Capsicum Genome Maping

8/3/2019 Capsicum Genome Maping

1/20

Copyright 1999 by the Genetics Society of America

Genome Mapping in Capsicum and the Evolution of Genome Structurein the Solanaceae

Kevin D. Livingstone,* Vincent K. Lackney,* James R. Blauth,* ,1 Rik van Wijk

and Molly Kyle Jahn*

*Department of Plant Breeding, Cornell University, Ithaca, New York 14853 and Keygene, n.v., 6708 PW Wageningen, The Netherlands

Manuscript received December 11, 1998Accepted for publication April 7, 1999

ABSTRACT

We have created a genetic map of Capsicum (pepper) from an interspecific F2 popu lation consisting

of 11 large (76.2192.3 cM) and 2 small (19.1 and 12.5 cM) linkage groups that cover a total of 1245.7

cM. Many of the markers are tomato probes that were chosen to cover the tomato genome, allowing

comparison of this pepper map to the genetic map of tomato. Hybridization of all tomato-derived probes

included in th is studyto positions throughou t the pepp er m ap suggests that no m ajor losses have occurred

during the divergence of these genomes. Comparison of the pepper and tomato genetic maps showed

that 18 hom eologous linkage blocks cover 98.1% of the tomato gen ome and 95.0% of the pep per genome.

Through these maps and the potato map, we determined the number and types of rearrangements that

differentiate these species and reconstructed a hypothetical progenitor genome. We conclude there havebeen 30 breaks as part of 5 translocations, 10 paracentric inversions, 2 pericentric inversions, and 4

disassociations or associations of genomic regions that differentiate tomato, potato, and pepper, as well

as an additional reciprocal translocation, nonreciprocal translocation, and a duplication or deletion that

differentiate the two pepper mapping parents.

T HE field of comparative plant genomicswasprecipi- linkage blocks between related genomes, even whentated in 1988 by two studies in th e Solanaceae r elat- comparing species that vary widely in DNA content anding the genetic maps of tomato and potato (Bon ier bal e karyotype morphology ( Gebh ar dt et al. 1991; Tanks-

et al. 1988) and tomato and pepper ( Tanksl ey et al. l ey et al. 1992; Weeden et al. 1992; Menancio-Haut ea

1988), each of which was constructed using common et al. 1993; Kowal ski et al. 1994; Bennet zen an d Fr ee-

restriction fragment length polymorphism (RFLP) l ing 1997; Cheung et al. 1997; Bennet zen et al. 1998;probes. The first study found th at the tomato and p otato Gal e an d Devos 1998a,b; Lager cr ant z 1998).genomes differed only by paracentric inversions, and There are other previously published and unpub-further studies ( Gebh ar dt et al. 1991; Tanksl ey et al. lished genetic maps of Capsicum based on either inter-1992) showed th at five in version s differentiated the se specific Capsicum annu um C. chinense populationsspecies. The tomato-pepper study also suggested that ( Tanksl ey 1984; Tanksl ey et al. 1988; Pr inc e et al.pepper had maintained genomic content similar to to- 1993; Kim et al. 1998a), intr aspecific C. annuum doubled-mato, as defined by the presence of pepper sequences haploid popu lations ( Lefebvr e et al. 1995, 1997; Lefeb-complementary to all tomato cDNAs tested, but that th e vr e an d Pal l oix 1996; Car ant a et al. 1997a,b), otherpep per gen ome was rearr anged substantially, with man y interspecific crosses ( Z h an g 1997; Y. Zh an g, unpub-pepper chromosomes containing three to four distinct lished results), or an intraspecific C. annu um F2 popula-tomato segments. A later, more detailed comparison of tion ( Massoudi 1995). To date, however, there is nopepper and tomato concluded that pepper had lost map of Capsicum that achieves the goal of completelyregions hom ologous with the tomato genome and failed delineating and saturating the pepper chromosomes.

to change the perception that the ho meologous linkage To answer questions remaining from these earlierblocks in th e pep per genome were fragmented substan- studies of Capsicum, a complete genetic map with 12tially( Pr inc e et al. 1993). As a result, the p epp er-tomato linkage groups anchored in and completely represent-comparison remains the frequently cited exception to ing the tomato genome is required. Toward this end,nu merou s studies that have shown con servation of large we have constructed a mo lecular map of Capsicum u sing

rand omly amplified polymorp hic DNA (RAPD), iso-

zyme, amplified fragment length polymorphismCorresponding author: Molly Jahn, Department of Plant Breeding, (AFLP), and RFLP an alyses with tomato- and pepp er-

252 Emerson Hall, Cornell University, Ithaca, NY14853. der ived pro bes, which has allowed us to reexamine qu es-E-mail: [email protected]

tions of gen ome structure and karyotypic evolution in1 Present address: Division of Biological Science s, Alfred Un iversity,Alfred, NY14802. pepper, tomato, and potato.

Genetics 152: 11831202 ( July 1999)


2/20

1184 K. D. Livin gston e et al.

MATERIALS AND METHODS Genetic map co nstruction: The genotypes of the RFLPsand RAPDs were scored ind epen dently to obtain a consensus

Population construction, DNA e xtractions, and cytological genotype. If a probe produced multiple segregating bands,examination: T h e F2 mapping population of 75 plants was then each band was initiallyscored as a dominan t band . Somedeveloped byself-pollinating one F1 hybrid plant ofC. annuu m of these genotypes were subsequently converted to codomi-cv. NuMex RNaky ( Nakayama an d Mat t a 1985) C. chi- nant pairs if two dominant bands, one from each parent,nense PI 159234, obtained from S. Tanksley (Cornell Un iver- mapped to the same position.sity, Ithaca, NY) . The pare nts and F1 and F2 plants were grown The initial RFLP d ata were then merged with isozyme,in the greenhouse at Cornell University, and DNA was ex- RAPD, and AFLP marker genotypes. A test of departure fromtracted from harvested leaf tissue following the procedure of expected Mendelian ratios was conducted where possible;

