range of fundamental developmen-tal and metabolic processes have beenidentified by mutational analysis andplaced on classical genetic linkage maps(1). In most cases, while the mutant phe-notypes and genetic map locations areknown, virtually nothing is known aboutthe gene product. The cloning of these locitherefore relies solely on their mutantphenotype and genetic map position. Therelatively large genome sizes and highcontent of repeated sequences of the ma-jority of plant genomes have meant thatcloning by chromosome walking is not afeasible prospect in most plant species.The development of map-based cloning

has focused on three plant species, Arabi-dopsis, tomato, and rice. The first genes tobe cloned this way were reported in 1992(2, 3). Since then, there has been a massiveincrease in the number of laboratoriesusing this approach, such that, to date,probably >100 loci are being targeted.Most of this effort is centered on Arabi-dopsis, making the availability of a physi-cal map of the Arabidopsis genome a highpriority for the Arabidopsis research com-munity. The immediate benefits of havinga physical map are twofold. First, the mapprovides ready access to any region of thegenome which can be genetically identi-

fied. In other words, the physical mapserves as a cloning tool by facilitating themovement from the genetic locus to thecloned gene. Given a mutation of knowngenetic map location, the physical map canbe used to easily isolate an overlappingcollection of clones encompassing the lo-cus of interest. Second, the physical mapprovides a starting point for studyingglobal genomic organization. As an in-creasing number of genes are cloned andmolecular biological information is accu-mulated, one can begin to investigate thephysical linkage of cloned genes, study theorganization and distribution of repetitiveelements, and address questions such ashow physical distance and genetic distanceare correlated. In this context, the mapprovides the framework for catalogingand integrating molecular biological infor-mation. Ultimately, genome organizationwill be investigated at the nucleotide level.Clearly, physical maps are the logical sub-strates for genome-sequencing projects.

Why Arabidopsis?

Over the past several years, Arabidopsisthaliana, a typical flowering plant and amember of the mustard family, has gainedincreasing popularity as a model systemfor the study of plant biology. Its short lifecycle, small size, and large seed outputmake it well suited for classical geneticanalysis (reviewed in refs. 4 and 5). Mu-tations have been described affecting awide range of fundamental developmentaland metabolic processes (reviewed in ref.6). The pioneering work of Redei andcoworkers (7, 8) and Koornneef and co-workers (9, 10) using classical segregationanalysis led to the construction of theinitial genetic maps of Arabidopsis thatcontained -90 loci (9). Significantprogress has been made in the last severalyears in expanding the number of markersand the current map contains >280 visiblemarkers (10). An increasing number ofcloned genes and restriction fragmentlength polymorphisms (RFLPs) are avail-able for the alignment of the genetic mapwith the physical map (11-13).Arabidopsisis well suited for physical mapping studiessince it has a very small genome (5) and aremarkably low content of interspersedrepetitive DNA (14). The genome size ofArabidopsis has been estimated by using a

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variety of different methods (see refs. 5and 15 for a more complete discussion)including reassociation kinetics ('80 Mb;refs. 15 and 16), flow cytometry (86-145Mb; refs. 17 and 18), chromosome volume(100 Mb; ref. 19), and physical mapping ofcosmids (100 Mb; ref. 20). These estimatesrange from about 50 to 150 Mb, with 100Mb being taken as a convenient compro-mise. A more accurate estimate awaits thecompletion of the individual chromosomemaps (see below) and eventually nucle-otide sequence analysis. Therefore, thepositive features of Arabidopsis that rec-ommend it for genome research are itssmall genome size, the presence of rela-tively few repetitive sequences, and thelarge number of mapped markers. Thesefeatures have been exploited in physicalmapping strategies. The lack of single-copy gene in situ hybridization, flow sort-ing of chromosomes, and well-character-ized hybrids with other plant species hasprecluded other strategies that have beeneffective in the Drosophila and humanphysical mapping projects.

