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Proc. Nati. Acad. Sci. USA Vol. 89, pp. 1477-1481, February 1992 Genetics Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs (restriction fragment length polymorphisms/chromosome walidng/genetic map) ROBERT S. REITER*, JOHN G. K. WILLIAMS*, KENNETH A. FELDMANN*t, J. ANTONI RAFALSKIt, SCOTT V. TINGEYt, AND PABLO A. SCOLNIK*§ *Central Research and Development and tAgricultural Products, E. I. Du Pont de Nemours & Company, Experimental Station, Wilmington, DE 19880-0402 Communicated by Nina V. Fedoroff, November 15, 1991 (received for review August 5, 1991) ABSTRACT A population of Arabidopsis thaliana recom- binant inbred lines was constructed and used to develop a high-density genetic linkage map containing 252 random am- plified polymorphic DNA markers and 60 previously mapped restriction fragment length polymorphisms. Linkage groups were correlated to the classical genetic map by inclusion of nine phenotypic markers in the mapping cross. We also applied a technique for local mapping that allows targeting of markers to a selected genome region by pooling DNA from recombinant inbred lines based on their genotype. We conclude that random amplified polymorphic DNAs, used in coglunction with a recombinant inbred population, can facilitate the genetic and physical characterization of the Arabidopsis genome and that this method is generally applicable to other organisms for which appropriate populations either are available or can be developed. The crucifer Arabidopsis thaliana is a useful system for basic studies in plant molecular genetics due to its relatively small genome size, small amounts of dispersed repetitive DNA, and rapid generation time (1). These attributes have made Arabidopsis an attractive model system for the analysis of genome organization and the development and use of tech- nology to clone genes known only through their genetic map position. High-density genetic maps based upon DNA markers can provide starting points for chromosome walking experi- ments. Markers closely linked to a mutation of interest can reduce the amounts of DNA to be cloned and help establish the direction of the chromosome walk. Restriction fragment length polymorphisms (RFLPs) have been used as markers to construct genetic maps (2) and as starting points for chro- mosome walking (3). To date, two different RFLP maps have been reported in Arabidopsis (4, 5). Recently another class of genetic markers [random ampli- fied polymorphic DNAs (RAPDs)] has been described (6, 7), which relies on the observation that a single oligonucleotide primer, of arbitrary nucleotide sequence, will direct the amplification of discrete loci (for a more detailed description of this method, see ref. 8). We report here the use of RAPD markers to construct a genetic map of A. thaliana. This map has been constructed with unprecedented speed by using RAPD markers and a recombinant inbred (RI) population. For many mapping purposes RI populations are superior to F2 or backcross populations because they constitute a per- manent population in which segregation is fixed (9). Addi- tional markers scored on the same RI population are auto- matically integrated with the existing map, making map information cumulative (9). Near-isogenic lines have been used to target RFLP (10) or RAPD (11) markers to specific segments of a genome. However, construction of near-isogenic lines is time con- suming, and unlinked portions of the donor genome remain even after several crosses to the recurrent parent (12). Pooling DNA based on phenotype has been used as a means of either identifying additional RFLP loci (13) or mapping existing RFLP loci (14) near genes of interest. Recently, Michelmore et al. (15) have shown that DNA pools based on phenotype can be used to target markers to a locus respon- sible for the phenotype. This technique allowed them to quickly identify three additional RAPD markers linked to a disease-resistance locus in lettuce. Pooling DNA from seg- regants is an attractive alternative to constructing near- isogenic lines. We demonstrate a strategy for targeting mark- ers to discrete regions of the genome, which involves pooling segregants based on genotype. Using RI lines that constitute a permanent set of fixed genotypes in combination with RAPD markers, one can quickly target markers to virtually any portion of a genome from a single locus up to an entire chromosome. This method is generally applicable to any organism in which a set of genotyped individuals is available. MATERIALS AND METHODS Population Development. Arabidopsis marker line W100, which carries nine phenotypic markers (an, ap-1, er, py, hy-2, g1-J, bp, cer-2, and tt-3; ref. 16) was crossed with pollen from wild-type A. thaliana ecotype Wassileskija (WS). After self- fertilization of the F1 hybrid, we generated 150 RI lines to F8 from individual F2 plants using single-seed descent (17). DNA Isolation. DNA was isolated from 3- to 4-week-old plants grown in liquid culture. Five to 20 surface-sterilized Arabidopsis seeds were inoculated into 50 ml of sterile Gamborg's B5 liquid medium (GIBCO-BRL) and grown under continuous illumination on a rotary platform (50 rpm). Harvested tissue was frozen at -70'C, lyophilized, and ground before DNA isolation. DNA was isolated by the method of Murray and Thompson (18), but in which an additional phenol/chloroform extraction and ethanol precip- itation were included as a final step. Prinmer Synthesis. Oligodeoxynucleotide primers were syn- thesized in a Du Pont Coder 300 automated DNA synthesizer or were obtained from either National Biosciences (Hamel, MN) or Operon Technologies (Alameda, CA). Primers were purified by gel filtration on Sephadex G25 (NAP-5 columns, Abbreviations: RAPD, random amplified polymorphic DNA; RFLP, restriction fragment length polymorphism; cM, centimorgan(s); RI, recombinant inbred; WS, Arabidopsis thaliana ecotype Wassiles- kija; LOD, logarithm of odds. tPresent address: Department of Plant Science, Forbes Hall, Uni- versity of Arizona, Tucson, AZ 85721. §To whom reprint requests should be addressed. 1477 The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. Downloaded by guest on August 27, 2020
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Page 1: Global and local Arabidopsis DNAs · Genetics: Reiter et al. Mendelian fashion or were not reproducible. Ninety-eight percent ofthe polymorphisms identified by a single primer were