Pr inc e et al. (1997). Immature F1 flower buds were collected however, a number of the AFLP genotypes included A, B, H,and fixed in Carnoys solution for cytological examination. and C ( B or H) or D (A or H ) callsp recluding this analysis.The buds were transferred to a 70% ethan ol solution and The markers were also divided into classes on the basis of athen squashed with gentle h eating in a 2% acetocarmine:45% subjective measure of the certainty with which the genotypeacetic acid solution. Metaphase I and anaphase I in pollen was ascertained. These classifications were used to find themother cells were then observed by light microscopy. RFLP markers that could be unambiguously read and whose

Molecular markers: RFLP: Pepper, tomato, and tobacco deviations from the expected Mendelian frequencies were P DNA fragments were used as probes for RFLP. Three types 0.01 for dominant markers and P 0.001 for codominantof tomato clones described in Tanksl ey et al. (1992) were markers. The more distorted m arkers were excluded fromsupplied by S. Tanksley: tomato random gen omic DNA (TG) , the initial framework con struction phase to protect againsttomato whole-leaf cDNA (CD), and tomato leaf epidermal mapping errors stemming from either pseudolinkages con-

joining independent chromosomal regions or incorrect esti-cDNA (CT). Pepper leaf epidermal cDNA (PC) and peppermates of map distances ( Lor ieux et al. 1995; Cl out ier et al.random genomic (PG) DNA clones, described by Pr inc e et1997).al. (1993) and Bl au t h (1994), were either supplied by S.

The MAPMAKER/ EXP v3.0b program ( Lincol n et al. 1993)Tanksley or generated in our lab. In addition to these, other

was used for map construction. The subset of markers defin edclonesused asprobesincluded the following:the tomato genesabove was divided into linkage gro ups using the group com-Prf, supplied by G. Martin (Boyce Thom pson In stitute, Ithaca,mand (parameters: LOD 3, 20 cM), and then arrangedNY), and Sw-5, supplied by S. Tanksley; four p epper genomicinto a framework map using the order command (parame-clones (UB) from U. Bonas (Martin Luther University, Dom-ters: LOD 3 for linkage, 20 cM, initial group size of 3,platzl, German y); and th e tobacco NcDNA(pN18C) providedLO D 3 vs. alternative order s). The resultant ord ers for eachby B. Baker (U .S. Departmen t of Agriculture, Albany, CA).group were checked bym ultiple iterations of thisp rocess afterSurvey filters were prep ared to assess polymorp hism be-scrambling th e marker input order. When multiple markerstween paren tal DNA digested with 12 differen t restrictioncosegregated, codominant markers were given preferen ce forenzymes:DraI,EcoRI,EcoRV,HindIII,BstNI, TaqI,XbaI,BamH I,inclusion in the framework. Framework o rder s were checkedBglII, BclI, SacI, and StuI. Mapping filter sets for each of theby manu al examination of the LOD table, the ripple com-12 restriction enzymes were also prepared, including bothmand (parameters: 3 markers, reporting alternative orders ifparents and all 75 F2 progeny. All filters were prehybridizedLO D 3 compared to the set framework), and finally byfor at least 4 hr in 70 ml of hybridization buffer before use.checking the p airwise linkages between all framework marker sThe cloned inserts used as probe s were am plified by PCR andfrom different linkage groups.then purified on Sephadex G50 spin columns equilibrated

AFLP markers were added to the linkage groups via thewith Tris-EDTA to reduce background signal. These productsassign command (parameter values LOD 3 and 20were then radiolabeled using a protocol modified from Fein-cM), and they were added to the chromosomal frameworksber g an d Vog el st ein (1983) as follows. The am oun ts of theusing th e build command if the placement of a m arker intofollowing reagents were doubled to increase the signala particular interval was significantly better (LO D 3) thanstrength when using heterologous probes: cloned DNA (200all alternative placements. This addition procedure was thenng instead of 100 ng DNA), labeling solution (22 l insteadrepeated for the remaining initial RFLP m arkers and the

of 11 l), Klenow enzyme (8 units instead of 4 units), andskewed markers. The resultant orders for each linkage group

[ 32P]dCTP (0.1 mCi instead of 0.05 mCi). After a 90-min incu-were then checked again by manu al examination of the LOD

bation at 37, the labeled clones were purified on Sephadextable and the ripple command, as described above. Finally,

G50 spin column s in 1% SDS and 25 m m EDTA spun at 2500the p ositionsfor all remaining markerswere determined using

rpm for 8 min. The clones were denatured by heating atthe try command. Markers were given either a position be-

100 for 10 min and then added to the h ybridization buffer.tween framework markers if 2 LO D 3 for the interval

Hybridization was carried out overnight at 65. Filters wereand all other placements were unlikely (LOD 1), or they

washed with one low-stringency ( 2 SSC, 0.1% SDS) washwere added into haplotype groups. Haplotype groups con-

and two moderate-stringency (1 SSC, 0.1% SDS) washes at

sisted of markers that were separated from framework markers65 and placed o n Kodak XAR-5 film for 312 days, dep end ing by 5 cM and placement on either side of the frameworkon signal strength. marker was equally likely. These markers were assigned posi-

Isozyme analysis: The procedures ofLoaiza-Figu er oa et al. tions with the framework marker(s), but they are differenti-(1989) were carried out in th e laboratory of N. Weeden (New ated on the map (see Figure 1 legend). Some markers wereYork State Agricultural Expe rimen t Station, Gen eva, NY) to placed beyond the framework en ds of the linkage groups ifanalyze Idh-1, Gpi-1, Gpi-2, 6-Pgdh, Pgm-1, Pgm-2, and Tk. they mapped to the end of a linkage group (2 LO D 3)