Molecular Markers

Mapping of mutations in Arabidopsis hastypically been carried out by using classicalmorphological markers (10) or RFLPs(11, 13). Classical morphological markersare simple to use and require no use ofexpensive molecular reagents but may suf-fer from ambiguities in scoring, interfer-ence with the phenotype to be mapped,and, in most cases, only a few markerscan be reliably followed in a single cross.Random amplified polymorphic DNAs(RAPDs) are easily generated, simple toscore, and amenable to automation, and ahigh-density RAPD map of theArabidop-sis genome has been constructed (21).However, a major drawback is that thesemarkers are generally dominant, and themethod is exquisitely sensitive to DNAconcentration and PCR conditions. Thus,as a practical matter, the transfer of suchmapping information among laboratorieshas been difficult. For these reasons,

Abbreviations: RFLP, restriction fragmentlength polymorphism; YAC, yeast artificialchromosome.ITowhom reprint requests should be sent at thet address.

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RFLPs are commonly used for mapping ofgene mutations. Initial RFLP maps wereconstructed of the Arabidopsis genome byusing various different independent map-ping populations (11, 13). As common

markers were incorporated into bothmaps, it was possible to mathematicallyintegrate the two data sets (22). RFLPmarkers from both maps have been fin-gerprinted and integrated into the over-lapping cosmid map (see below), therebyestablishing contact with the genetic link-age map. These early maps have beenlargely superseded by the development of"recombinant inbred" or "single seed de-scent" mapping populations (12, 21) thatare now the standard for the field and onwhich >430 DNA-based markers havebeen mapped (C. Lister and C.D., unpub-lished data).More recently, PCR-based markers,

such as simple sequence length polymor-phisms (SSLPs) (23), cleaved amplifiedpolymorphic sequences (CAPS) (24), andamplified fragment length polymorphisms(AFLPs) (25) have been developed forArabidopsis. These markers offer a con-siderable advantage over RFLPs in thatonly small amounts of tissue are requiredand the polymorphisms are visible byelectrophoresis rather than blotting andhybridization. While SSLPs and CAPSproduce codominant markers by usingstraightforward PCR (the primers areknown DNA sequences), AFLP markersare largely dominant, and the technologyrequires much more complex manipula-tion for each DNA sample (adapters/ligation/PCR/affinity capture/differen-tial display). Additionally, sophisticatedimage analysis capability is also requiredto interpret the complex pattern of band-ing that is produced for each sample.However, the distinct advantage ofAFLP technology is that literally thou-sands of markers can be identified in ashort time, and, when combined withbulked segregant analysis (26), markerscan readily be identified within 10 kb ofa locus of interest (C. Thomas and J.Jones, personal communication).

Physical Map

Due to the success of the cosmid-fingerprinting strategy in Caenorhabditiselegans and the similar size and complexityof the C. elegans andArabidopsis genomes,

this method was also chosen as the initialstrategy for Arabidopsis.Random Linking of Cosmid Clones.

The construction of the cosmid map in-volved the characterization of randomclones by fingerprint analysis (20, 27-29).Approximately 20,000 clones (-8-foldsampling redundancy) from a primarycosmid library were fingerprinted. By us-

ing computer matching programs, theclones were aligned into some 750 over-lapping groups or contigs. The 750 contigsencompass -91,000 kb representing be-tween 90% and 95% of the Arabidopsisgenome. Having fingerprinted eightgenomic equivalents, the practical limit ofrandom clone mapping was reached-i.e.,the stage of the project where the rate offinding new joins was unacceptably lowdue to the scarcity of the linking clones.

Linking Cosmid Contigs by Using YeastArtificial Chromosome (YAC) to ContigHybridization. The majority of the gaps inthe cosmid contig map were expected tobe small and attributable to the fact thatthe linking cosmids were either nonexist-ent or underrepresented in the cosmidlibraries. Another potential difficulty wasthe instability of the cosmids-i.e., theyare very prone to delete during growth ofthe cells and tend to give low yields ofDNA-hence, they have to be handledwith considerable care (20). An attemptwas made to join the cosmid contigs byusing linking clones from two (EG andEW) of the available Arabidopsis YAClibraries listed in Table 1 (30-33). Thelarge insert sizes which can be propagatedin YAC vectors (35) means that fewerclones need be examined, but more im-portant, the yeast cloning system offersthe potential to give a random or at leastdifferent representation of sequences thanare obtained with cosmids. The linkingstrategy was to use YAC clones to probeordered cosmid grids representative of thecontigs and the unattached clones (36).Cosmids within a contig were chosen sothat there was minimal overlap betweenflanking clones, yet the clones were rep-resentative of the entire contig. The col-onies were then gridded at high density byinterleaving 16 Microtiter dish patternsover an area of 8 x 12 cm. The represen-tative collection of cosmids could there-fore be arrayed on two filters the size of aMicrotiter plate. The YAC clones used as