Proc. Nati. Acad. Sci. USAVol. 89, pp. 1477-1481, February 1992Genetics

Global and local genome mapping in Arabidopsis thaliana by usingrecombinant inbred lines and random amplified polymorphic DNAs

(restriction fragment length polymorphisms/chromosome walidng/genetic map)

ROBERT S. REITER*, JOHN G. K. WILLIAMS*, KENNETH A. FELDMANN*t, J. ANTONI RAFALSKIt,SCOTT V. TINGEYt, AND PABLO A. SCOLNIK*§*Central Research and Development and tAgricultural Products, E. I. Du Pont de Nemours & Company, Experimental Station, Wilmington, DE 19880-0402

Communicated by Nina V. Fedoroff, November 15, 1991 (received for review August 5, 1991)

ABSTRACT A population of Arabidopsis thaliana recom-binant inbred lines was constructed and used to develop ahigh-density genetic linkage map containing 252 random am-plified polymorphic DNA markers and 60 previously mappedrestriction fragment length polymorphisms. Linkage groupswere correlated to the classical genetic map by inclusion of ninephenotypic markers in the mapping cross. We also applied atechnique for local mapping that allows targeting of markers toa selected genome region by pooling DNA from recombinantinbred lines based on their genotype. We conclude that randomamplified polymorphic DNAs, used in coglunction with arecombinant inbred population, can facilitate the genetic andphysical characterization of the Arabidopsis genome and thatthis method is generally applicable to other organisms forwhich appropriate populations either are available or can bedeveloped.

The crucifer Arabidopsis thaliana is a useful system for basicstudies in plant molecular genetics due to its relatively smallgenome size, small amounts of dispersed repetitive DNA,and rapid generation time (1). These attributes have madeArabidopsis an attractive model system for the analysis ofgenome organization and the development and use of tech-nology to clone genes known only through their genetic mapposition.