PCR-based markers: RAPD markers were generated following and all altern ative locations within the group were unlikelythe pr ocedures ofPr inc e et al. (1995). RAPD 10-mer primers (LOD 1). Pairwise linkages with the terminal frameworkwere obtained from th e National Science Foun dation/ Depart- markers were checked to ensure correct placement. Thesemen t of Energy/ U.S. Departmen t of Agriculture Plant Science markers were add ed to th e map; however, they were n ot con-Center at Cornell Un iversity and from Gilroy Foods ( Gilroy, sidered framework markers for further linkage group exten-CA). AFLP markers were generated by Keygene n.v. (Wagen- sion. All mapping was done without reference to the order ofingen, The Netherlands) using the procedure of Vo s et al. markers on th e tomato m ap, and all distances were comp uted

using the Kosambi mapping function ( Kosambi 1944).(1995).


3/20

1185Genome Evolution in the Solanaceae

Construction o f the synteny map: A second genetic map pected single-locus Mende lian ratios. Slightly mor e th anwas constructed to maximize the number of tomato-derived half of the tested subset (337 50.7%) showed devia-markers for comparative analysis. For this map, all nontomato

tion from the expected ratios ( P 0.01); 81 of thesemarkers were removed, and positions for the remaining to-(12.2%) were severely distorted ( P 0.001), with Pmato-derived markers were estimated by reducing the strin-

gencyfor addition to haplotype groups ( 8 cM) or placement values as low as 2.69 1025. Two common causes ofbetween framework loci ( LOD 1.5). Other markers that misclassified segregation distortion (residual heterozy-mapp ed into several contiguous intervals were placed at their gosity and comigrating RFLP or PCR fragments) weremost likely positions. The tomato map ofPil l en et al. (1996)

ruled out because (1) all F2 plants came from only onewas then reduced to only the markers in common between

F1 individual that could carry only one allele from eachthe two maps.parent; and (2) within a distorted region, all RFLP and

AFLP marker s were distorted an d com igration of multi-RESULTS ple indepen den t markers is extremely un likely.

The distorted regions (0.01 P 0.001) includedCytology of meiosis in ( C. annuum NuMex RNaky the middle of pepper linkage group (P)1 between TG70C. chinensePI 159234) F1 plants:Cytological examinationand A211, distorted in favor ofC. annu um homozygotesof meiotic chromosome spreads from pollen motherover C. chinense ho mozygotes; the midd le of P3 betweencells ofC. annuum C. chinense F1 revealed multivalentsTG74 and TG290a, distorted in favor of C. chinense h o-and bridges extending across the metaphase plate atmo zygotes over C. annu um homozygotes; the bottom oflate anaphase I ( M. Cad l e, unpublished results). TheseP6 n ear CT109, distorted in favor of h eterozygotes overdata are consistent with the presence of at least oneC. annuum ho mozygotes;an d the middle of P11 betweenreciprocal translocation between these species, as de-CT70 and CD127a, distorted in favor of C. annuum h o-scribed pre viously by Tanksl ey (1984), Kumar et al.mozygotes over C. chinense homozygotes. Severely dis-(1987), and Lant er i an d Picker sgil l (1993).torted regions ( P 0.001) included the upper endMarker genotyping and analysis: RFLP: A total of 399of P2 d own to CT128a, with an excess of C. chinensetomato probes selected to represent the tomato genomeho mozygotes over C. annuum hom ozygotes; the upp erwere assayed for p olymorp hism (270 TG, 89 CT, 33end of P3 at CT220, with an excess of heterozygotesCD, and 7 other tomato cDNAs). Furthermore, 184 PGover C. chinense homozygotes; the upper end of P11 atclones, 4 PC clones, 4 other pepper genomic (UB)CD127d and CD186d, again with an excess of he terozy-clones, and pN18C were also tested. All tomato clonesgotesover C. chinensehom ozygotes; all of P7,d istorted intested hybridized to pep per gen omic DNA, and 203 TG,favor ofC. chinense ho mozygotes, almost to the comp lete58 CT, 28 CD, 7 othe r tom ato cDNA, 2 PC, 3 UB, pN18C,exclusion o fC. annuu m alleles in some re gions; and theand 43 PG clones were used as probes. The lower per-upper end of P12 down to A3, with an excess of C.centage of PG clones used (23 vs. 75% for TG, 65% forchinenseho mozygotes over C. annuum hom ozygotes. TheCT, and 85% for CD) resulted from the number of PG

regions correspon ding to P1, P2, P3, P6, P11, and P12clones(74 40.2%) th at produ ced a smear of un resolv-were also distorted in either one or both of the tomatoable bands. Some survey autoradiograms are availablepopulations of de Vicent e an d Tanksl ey (1993) orfrom the Solgenes database2 ( Paul et al. 1994). TheBer nac ch i an d Tanksl ey (1997), and markers fromprobes produced 460 segregating RFLP; 227 (49.3%)P7 and P12 were also distorted in the earlier pepperwere codominant.population ofPr inc e et al. (1993) and the potato popu-Isozymes: Genotypes were obtained for all seven iso-lation ofTanksl ey et al. (1992).zymes.