probes were first separated from the host

chromosomes by clamped homogeneouselectric field (CHEF) gel electrophoresisand cut out of the gel. The gel slicescontaining the YACs were then labeled byrandom priming in Microtiter plates (20).Consequently, 96 probes could be pre-pared simultaneously, thereby facilitatingmultiple hybridizations. Since the cosmidlibraries were constructed in the loristseries of vectors (37), which have no sig-nificant homology with the YAC vectors(35), there was no need to separate theinsert from the vector sequences. Theoverlaps were established by probing theordered cosmid grids with the labeledYAC clones. The YACs to be used as

probes can either be picked at random orpreselected by hybridization. The latterapproach has the advantage that it can beused to rapidly establish linkage in spec-ified regions of the genome. The disad-vantage is that two hybridizations are re-quired: preselection of the YAC clonesfollowed by hybridization to the cosmidgrid. Both approaches were employed,with the primary emphasis being the useof randomly selected YAC clones. Al-though this approach of YAC to cosmidcontig hybridization was somewhat fruit-ful (B. M. Hauge and H.M.G., unpub-lished data), it was considerably less valu-able for contig linking than originally an-

ticipated (36) because the two YAClibraries (EG and EW, see Table 1) usedmore or less exclusively for these experi-ments were highly chimeric and manyalso contained chloroplast or ribosomalDNA. However, the gridded cosmids andtheir filters have been helpful for linkingthe YAC contigs and as substrates forgenomic sequencing (see below).

Physical Mapping by Anchoring ofYACClones with Molecular Markers. TheAra-bidopsis genome has ideal properties toundertake a strategy for physical mappingby anchoring YAC clones with geneticallymapped molecular markers (38-40). Thebasis of this method is to identify clustersof overlapping YAC clones that shareshort "anchor" sequences; with a greatmany such anchors scattered randomlythroughout the genome, contiguous arrays(contigs) of YACs sharing common an-chors may be identified. With a sufficientnumber of anchors, these contigs becomeassembled into a true physical map withlong-range continuity. Furthermore, byusing genetically mapped markers as an-

Table 1. Characteristics of available Arabidopsis YAC libraries

Average % of clones in the library (n) DNALibrary insert size, No. of With With 180 With Chl DNA used fragmentationname kb clones rDNA bp DNA With 160 bp for library method Vector Ref.EG '150 2300 15.4 (354) 1.6 (37) 26.4 (606) ? COL nuclear BamHI partial pYAC41 33EW -150 2200 2.3 (51) 8.45 (186) 6.6 (146) ? COL nuclear Random shear pYAC3 30yUP -250 2300 9.5 (218) 0.7 (16) 7.8 (180) ? COL nuclear EcoRI partial pYAC4 31CIC -450 1152 8.9 (103) 5.8 (67) 12.9 (148) 0.09 (1) COL nuclear EcoRI partial pYAC4 34

Chl, chlorophyll; COL, Columbia ecotype.

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chors, the meiotic and physical maps willbe tightly aligned and facilitate the pre-diction of physical map positions on thebasis of linkage data. This is a majorbenefit for the positional cloning of genes.

Mathematical analysis of a generalscheme for mapping the Arabidopsis ge-nome by anchoring has been described(40). Several additional theoretical studiesabout the efficiency of mapping strategieshave also been published for other ge-nomes (41-44). Although different as-sumptions need to be applied for each ofthe different strategies, important similar-ities are found in these predictions. Inde-pendent of the chosen strategy, physicalmapping projects will be more successful ifboth the number of molecular markersand the insert size of the library are large.Insert size dramatically affects the numberand the size of contigs for a specific num-ber of markers, and these two parametersare decisive in the evaluation of the pos-sibilities for map closure (39).Anchoring strategies have several im-

portant advantages over the random-content mapping approaches. Of primaryimportance is the knowledge of wherecontigs are being built. When a set ofYACclones are detected with a geneticallymapped probe, their position in the ge-nome is immediately known and allows forthe correlation of the physical and geneticlinkage data. Additionally, the potentialrelationships between genetically posi-tioned contigs can be assessed and it maybe possible to predict which contig endsare likely to cross-hybridize. In this sense,anchoring resembles the approach beingused for physical mapping of the Drosoph-ila genome (45) in which YACs have been"cytologically anchored" by in situ hybrid-ization to salivary gland chromosomes (46,47).