High-density genetic maps based upon DNA markers canprovide starting points for chromosome walking experi-ments. Markers closely linked to a mutation of interest canreduce the amounts ofDNA to be cloned and help establishthe direction of the chromosome walk. Restriction fragmentlength polymorphisms (RFLPs) have been used as markers toconstruct genetic maps (2) and as starting points for chro-mosome walking (3). To date, two different RFLP maps havebeen reported in Arabidopsis (4, 5).

Recently another class of genetic markers [random ampli-fied polymorphic DNAs (RAPDs)] has been described (6, 7),which relies on the observation that a single oligonucleotideprimer, of arbitrary nucleotide sequence, will direct theamplification of discrete loci (for a more detailed descriptionof this method, see ref. 8). We report here the use of RAPDmarkers to construct a genetic map ofA. thaliana. This maphas been constructed with unprecedented speed by usingRAPD markers and a recombinant inbred (RI) population.For many mapping purposes RI populations are superior toF2 or backcross populations because they constitute a per-manent population in which segregation is fixed (9). Addi-tional markers scored on the same RI population are auto-matically integrated with the existing map, making mapinformation cumulative (9).

Near-isogenic lines have been used to target RFLP (10) orRAPD (11) markers to specific segments of a genome.However, construction of near-isogenic lines is time con-suming, and unlinked portions of the donor genome remaineven after several crosses to the recurrent parent (12).Pooling DNA based on phenotype has been used as a meansof either identifying additional RFLP loci (13) or mappingexisting RFLP loci (14) near genes of interest. Recently,Michelmore et al. (15) have shown that DNA pools based onphenotype can be used to target markers to a locus respon-sible for the phenotype. This technique allowed them toquickly identify three additional RAPD markers linked to adisease-resistance locus in lettuce. Pooling DNA from seg-regants is an attractive alternative to constructing near-isogenic lines. We demonstrate a strategy for targeting mark-ers to discrete regions of the genome, which involves poolingsegregants based on genotype. Using RI lines that constitutea permanent set of fixed genotypes in combination withRAPD markers, one can quickly target markers to virtuallyany portion of a genome from a single locus up to an entirechromosome. This method is generally applicable to anyorganism in which a set of genotyped individuals is available.

MATERIALS AND METHODSPopulation Development. Arabidopsis marker line W100,

which carries nine phenotypic markers (an, ap-1, er, py, hy-2,g1-J, bp, cer-2, and tt-3; ref. 16) was crossed with pollen fromwild-type A. thaliana ecotype Wassileskija (WS). After self-fertilization of the F1 hybrid, we generated 150 RI lines to F8from individual F2 plants using single-seed descent (17).DNA Isolation. DNA was isolated from 3- to 4-week-old

plants grown in liquid culture. Five to 20 surface-sterilizedArabidopsis seeds were inoculated into 50 ml of sterileGamborg's B5 liquid medium (GIBCO-BRL) and grownunder continuous illumination on a rotary platform (50 rpm).Harvested tissue was frozen at -70'C, lyophilized, andground before DNA isolation. DNA was isolated by themethod of Murray and Thompson (18), but in which anadditional phenol/chloroform extraction and ethanol precip-itation were included as a final step.

Prinmer Synthesis. Oligodeoxynucleotide primers were syn-thesized in a Du Pont Coder 300 automated DNA synthesizeror were obtained from either National Biosciences (Hamel,MN) or Operon Technologies (Alameda, CA). Primers werepurified by gel filtration on Sephadex G25 (NAP-5 columns,

Abbreviations: RAPD, random amplified polymorphic DNA; RFLP,restriction fragment length polymorphism; cM, centimorgan(s); RI,recombinant inbred; WS, Arabidopsis thaliana ecotype Wassiles-kija; LOD, logarithm of odds.tPresent address: Department of Plant Science, Forbes Hall, Uni-versity of Arizona, Tucson, AZ 85721.§To whom reprint requests should be addressed.