Genetic map co nstruction: A genetic map consistingPCR-based markers:From the 116 RAPD primers tested,of 11 large (76.2192.3 cM) and 2 small (19.1 and 12.559 prod uced 75 reprod ucible polymorp hic bands (O PR,cM) linkage grou ps covering 1245.7 cM was constructedR, U, OPO, O PA, Q, and OPE markers). In addition,from the genotypic data (Figure 1). Although 2N 2X20 primer com bination s were u sed in AFLP. These reac- 24 for these species, th e reciprocal tran slocation intions yielded 465 segregating bands (A markers), ofthe paren ts would cause pseudolinkage between mark-which 340 could be scored as codominant by a prop rie-

ers near the interchange breakpoints on the chromo-tary algorithm. The primer sequen ces, fragmen t sizes,somes in volved ( Bur nh am 1991). P1 contains Idh-1 an dand paren tal lines showing am plification for all PCR-Pgm-2, which are described by Tanksl ey (1984) asbeingbased markers are available from Solgenes.3

near the exchange breakpoint in a similar interspecificSegregation distortion: Of the 1007 markers gener-cross; therefore, we propose that this linkage groupated, 665 could be tested for deviation from their ex-represents the two pepp er chromosomes involved in

this rearrangement. The two small linkage groups in

our map remained unlinked despite th e use of clones2 Go to http:// probe.nalusda.gov:8300/ and choose databases,then browse from the options of the Solgenes database, and look from the correspond ing regions of the tomato genom e.for image class objects with ACF in the title.

O f t he 1007 marker genotypes gener at ed, 6773 Go to http:// probe.nalusda.gov:8300/ and choose databases,

(67.2%) were eith er given p ositions in the LOD 3 frame-then browse from the options of the Solgenes database, and lookfor the marker under its name in the locus objects list. work or placed in framework intervals at 2 LO D


4/20


Figur e 1.A genetic map of Capsicum. Markers in boldfaced type at tick marks are framework markers ordered at LOD 3, and multiple markers at a tick mark cosegregated. Markers listed in plain type after framework markers were closely linkedto the framework mar kers (5 cM), bu t placed equ ivalentlyon either side of the framework po sition at LO D 2 when comparedto other positions in the linkage group. Markers in parentheses placed between framework positions at 2 LO D 3. Markertypes and designations are as follows: tomato genom ic RFLP (T G); tom ato cDNA RFLP (CD, CT, Sw5, and Prf); pep per genomicRFLP (PG and UB); pepper cDNA RFLP (PC); tobacco cDNA RFLP (pN18C); AFLP (A); RAPD (OP, U, R, Q); and isozyme( Gpi-2, Idh-1, and Pgm-2). Lowercase letters at the end of the marker names indicate that the marker is one of at least twosegregating loci detected by a single assay. Distances between framework positions in centimorgans ( Kosambi) are to the left o feach chrom osome.


5/20


Figur e 1.Continued.

3, while 5 marker s (1 isozyme, 1 TG, 1 CT, and 2 AFLP) this classification placed equ ally well into a small num -

ber ( 35) of contiguous intervalsin th e framework areasremained unlinked. The remaining 325 markers group-

ed (LOD 3) with the linkage groups but did not place with high marker densities. There were, however, 29

markers in this group that placed in a greater numberwell within th e frameworks (m ultiple equ ivalent LO Ds).

The number of these markers from each linkage group of intervals all along the length of a particular chromo-

some. A hallmark of these loci was moderate pairwisecould be a function of the length of the linkage group

( r2 0.77, P 8.4 105). Onlygroups 1 and 4 deviated linkage with a framework locus (LOD 3, 1520 cM),

but no linkage to the flanking framework markers.significantly toward more of these loci than expected

(data not shown) . The majority of the markers that fit The 677 markers across 1245.7 cM provide an average


6/20



marker density of 1 marker per 1.8 cM; however, the allowed Tanksl ey et al. (1992) to show that the clus-

ters represented regions of suppressed recombinationmean distance between framework positions is 9.0 cM.There isgreat variabilityin these den sities because many aroun d tomato centromeres. Pepper centromeres have

been mapped u sing C banding ( Moscone et al. 1993);markers showed pr onou nced clustering (Figure 1). On e

region of marker clustering occurs on each of the large however, pepper lacks both the classical map and dele-

tion studies to correlate our map with these data. Thus,linkage group s and includes 4466% of the markers in

that linkage group. Overall, 54% of the markers are while all the clusterson our map contain markers linked

to centromeres in tomato, an observation also made forlocated in th ese clusters. This figure m ay be an overesti-

mate, however, as some of the AFLP markers may be several of the linkage groups of the map in Pr inc e

et al. (1993), we can only presume that these regionsallelic pairs.

The nonrandom distribution of markers within link- correspond to the centromeric regions of each of the

linkage groups.age groups is similar to tomato, where cytogenetic data


7/20


Genome content: Most probes used ( 66%) pro duced Comparative map of pepper and tomato: The probes

used detected 308 loci on the tomato map ofPil l en et26 bands; 21% gave 610 bands, and 12% revealed

segments of the genome that had been duplicated ex- al. (1996) and 352 loci on our augmented pepper map

(Figure 2). We then defined h omologous segments con-ten sively ( 10 ban ds) b ut still provided distingu ishab le

polymorphisms. To examine the relative copy number taining common markers from contiguous regions of

the genetic maps of both species. Breaks in h omeologyof sequences detected by hybridization, we compared

a subset of 30 pepper survey blots with tomato survey were not declared if the intervening markers not from

the contiguous region of the other species were eitherblots from the Tanksley laboratory using the same

probe-enzyme combinations. Five of the tomato blots from probes detecting multiple segregating loci or frommore than one different chromosome.also included a lane with DNA from our C. annuum

parent. In 2 of these 5 control comparisons, our surveys There were only four regions in pepper and one re-

gion in tomato where h omeo logy was either d ifficult toshowed more bands th an the Tanksley surveys (6 vs. 2

and 9 vs. 3). In the other three cases, results were more assign or not apparent: the top of P4, which included

markers from throughout the tomato genome; the topsimilar (3 vs. 1, 5 vs. 4, and 11 vs. 10), although in every

case the larger number came from our laboratory. This of P5, which is duplicated in and represented on ly by

dominant m arkers from the C. chinense parent; the toplimited samp le suggests that some differen ces observed

between tomato and pepper in the copy number of of P7, which contains a large number of markers that

are spread throughout the tomato genome and someprobes may result from specific laboratory procedu res.