Construction of an ordered series ofoverlapping YACs by using molecularmarkers has been ongoing in several lab-oratories (32, 34, 38, 39). Screening of theEG, EW, yUP, and CIC YAC libraries(30-34) to isolate clones containing thesemolecular markers has been carried out byDNA hybridization or by using PCR. Byidentifying YACs that contain two ormore anchors, contigs have been builtwhich consist of overlapping YACs thatshare common sequences. This approachhas provided a facile means of construct-ing large contigs relatively quickly. Thusfar, the experimental progress has closelyparalleled the outcome predicted from themathematical analysis (ref. 38; P. Dunnand J.R.E., unpublished data). Long-range continuity of the physical map isnow being achieved by a directed ap-proach toward linking the contigs togetherwith additional YACs and using otherlarge-insert clone libraries (see below).

Directed Linking of YAC Contigs. Thedirected approach to linking YAC contigshas generally taken the form of utilizing

YAC ends as hybridization probes to ar-rayed YAC libraries (30-34). The endprobes were sometimes generated by plas-mid rescue or vectorette PCR (48), but,for most of the probes, inverse PCR wasthe method of choice (49).The inverse PCR or vectorette PCR

products and gel-purified plasmid rescueinserts were radioactively labeled by PCR,hybridized to high-density YAC grids orSouthern blots of pulsed-field gel electro-phoresis fractionated YAC clones, and allpositive signals confirmed by Southernblot analysis to yeast DNA isolated fromthe YAC-bearing clones. While the link-ing ofYAC clones by using end probes hasproven to be straightforward and criticalfor the linking, it is, nonetheless, laborintensive. YAC-contig expansion with atleast two of the early YAC libraries (EGand EW; refs. 30 and 33) was difficultbecause of their generally small insertsizes ("150 kb), chimeric nature, and in-stability of the clones carrying tandemlyrepeated DNA sequences (Table 1). Theproblems that arise when trying to con-struct contigs with libraries with a highproportion of chimeric clones are fairlyobvious-e.g., one needs at least two in-dependent YACs confirming each poten-tial join. As a specific example, a contig onchromosome IV utilizing three of the li-braries (EG, EW, and yUP; Table 1) con-tained 84 clones, 22 of which were chimer-ic-i.e., had both repetitive and uniqueDNA-and of the 57 end probes gener-ated, only 44 were usable, while 13 re-mained unlinked or contained repetitiveDNA.The availability of a new library (34) in

1994 (called CIC, see Table 1) consistingof 1152 clones with an average insert sizeof -450 kb and developed by a collabo-ration among the Center for the Study ofHuman Polymorphisms, Institut Nationalde la Recherche Agronomique, and Cen-tre National de la Recherche Scientifiquein France has facilitated rapid progress inthe last year. In many cases, by using theCIC library with larger and less chimericinserts, the contigs anchored around theRFLP markers coalesce without the use ofmore markers or chromosome walking.However, integration of the CIC cloneswith the smaller YAC clones meant thatmarker order could be established andphysical distances reliably estimated.The current status of the YAC contig

map is as follows: chromosome I contains42 contigs with -65% coverage (P. Dunnand J.R.E., unpublished data), chromo-some II contains 4 contigs (5 gaps) with-80% coverage (Ming-Li Wang, EveZachgo, and H.M.G., unpublished data),chromosome III contains 42 contigs with"60% coverage (P. Dunn and J.R.E.,unpublished data), chromosome IV con-tains 4 contigs (3 gaps) with >90% cov-erage (64), and chromosome V contains