1477

The publication costs of this article were defrayed in part by page chargepayment. This article must therefore be hereby marked "advertisement"in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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Page 2: Global and local Arabidopsis DNAs · Genetics: Reiter et al. Mendelian fashion or were not reproducible. Ninety-eight percent ofthe polymorphisms identified by a single primer were

Proc. Natl. Acad. Sci. USA 89 (1992)

AB

FIG. 1. Example of RAPD band seg-regation in RI populations. Ethidium bro-mide-stained electrophoretic pattern ofDNA amplified from individual RI orparental lines. Arrows indicate two inde-pendent dominant markers amplified byprimer r239 (A and B) and a singlecodominant marker amplified by primer

]-- C rapl4e (C). Asterisks indicate heterozy-gotes identified by primer rapl4e.

Pharmacia). Primer length was 10 nucleotides, except for 96primers that were nine nucleotides long.RAPD Markers. Amplification was done in a Biocycler

oven (Bios, New Haven, CT). Amplification parameterswere 920C for 3 min followed by 45 cycles with 3YC toleranceat 950C for 30 sec, 340C for 15 sec, and 740C for 1 min. A 720Cincubation for 8 min was included as a final step. Twenty-five-microliter amplification reactions contained 80 mMTris-HCl (pH 9.0), 20mM(NH4)2SO4, 3.5mM MgCl2, 100 JuMof each dNTP (Boehringer Mannheim, pH 7.0), 0.4 AuMprimer, 1 unit ofAmpliTaq DNA polymerase (Perkin-Elmer/Cetus), and 25 ng of genomic DNA. Reactions were held in96-well polycarbonate microtiter plates (Techne, Princeton,NJ) and overlaid with 20 1,u of mineral oil. With a mappingpopulation of46 RIs, two RAPD primers can be examined per96-well microtiter plate. Amplification products were ana-lyzed by gel electrophoresis in 1.2% agarose gels and visu-alized by ethidium bromide staining. Markers were scored forthe presence or absence of the corresponding DNA bandamong the segregating RI populations.RFLP Markers. Genomic DNA (1 ug) was digested with

one of five restriction enzymes (BamHI, EcoRI, EcoRV,HindIII, and Xba I) and transferred to Immobilon-N (Milli-pore), according to the manufacturer's instructions. Prehy-bridizations and hybridizations were done at 65°C in 5xstandard saline phosphate/EDTA (SSPE) (lx SSPE is 0.18M NaCI/10 mM phosphate, pH 7.4/1 mM EDTA)/0.5%SDS/5 x Denhardt's solution/5% dextran sulfate/denaturedsalmon sperm DNA at 100 ,ug/ml. DNA isolated either fromA phage (19) or from cosmids (20) was labeled by the randomhexamer method (21).

Linkage Analysis. Segregating markers were scored aseither A (WS homozygote) or B (W100 homozygote). Resid-ual heterozygotes and ambiguous data were scored as M(missing). Linkage analysis was done by using a Macintoshimplementation of the MapMaker program (22) provided byS. V. Tingey and J. A. Rafalski. The data were analyzed asan F2 population because MapMaker does not handle RI data;this results in a doubling of the logarithm of odds (LOD)scores; thus a LOD score 6.0 was set for linkage threshold.The recombination frequency (r) in a single meiosis wascalculated from the fraction of recombinants (R) using therelationship r = R/2(1-R) (23). Map distances in centimor-gans (cM) were calculated from recombination frequencies(r) by using Kosambi's mapping function (24).

Targeting Markers to Chromosome 1. Two DNA pools,each containing equal amounts ofDNA from six different RIpopulations, were used to identify additional polymorphismsresiding on chromosome 1. These pools were constructedbased upon their genotype at all RFLP loci mapped onchromosome 1. The WS pool contained DNA from RI linesthat were homozygous for WS alleles at each locus tested on

chromosome 1. The W100 pool was analogous, except RIpopulations were homozygous for W100 alleles. Amplifica-tion reactions were done as described using 25 ng of pooledDNA.