When all 30 comparisons between pepper and tomato loci that were uniquely duplicated in pepper; the bot-

tom of P7, which con tained markers from different to-were considered, 14 showed more bands for a given

probe in pepper than tomato, and 16 were approxi- mato chromosomes;and the top oftomato chromosome

(T)7, which is represented in the pepper (all probesmately similar.

In our study, 43 clones (6 pepper genomic DNA, and hybridized) but appears to be scattered throughout the

pepper genome. It is impossible to tell whether these37 tomato probes, 17 cDNA, and 20 genomic clones)

detected multiple segregating loci in p epper. Seven of regions are the result of novel associations of markers

in on e of the genera or the disassociation of a group ofthe 37 tomato clon es also detected m ultiple segregating

loci in the tomato ( Pil l en et al. 1996), but the duplica- markersin another. Overall, 98% of the tomato genome

and 95% of the pepper genome were included in de-tions in each species appeared to be d istinct. The m ajor-

ity (93%) of the pepper duplications appeared to be fined regions of homeology.

Within hom eologous segmen ts, 30% of the lociun linked d up lication s of single loci. The re was on lyo ne

set of multiple linked loci that revealed a d uplication mapped in onlyone genome, perhaps because no corre-

sponding homolog was present in the other genus orin the Capsicum genome: CD42, CD44, CT205, TG51,

TG174,TG215,and TG314 produced loci on the middle the homolog wasn ot segregating. We cannot distinguish

between these two alternatives because nonsegregatingof P1 in C. annuum and t he t op of P 2 and P 5 i n C.chinense. The frequencyof tandemly duplicated loci sep- bands were detected by most probes in at least one of

the populations, but we can resolve two classes of loci.arable by recombination within intervals 10 cM was

0.87%. Some loci appear to be un iquely duplicated in on e

Figur e 2.Homeologous relationships between the genetic maps of Capsicum and tomato. The genetic map of tomato wasmodified from the map of Pil l en et al. (1996): only the markers in common between the two maps are presented, and theorientation of tomato chromosome 8 is reversed. For the tomato map, markers in plain type at tick marks are framework lociordered at LOD 3, markers in parentheses are placed in intervals at LOD 3, and positions of un derlined loci wereapproximated from other maps. The pepper map is based on Figure 1, but all markers except those in common to the two mapshave been removed. Markers in bold represent framework m arkers ordered at LOD 3. Markers in plain type listed with theframework markers may be up to 8 cM from the framework mar ker, based on pairwise linkage estimates. Pepper markers

enclosed in parentheses are placed at 1.5 LO D 3, and underlined markers are placed at their maximum likelihood position(LOD 1.5). When a chromosome is homeologous to two chromosomes from the other species, one side of the chromosomehas been widened out. Marker types and designations are as follows: tomato genomic RFLP ( TG); tom ato cDNA RFLP ( CD andCT); pepper cDNA RFLP (PC); cloned genes [ Pto (CD186), Fen (CD127), and Prf]; and isozymes (Idh-1, Pgm). Numbers insquare brackets after locus names indicate the nonh omeologous chromosome in the other species where a map position wasobtained for that particular probe. An asterisk after a locus name denotes a locus mapped uniquely in one species from a probethat produced multiple segregating loci, with the other loci mapping to syntenous positions; e.g., if a probe produced twofragments in tomato and one fragment in pepper that mapped to a syntenous position, the second locus would be marked withan asterisk. A dagger indicates that a homolog groups with the syntenous linkage group, but a definitive position cannot beassigned. The markers that grouped (LOD 3) but did not place well within the linkage group frameworks for each of thelinkage groups are as follows (ann otations are the same as above): P3TG16b*; P4CD55, CD64c*, CD64d*, CD64g*,CT205c *, TG503a [ 5], T G503b [ 5]; P7CD39d*, CT32a [9] , CT129a*, TG47 [11], TG220b*, TG418; the two unlinked markersare CT182 [ 11] and TG214 [3].


8/20


Figur e 2.


9/20



genus (a probe reveals a pair of loci that map to synten - appear to be un iquelydu plicated, while 67 loci (21.8%)

lack a counterp art in the h omeologous pepp er segment.ous positions and an additional locus in one species);

some loci are represented only once on each map not In pepper, 40 loci (11.4%) appear to be uniquely dupli-

cated, and 70 loci (19.9%) lack a counterpart on thein homeologous segments. In tomato, 11 loci (3.6%)


10/20




11/20




12/20




13/20


homeologous tomato segment. When all 660 loci are sented by 18 homeologous segments with unique rela-

tionships in each gen us. The majority of these segmentsconsidered , 51 loci (7.7%) are un iquely duplicated on

1 map, and 137 loci (20.8%) lack a homolog in the maintain strict syntenic order throughout, while a few

maintain locus content but have und ergone paracentrichomeologous segment of the other genome. This is

comparable to the percentage of markers (2040%) inversions within the segment. Despite the number of

rearrangements, chromosomes from both genera ap-withou t mean ingful synten y in comparisons amon g the

grasses ( Bennet zen an d Fr eel ing 1997) . p ear to co ntain at m ost o nly two co nse rve d se gm en ts.