35 contigs with -85% coverage (R.Schmidt and C.D., unpublished data).A potential obstacle to closure of the

physical map is the absence of certainsequences from the YAC and cosmid li-braries. Thus, to construct a "complete"map, it is almost certain that other large-insert clone libraries will be necessary.The recent availability of both bacterialartificial chromosome (**; P. Ronald, per-sonal communication) and P1-based Ara-bidopsis genomic (50) libraries has ex-panded the possibilities for completing thechromosome physical maps.AAtDB. A continuously updated collec-

tion of relevant information on Arabidop-sis is available in An Arabidopsis thalianaData Base (AAtDB) (51). The focus ofAAtDB is on the genetic and physicalmaps of the Arabidopsis thaliana chromo-somes. Genetic maps continue to be re-fined, and AAtDB contains informationon several versions of the five chromo-some maps, with visible as well as molec-ular markers. The physical maps containdata on cosmid and YAC contigs, as wellas some sequence information. Additionalinformation related to Arabidopsis genet-ics and genetic research is also included,such as literature citations, Arabidopsissequences from GenBank, germ plasmand DNA resources, and images. AAtDBuses the ACeDB software developed byRichard Durbin (Medical Research Coun-cil-Laboratory of Molecular Biology,Cambridge, U.K.) and Jean Thierry-Mieg(Centre National de la Recherche Scien-tifique, Montpellier, France) for the C.elegans genome project. The software runson UNIX workstations (a Macintosh ver-sion is also available) and provides theuser with a dense network of graphicaland hypertext links to examine datathreads of interest. This is accessiblethrough the Internet worldwide computernetwork. AAtDB also features a widevariety of public information that is pre-sented using graphical, text, and tabularformats. The user interface, which wasdesigned to invite browsing, allows usersto explore information by pointing andclicking with the workstation mouse or byusing a versatile query facility (Table 2).All the AAtDB information in text form isavailable via the Arabidopsis ResearchCompanion, an Internet Gopher server atMassachusetts General Hospital.

Sequence Analysis

Most of the genomic sequence data cur-rently available in the data bases (1016entries) have been obtained by individualsequencing of cloned genes of interest.Large-scale sequencing of the Arabidopsis

**Choi, S., Creelman, R. A., Mullet, J. E. &Wing, R. A. (1955) Weeds World (http://weeds.mgh.harvard.edu., Mass. General Hos-pital, Boston), Vol. 2.

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Table 2. Numbers of objects in selectedclasses of AAtDB (version 3-5)

Object

MapAlleleAuthorCloneContactDNA ResourceGene_ClassGene_ProductGermplasm_ResourceImageJournalLocusMap PopulationMotifPaperProbeSequenceSequence_ESTSequence HomolSequence GenomicSource2_point data

No.

31129554251916314192869244791

3520819395192626

3434192528

3468614915172572495

604877

genome is now underway with a majorexpansion of activity planned for the next10 years. The focus will be on the sequenceanalysis of the ecotype Columbia, usedextensively in production of the YAC, Pl,and cosmid libraries and a parent in oneset of recombinant inbred lines. The firstcontribution to the large-scale genomicsequencing has been the completion oftwo 40-kb cosmid clones (H.M.G., P. Gal-lant, and G. Church, unpublished data). Aprogram to sequence just under 2 Mb ofArabidopsis genomic DNA was funded bythe European Economic Community pro-gram in 1993 and is being coordinated byM. Bevan (John Innes Centre, Norwich,U.K.). A total of 1.5 Mb of contiguoussequence is being generated on the longarm of chromosome IV, centered arounda locus controlling flowering time (FCA).In addition, 150 cDNA clones transcribedfrom this 1.5-Mb region will be sequenced.Information from the comparison of thecDNA and genomic sequences will beused to "teach" the GENEFINDER or equiv-alent software to recognize Arabidopsissplice consensus sites. The rest of thegenomic sequence is made up of 400 kbthroughout the genome, although a largepart of this is centered on a region arounda locus on chromosome IV controllingfloral morphology (AP2). This project,termed the ESSA project (for EuropeanScientists Sequencing Arabidopsis) is be-ing considered as a pilot program (to becompleted by 1996) for a future large-scale project (covering on the order of 10Mb), funded by the European EconomicCommunity.The templates for the sequencing of the

1.5 Mb of chromosome IV have so farbeen exclusively cosmid clones necessitat-

ing the production of overlapping cosmidclones from the detailed YAC physicalmap of that region. Cosmid clones havebeen identified by hybridization of wholeYAC clones to filters carrying represen-tative cosmids from the fingerprinting ex-periments (see earlier section). In addi-tion, a second cosmid library made fromthe Columbia ecotype was screened (I.Bancroft, K. Love, and C.D., unpublisheddata). Approximately 80% cosmid cover-age was achieved with this YAC to cosmidhybridization strategy. Currently purifiedYAC clones are being subcloned into cos-mid vectors. The high-redundancy librar-ies that can be achieved this way (average30-fold) have so far given complete cov-erage.