RESULTSGenetic Mapping with RAPD Markers. In an initial screen

for polymorphisms between WS and W100, we tested =1200RAPD primers. Twenty percent (245) of these primersshowed polymorphisms between the two lines. The totalnumber of polymorphic DNA bands was 392. These poly-morphisms were mapped in a population of46 RI lines. Ofthe392 polymorphic DNA bands, 225 polymorphisms segregatedin a Mendelian fashion in the RI subpopulation (Fig. 1). Theremaining polymorphisms either segregated in a non-

C E

S

D F

II

FIG. 2. Blot analyses ofRAPD bands. Amplifications used eitherprimer rli (A) or primer r315 (B). After agarose gel electrophoresis,the appropriate polymorphic bands (arrows) were excised and usedas hybridization probes to blots of duplicate amplification reactions(C and D) and genomic DNA digested with BamHI, EcoRI, andEcoRV (E and F, left to right).

W,-FORIR12.14

.I.-

46 I.,.-,...

1478 Genetics: Reiter et al.

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Page 3: Global and local Arabidopsis DNAs · Genetics: Reiter et al. Mendelian fashion or were not reproducible. Ninety-eight percent ofthe polymorphisms identified by a single primer were

Genetics: Reiter et al.

Mendelian fashion or were not reproducible. Ninety-eightpercent of the polymorphisms identified by a single primerwere >10 cM apart.The genomic sequence complexity of amplified loci is

important if RAPDs are to be used as genetic anchors forphysical mapping or as starting points for chromosomewalking. To determine the copy number of our RAPD mark-ers, we hybridized DNA from 18 polymorphic RAPD bandsto DNA blots (Fig. 2). Results indicate that 9 of the RAPDfragments hybridized to sequences present at 3 copies or lessin the genome, whereas the remaining RAPD fragmentshybridized to sequences present at 3-10 copies. Thus, one-half of the RAPDs identified may be useful as hybridizationprobes representing a specific genomic target. Interestingly,16 of 18 RAPDs (89%), which were used as hybridizationprobes, also identified an RFLP between WS and W100. Thisfrequency is greater than that seen with genomic A clones(50%o) or cosmids (65%). RAPDs may, thus, be useful inidentifying traditional RFLPs.

Genetic Mapping with RFLP Markers. To provide integra-tion with the two existing Arabidopsis RFLP maps, weremapped 44 genomic A clones (4) and 16 cosmid clones (5)by using a collection of 115 RI lines that included the same 46lines used for RAPD mapping.

Genetic Map Construction. A genetic map was constructedbased on the segregation of all three marker types (RAPD,

Proc. Natl. Acad. Sci. USA 89 (1992) 1479

RFLP, and phenotypic; Fig. 3). Five linkage groups wereidentified and assigned to the five Arabidopsis chromosomesby their linkage to phenotypic markers (16, 25). A subset of126 markers that could be ordered with a LOD score >3provided a core map with an average distance of 5 cMbetween markers. The remaining markers could not be or-dered unambiguously with the same LOD score, and they areshown in relation to the core map. Ordering of these regionscan probably be improved by increasing the mapping popu-lation size to provide more recombination information.

Local Mapping. A large number of RAPD markers couldprovide additional genetic anchor points and fingerprintinginformation. To increase the marker density on chromosome1, we have created two DNA pools from RI lines, asdescribed, to collaborate on a project with J. Ecker (Univer-sity of Pennsylvania) to physically map Arabidopsis chro-mosome 1 by using RAPDs and RFLPs as hybridizationprobes to yeast artificial chromosomes (26). By testing 384additional primers we identified 32 more polymorphismsbetween each pool (Fig. 4). Of these polymorphisms, 23mapped to chromosome 1 (Fig. 3), 4 mapped to other regionsof the genome, and the remaining 5 did not segregate in aMendelian fashion.