Genome structure in the Solanaceae: The pepper-To provide a concise representation of synteny be-

tween tomato and pepper, we modified Figure 2 as tomato comparative map can be used with the phylog-eny of Capsicum, Lycopersicon, and Solanum ( Spoonerfollows to create Figure 3: all marker names were omit-

ted, indicators for markers with no homologs mapped et al. 1993) and the tomato-potato comparative m ap

( Tanksl ey et al. 1992) to identify conserved linkagein th e h omeologous region were om itted, the positions

of the tomato centromeres and the regions of sup- blocks, to reconstruct portions of the genome of the

most recent ancestor of these species, and, in somepressed recombination on the pepper linkage groups

were added, and the lines connecting pairs of loci were cases, to determine in which lineage rearrangements

occurred. Where pepp er and tomato/ potato differ, thechanged to dashed if one of the loci in a pair was not

mapped at framework stringency, was inferred from an- number of ad hoc hypotheses is the same using either

condition as the ancestral state, so only two alternativeother map, or was duplicated such that orthology was

suspect. arran gemen ts can be presented. We assumed th at para-

centric and pericentric inversions and translocationsFigures 2 and 3 show that the tomato and pepper

genomes share large linkage blocks that have un der- were the prominent mechanisms of structural change,

and we did not equate nonsyntenous markers withgone various typical rearran gements during speciation4.

Four pairs of chromosomes show conservation of con- breaks because no simple way exists to explain th ese

loci concordantly with these typical chromosomal re-tent of entire chromosomes: T2-P2, T6-P6, T7-P7, and

T10-P10. Both marker locus content and overall struc- arrangements.

A1: The ancestral hom eologs of chromo some 1 ( A1)ture in the T6-P6 pair appears to have been maintained

completely. Two of the other pairs show paracentric in tomato and potato are identical (Figure 4). The pep-

per species differ by a reciprocal translocation with A8inversions, a small part of the lower end of T2/ P2, and

the lower arm of T10/ P10. The T2-P2 pair also includes and th e small linkage block foun d on P1 in C. annuum

and P2 and P5 in C. chinense, but not found in tomato/the region at the top of P2,which isun ique to C. chinense,

and three markers (TG205, CT140, and CT176) that potato. We conclude that A1 was most like tomato/

potato, with at least two breaks in the pepper lineages,map to nonsyntenous positions. The T7-P7 pair main-

tains a common core, but differs in the position of one to create the A1-A8 translocation and the other to

account for the position of the duplicated region in C.TG183 and u nique linkages at both en ds of P7 and oneend of T7, as me ntioned previously. annuum.

A2: The tomato/ potato A2 hom eologs are identical,The rest of the genome appears to have been con-

served in linkage blocks correspon ding to chromosome while pepp er and tomato/ potato differ by a paracentric

inversion. The pepper species also differ in the distalarms rearranged byn onreciprocal translocations as well

as pericentric and paracentric inversions. The complex- region of P2; therefore, at least two breaks differentiate

the pepper and tomato/ potato lineages, with at leastityof the rearrangements ranges from a single nonrecip-

rocal translocation, in the case of the T4-P4, to multiple one m ore break in one of the pepper lineages.

A3: The tomato/ potato homeologs are identical tonested translocations and inversions seen in the T9-P9-

T12 comparison. The rearrangements must also h ave each other and to a segment of pepper, but at least two

breaks must have occurred in one of these lineages toincluded mu ltiple per icentric inversions in th e P12-T11-

P11-T5 chromosomes. The T1-P1-T8 comparison is account for the differences between pepper and to-

mato/ potato.un ique be cause of the major tr anslocation within Capsi-

cum, b ut it also app ears to con serve who le arms as link- A4: The tomato/ potato A4 h omeologs and most ofpepper A4 occur as a single linkage block. The segmentage blocks. The possible exception is the upp er arm of

T1, although the observed lack of synteny could be attached to tomato/ potato A4 is attached to the A5

homolog in pepper in a reversed telomere-centromerecaused by mapping artifacts arising from the transloca-

tion within pepp er. Finally, Figure 3 illustrates the align- orientation an d is distinct in th e two pepp er species: C.

chinense has an additional linkage block not found inment of tomato centromeres with the regions of sup-

pressed recombination in pepper. C. annuum. As a re sult, we infer at least o ne break with

a reversal of orientation between tomato/ potato andThe pepper and tomato genomes can then be repre-

pepper, as well as a break in one of the Capsicum spe-

cies.

A5: The potato and tomato homeologs of A5 are4 A more exhaustive description of the differences between thetomato an d pepper genomes is also available ( Livingst on e 1999). identical for one arm, but differ by a paracentric inver-


14/20


Figur e 3.Comparative ge-nome structure of pepper and

tomato. The genetic maps ofFigu r e 2 [ p ep p er ch r om o -somes (P), gray bars; tomatochromosomes (T), white bars]h a ve b e en re d uc ed t o o n lymarkers that map to h omeolo-gous segments of the genome.These points are connected bysolid lines, except where eithera clone prod uced m ultiple seg-regating loci in one or both ofthe species with loci mappingto nonsyntenous positions,making the assignmen t of para-logous pairs questionable, or

one or both of the marker(s)ma p pe d a t LOD 2 or wasmapped in a different popula-tion. These marker pairs areconnected by dashed lines.The positions of the tomatocentromeres are indicated byshaded bars or points on thetomato chromosomes. The re-gions of suppressed recombi-nation on the pepper chromo-somes are indicated by whitecircles or bars. The locations ofpepper linkage groups A andB are indicated by bars next to

tomato chromosomes 8 and 3.