In parallel to these genomic sequencingprograms, expressed sequence tags (ESTs)are being generated (52, 53). These arepartial sequences of random cDNA clonesisolated either from one cDNA librarymade from mRNA isolated from a mix-ture of tissues and conditions (52) or fromdifferent cDNA libraries made from avariety of tissues and cultured cells (53).So far, 14,915 EST sequences are in thedbEST data base. A first analysis hasrevealed that 40% of the clones showsignificant similarity to known genes.

Interim Lessons Learned

What has been learned from the study ofthe genome of Arabidopsis thaliana andhow has this contributed to our under-standing of plant biology?Genome Structure. A considerable

amount of information on the genome ofArabidopsis has been accumulated as out-lined in the previous sections. In addition,the first plant telomeres were isolatedfrom Arabidopsis, and their partial mappositions were determined (54). A recentreport also indicates that the genes codingfor ribosomal RNA that exist as largerDNA tandem repeats (together these ac-count for -6% of the genome) occur intwo nucleolar-organizer regions whichmap near the telomeres of chromosomesII and IV (55). The positions of the cen-tomeres were initially defined geneticallyfor chromosomes I, III, and V by usingtrisomic lines (9), and later clones wereisolated that mapped close to CENI (56).Recently, centromeres have been locatedmore precisely on the YAC contig maps ofchromosomes II (H.M.G., unpublisheddata) and IV (64) by hybridization to aprobe, pALl (57), containing a 180-bpHindIII repeat. This had been shown byusing in situ hybridization to colocalize thecentromeres with the paracentromericheterochromatin of all five chromosomes(58). For chromosome IV, the centromerewas located close to the marker mi87,indicating that the short arm of this chro-mosome contains -3.5 Mb of the coding

DNA and -3 Mb ofrDNA at the terminus(55, 64).The data on genome structure and ac-

cumulated sequence data have confirmedprevious information that Arabidopsisgenes are on the average rather small(-4-5 kb) and in general contain smaller(usually <200 bp) and fewer introns thanother plant species. In addition, it appearsthat there is little space between genes. Itcan therefore be predicted thatArabidop-sis contains -25,000 genes. On a globalscale, the correlation between the geneticand physical maps indicates that there is"200 kb per centimorgan (cM), while datafrom the physical mapping of chromo-some IV indicates - 175 kb per cM for thatchromosome. This number can differ sig-nificantly in any local region.Gene Isolation. A large number ofAra-

bidopsis genes have been isolated by tak-ing advantage of the integrated genetic,physical, and RFLP maps. As examples,among the first twoArabidopsis genes thatwere isolated by using map-based or po-sitional cloning were the genes corre-sponding to thefad3 locus that encodes anw - 3 desaturase (2) and ABI3 (3), thewild-type gene corresponding to one ofthe abscisic acid insensitive mutants (abi3)of Arabidopsis. These abi mutants are al-tered in various aspects of seed develop-ment and germination due to a decreasedresponsiveness to the hormone abscisicacid. On the basis of its properties, thisgene is thought to be involved in theabscisic acid signal transduction pathway.Of particular note was the recent isola-

tion of a plant disease resistance gene,RPS2, from Arabidopsis (59, 60). Arabi-dopsis mutant plants were isolated thatwere resistant to infection by the bacterialpathogen Pseudomonas syringae and usedfor positional cloning of the gene. Thisgene encodes a protein with 14 imperfectleucine-rich repeats and is probably a re-ceptor for a molecular signal of the patho-gen (59, 60). This becomes even moreinteresting (61) since RPS2 is similar toanotherArabidopsis gene, RPP5, that con-fers resistance to a fungal pathogen Per-onospora parasitica (ref. 62; J. Parker andJ. Jones, personal communication) and tothe N gene of tobacco that confers resis-tance to tobacco mosaic virus (63).

Conclusions

Considerable progress has been made in arelatively short period of time in isolatingand mapping genes and developing a phys-ical map of the model plant Arabidopsisthaliana. Work is in progress to completethe physical maps of each of the fivechromosomes and to initiate large-scalegenomic sequencing. These studies andothers have contributed to our under-standing of the biology ofArabidopsis andof plants in general.

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