DISCUSSIONWe have used an A. thaliana RI population to demonstratethe use ofRAPD markers for constructing genetic maps. The

Chrc

0.02.53.65.9

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101.3103.6107.4

125.3129.2

137.4

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- rap8k /XAt241, 3.0 00-i X/At488, 1.5

XAt322, 3.0r1356 c4715, 3.0 7-5r315.1 I 1029, 1.5

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r916.4 r694, 7.0r1383, 7.5r731, 6.0rap4c, 0.0I1261.1, 0.0

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Chromosome 5

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FIG. 3. Linkage map of A. thaliana. The 126 markers along the five vertical bars were ordered with LOD score differences (>3.0; see ref.22). Marker loci listed to the right of each chromosome bar could not be ordered with equal confidence (LOD score differences <3.0). All lociwere linked with a LOD score >6.0. The first marker at the top ofeach chromosome was assigned position 0.0, and approximate marker positionsare shown in cM to the left of each chromosome bar. Markers to the right are listed along with an approximate distance in cM from the markersplaced on the LOD 3.0 linkage map. Chromosome 1 RAPD markers with numbers >r1300 were placed by local mapping. Phenotypic markersare italicized; RFLP markers are designated either AAt (4) or c (5). The remaining markers are RAPDs.

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Page 4: Global and local Arabidopsis DNAs · Genetics: Reiter et al. Mendelian fashion or were not reproducible. Ninety-eight percent ofthe polymorphisms identified by a single primer were

Proc. Nat!. Acad. Sci. USA 89 (1992)

FIG. 4. Example of local map-ping for detection of polymor-

4 phisms with chromosome 1 DNApools. RAPD primers r15-9G andr1599 identify polymorphic bandsin parental lines. Only primer rl599identifies a polymorphism betweenWS-C1 and W100-C1 pools.Primer r1599 was subsequentlymapped to chromosome 1 near po-sition 83.1 (see Fig. 3). Arrowsindicate polymorphic bands.

final map contains 320 marker loci with an average distanceof 2 cM between markers. This map has a total length of 630cM, slightly greater than previous estimates (4, 5, 25). Wehave also integrated our RAPD map with the existing clas-sical and RFLP maps (4, 5, 25).We were able to construct this map in a reasonable time

and with a relatively small effort due to the speed with whichRAPD markers can be generated. By screening 1200 differentprimers, 225 marker loci were identified and mapped inArabidopsis by two full-time workers in a 4-mo period. Bycomparison, it took five full-time workers 2 yr to construct a600-marker soybean RFLP map (J.A.R. and S.V.T., unpub-lished work).We have used a different technique, which we call "local

mapping," to target a specific region of the Arabidopsisgenome for saturation with RAPD markers. This technique isbased upon pooling DNA from RI lines selected on the basisof their genotype. The targeted regions can range from anentire chromosome to a small region surrounding a singlelocus. The technique can be used with RFLP markers but isespecially useful with RAPD markers because large numbersof primers can be analyzed very quickly. Using this ap-proach, we targeted markers to chromosome 1, where weadded 23 additional markers to the 47 RAPDs obtainedthrough our global mapping efforts. In this experiment, fouradditional RAPD markers did not map to chromosome 1. Thisfinding is probably due to the fact that only six individuals inour genotyped population were homozygous for all parentalalleles tested with chromosome 1 RFLPs. These six individ-uals were also fixed for alleles from only one parent in otherregions ofthe genome. For experiments in which the mappingtarget is smaller than an entire chromosome, more individualsshould be available for pooling, thus decreasing the proba-bility ofhaving only alleles from one parent in regions outsidethe target (15).Our collection of genetically fixed and genotyped RI lines

allows targeting of markers to any part of the Arabidopsisgenome by pooling the appropriate RI lines by genotype. Theapproach has use for filling gaps in genetic maps and pro-viding either additional markers near single loci to supportchromosome walking or entire chromosomes to supportphysical mapping.Although we have used Arabidopsis as a model system, the

approach described here can be applied to any organism forwhich RI lines exist or can be developed (9, 27). RAPDmarkers can also be mapped efficiently in any populationwhere segregation can be scored in single recombinant ga-metes. Several examples include organisms where a haploidgeneration can be maintained, doubled haploid and backcrosspopulations, and F2 populations where only markers linked incoupling are considered.