sion for th e other. The noninverted arm of the A5 ho- A8: This chromosome is iden tical in tomato/ potato,

but is part of a reciprocal translocation pepper. Themeolog is also conserved in pepper, while the other

arm is attached to the A11 homeolog. The orientation other difference between pepper and tomato/ potato is

the small piece distal to the centromere in tomato/of this arm in p epp er an d po tato is superficially similar;

however, CD64 homologs occur in d ifferent linkage potato that is unlinked in pepper. At least one breakoccurred in one of the pepp er species, and anoth er mayblocks of pepper and tomato/ potato, indicating that

the inversions are independent and that a pericentric have occurred in either the tomato/ potato or pepper

lineage.inversion occurred early in either the tomato/ potato

or p epper lineage. We con clude that th ere was an early A9: The tomato and potato homeologs of this chro-

mosome differ by a p aracentric inversion. Tomato andpericentric inversion followed by indepen den t p aracen-

tric inversions in the potato and pepper lineages. pepper also differ by a similar paracentric inversion;

however, the positions of the breakpoints are different.A6: The structure of this homeolog is maintained in

all th ree species. These data are con sisten t with eith er tomato or pepper

being closest to the ancestral condition, as both config-A7: The structure is conserved, except for the unique

distal linkage blocks. uration s require two breaks an d two n ew telomeres.


15/20


lineage and a series of at least four breaks to account

for the position and arrangements of the G block.

A10: The potato/ pepper and tomato homeologs dif-

fer byone paracentric inversion, indicating the paracen-

tric inversion and break has occurred in the tomato

lineage.

A11: The tomato and potato homeologs differ by a

paracentric inversion. The corresponding p epper arm is

similar to that ofp otato, althou gh attached to a differen tchromosome. We presume the pepper/ potato orienta-

tion of this arm is ancestral. The position of TG104/

TG105 also differs in tomato/ potato and pepper. We

conclude that one break and a paracentric inversion

occurred in the tomato lineage, and another three

breaks and a per icentric inversion occurred in either the

tomato/ potato or pepper lineage that moved TG104/

TG105 and changed the attached linkage blocks.

A12: One arm of the A12 homeolog has been con-

served in pepper, tomato, and potato. Tomato and po-

tato differ by a paracentric inversion of the other arm

that requires one break in either tomato or potato to

accoun t for th e inversion and at least one b reak in either

the tomato/ potato or pepper lineages to change the

attached blocks.Figur e 4.Overview of genome structure within the Sola-naceae. The genetic maps of the 12 chromosomes of tomato, In total, we conclude that there have been at least 2potato, pepper (P), and an inferred configuration for their breaks in the tomato genome, 2 breaks in the potatomost recent common an cestor (A) are rep resented, along with genome, 1 break in either the tomato or potato genome,the d eviations from this common ancestor within each species.

1 break in th e pep per gen ome th at differentiates it fromWhite regions are conserved between the three species andtomato/ potato, and another 5 breaks to account fordefine the ancestral condition. Other white regions are con-

served between pepper and either potato or tomato, but n ot the differences between the 2 pepper species. Nineteenboth, indicating a derived condition in the nonidentical spe- other breaks must h ave occurred in either the p eppercies. Gray regions in the ancestral genome den ote areas wher e lineage or in the common ancestor of tomato/ potato.the ancestral condition cannot be defined. Gray regions in

These breaks were part of 5 translocations, 10 paracen-the other genomes show actual or potential differences be-

tric inversions, 2 pericentric inversions, and 4 disassocia-tween that species and the p roposed an cestral genome. In ver-sions are ind icated by white arro ws within graybars. An upward tions or associations o f genom ic regions that produ ceddirection is defined as the ancestral condition, except for the observed genome variation among genera. An addi-areas on A2, A9, and A12, where orientation could not be tional reciprocal tran slocation, no nr eciprocal tran sloca-determined on the basis of parsimony. On these segments,

tion, and a duplication or deletion differentiates thethe arrows in the A genome are double headed, and thetwo pepper mapping parents.direction of the arr ows in potato, tomato, and peppe r indicate

relative o rientation o nly. Rearranged segmen ts are identifiedbya letter to the right of the segment. In the ancestral genome,

DISCUSSIONall possibilities for a region are indicated (an X indicatesabsent), and the region present in potato/ tomato is under-

The Capsicum genetic map: The variability betweenlined. Asterisks den ote areas unique to pepper (the extensionsour mapping paren ts maximized intralocus polymor-at the ends of P7) and differen ces that have occurr ed between

Capsicum species (the extensions in C. chinense at the ends phism, but also included major st ruct ural r ear -of P2 and P5 and the r eciprocal translocation between P1 and ran gemen ts. As a result, we h ave d efine d m ore pre cisely

P8 in one species). Regions marked with a dagger denote the differences between the genomic structures of C.linkage blocks unique to tomato/ potato. The curved arrows

annuum an d C. chinense, knowledge that is important toto the left of A11 homeologs indicate possible movementsplant br eeders because C. chinense is a significant sourcewithin the linkage blocks.of character s for C. annuu m breeding. The major recip-

rocal translocation red uced th is map to 11 large linkage

groups; ho wever, throu gh comparative mapping, we

Furthermore, the location and arrangement of linkage could establish the locus order for two of the four link-

block G is distinct in all three species; th erefore, we age blocks of the two chromosomes involved. The

cannot ascertain the ancestral position or orientation marker order for the other two blocks will require intra-

of G, but all scenarios require at least four breaks. In specific populations genotyped with those markers.

This map contains two small, unlinked groups: P(A),conclusion, we infer at least one break in the potato


16/20


which is hom eologous to the telomeric region of T8, loci,whereasin the latter case, cross-hybridization would

not be expected, as demonstrated by Hu l ber t et al.and P(B), which is hom eologous to the telomeric region

of T3. In the two other interspecific maps constructed (1990), Bar a kat et al. (1997), and Bennet zen et al.