A disadvantage ofRAPD markers is that they typically aredominant, whereas RFLP markers are generally codominant.Therefore, the type of mapping population used is importantto maximize the amount of recombination information ob-tained. The relative two-point mapping efficiency of F2 andbackcross populations has been calculated by Allard (28). F2populations efficiently map codominant markers, such asRFLPs, but map dominant markers less efficiently (Fig. 5).Backcross populations map dominant and codominant mark-ers with equal efficiency (Fig. 5). We have calculated (Fig. 5legend) the mapping efficiency of RI populations for bothmarker types and found that dominant markers can bemapped as efficiently as codominant markers when RI pop-ulations are used (Fig. 5). In addition to mapping dominantand codominant markers with the same efficiency, RI linesare advantageous because they constitute permanent map-ping populations in which all marker information is cumula-tive (29). For example, when cloned genes are mapped, asingle hybridization provides linkage information to all pre-viously mapped loci in the population (27).RAPD bands observed in eitherWS or W100 lines may not

be detectable in other Arabidopsis ecotypes. Crossing plantsof these ecotypes to either WS or W100 would allow use ofthe corresponding RAPDs from our map. Additional RAPDmarkers specific for the other ecotype can be added by localmapping. Alternatively, many ofour mapped RAPD markerscould be used as hybridization probes and, thus, converted toRFLPs.We intend to use RAPDs as anchors for physical mapping

and starting points for chromosome walking; however,RAPDs corresponding to interdispersed multicopy DNAwould not be immediately useful to identify, by hybridiza-tion, particular cloned DNA corresponding to single genomiclocations. According to our results, this procedure couldconstitute a problem with approximately half of the markersreported here. At present, we foresee two possible ap-proaches to this problem. (i) Other RAPD markers identifiedby local mapping could be preselected for single copy byhybridization to genomic DNA. (ii) An alternative approachis the use of sequence information corresponding to the ends

0.0 0.1 0.2 0.3 0.4 0.5 0.4 0.3 0.2 0.1

Recombination Fraction (r)0.0

FIG. 5. Theoretical efficiency with which RI, F2, and backcross(BC) populations can detect recombinants by using either codomi-nant or dominant markers. The amount of information per individual(ip) in a mapping population is the inverse of the variance divided bypopulation size (28). For an RI population ip is approximately equalto 2/r(1 + 2r)2. Allard (28) previously derived ip for the otherpopulations shown. The amount of information per individual isrepresented by the logarithm of ip and is plotted against the recom-bination fraction (r) for repulsion- and coupling-phase linkage. An RIpopulation is equally efficient with either codominant or dominantmarkers and is very efficient for closely linked markers.

-j0-o

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U) 'r Un °-

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r15-9G r1599

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Page 5: Global and local Arabidopsis DNAs · Genetics: Reiter et al. Mendelian fashion or were not reproducible. Ninety-eight percent ofthe polymorphisms identified by a single primer were

Proc. Natl. Acad. Sci. USA 89 (1992) 1481

of multicopy RAPD fragments. Because these RAPD bandscorrespond to discrete loci the DNA sequences used aspriming sites for amplification are probably specific. Se-quence information would permit the conversion of RAPDsinto sequence-tagged sites (29). This procedure would allowthe use of the PCR to screen genomic libraries (30).

We acknowledge Roslyn Young for excellent technical assistance;Andrew Paterson for valuable comments; Michael Hanafey forassistance with mapping efficiency calculations; Elliot Meyerowitz,Brian Hauge, and Howard Goodman for providing RFLP probes; andTimothy Caspar, Forrest Chumley, Barbara Mazur, David Patton,and Barbara Valent for critical reading of the manuscript.

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