(1998).in our lab using a C. frutescens BG 2814-6 C. chinense

PI 159234 F2 and a C. frutescens BG 2814-6 C. annu um Differences between the tom ato and pep per genom es

with regard to the number of both homologous andRNaky F2, linkages are seen between TG176 on P(A)

and CT252 from the opposite end of T8, and between segregating locid etected bya probe were apparent, with

pepper generally showing a higher copy number. TheP(B) and the top end of P4 ( Z h an g 1997; Y. Zha ng ,

unpu blished results). The linkages between P(B) and greater number of probes detecting multiple loci inpepper relative to tomato could be a consequence ofP4 through TG132 are detectable in the C. annuum

C. chinense map; however, neither was strong enough the detection of more loci per probe in pepper, or

perhaps evidence of a higher degree of interspecific(LOD 2.5, 30 cM) in th is population to assert

linkage. Th e absence of linkage between P(A) and polymorphism within Capsicum compared to the inter-

specific cross used to construct the tom ato map. Regard-CT252 in our popu lation is puzzling; this linkage isclear

when either parent is crossed to C. frutescens, but it less, these differences in copyn umber between the spe-

cies lacked the patterns th at would be associated withdisappears when the C. annuum an d C. chinense parents

are intercrossed. Perhaps C. annuum an d C. chinense systematic duplications. Overall, our observations con-

cur with results from p revious work in th is system ( Tank-differ in the location of P(A), and the strength of the

linkage in the C. frutescens pare nt is causing the associa- sl ey et al. 1988) and the grasses (Bennet zen an d Fr ee-

l ing 1997) that have shown onlylimited species-specifiction in on e of the other m aps, or P(A) m aybe separated

enough from other detected markers in the linkage duplications and deletions. The absence of systemati-

cally duplicated or deleted genomic regions or individ-group in both C. annuum an d C. chinense that no linkage

is apparent. Th ere is support for both hypotheses: ual loci effectively rules out paleopolyploidy, duplica-

tion, or deletion as explanations for th e differences inKumar et al. (1987) and Lant er i an d Picker sgil l

(1993) have both reported that at least two transloca- genome size between pepper and tomato.

Increases in the amoun t of repeated DNA have bee ntions d ifferentiate these species, and Moscone et al.

(1993) observed heterochromatic segments at the telo- established as a cause of genome expansion in plants

( Fl avel l et al. 1974), and recent work in the Gramineaemeres of all C. annuum chromosomes.

Several Capsicum maps have related linkage groups has shown a pattern of increases in retroelements be-

tween the genes of large-genome species relative toto chromosomes thr ough a series of primary trisomics

generated by Pocha r d (1977). Unfortunately, this se- smaller-genome species ( SanMiguel et al. 1996; Chen

et al. 1997; Panst r uga et al. 1998). A study of rep etitiveriesis no longer complete or available.Because of incon-

sistencies between markers and their chromosomal asso- DNAin the pepper genome byAn et al. (1996) estimated

that 5% of the pepper genome was composed of ele-ciations among recentlyp ublished maps ( Lefebvr e an dPal l oix 1996; Car ant a et al. 1997a,b; Lefebvr e et al. ments with copynumber 10,000, 26% with copy nu m-

be r 150, and 65% single-copy sequen ces. This estimate1997), and some significant differen ces in observed link-

ages between these maps and our map, we h ave n ot of the single-copy fraction of the pepper genome ap-

pears high in light of our results, unless some of theassigned our linkage groups to named chromosomes.

Moscone et al. (1993) have succeeded in differentiating single-copy sequences are also unique to pepper, but

these data do show a significant amount of both high-the pepper chromosomes using C banding, indicating

that fluorescent in situ hybridization could be used with and medium-copy-nu mber sequen ces. Our observation

that a h igh percentage of pepp er genom ic DNA clonessingle-copy probes iden tified in this study to relate the

ge n et ic m ap t o Ca psicu m ch r om o so me s. d e te ct ed r ep e at ed se qu en ce s a lso p o in ts to r ep ea te d

sequences in the pepper genome. Moreover, retro-Genome size, structure, and evolution in the Solana-

ceae: Genome size and content: The 2C DNA content of transposons are well documented in Capsicum ( Fl a-

vel l et al. 1992; Pozuet a-Romer o et al. 1995; K. Living -pepper is two- to fourfold greater than that of tomato

( Ar umuga na t h an an d Ear l e 1991). We ob served th at st one, un published results). Th e extra DNA in pepp errelative to tomato cannot all be accounted for by theall tomato clones tested h ybridized to pe pper DNA and

covered the pepper genetic map. Our results conflict blocks of constitutive heterochromatin (7% of the total

karyotypic length) seen exclusively at the telomeres ofwith Pr inc e et al. (1993), who ob served th at clones from

regions of tomato chro mosome s 1, 2, 6, and 912 failed C. annuu m chromosomes ( Moscone et al. 1993). The re-

fore, it is probable that the retrotransposons inter-to hybridize with p epper DNA, p erhaps because these

clones were either more diverged from their pepper spersed equally across both the gene-rich and gene-

poor regions of the genome, as seen in the Gramineaehomologs or representative of intergenic sequences

unique to tomato ( Ganal et al. 1988) . In th e case o f ( Bar aka t et al. 1997), will account for differences in

nuclear DNA content between pepper and tomato.the former, perh aps different h ybridization conditions

in o ur RFLP analysis revealed th ese mor e weaklyr elated Conservation of linkages: Our comparison of the pepper


17/20


and tomato genomes demonstrates overwhelmingly the upper arms of T5 and T9 in pepper and potato and

those seen by C acco n e et al. (1998) in mosquitoes.conservation of marker order from whole-tomato chro-

In the recent comparison of Arabidopsis and B. nigra,mosome arms, and even entire chromosomes, in pep-

Lager cr ant z (1998) reported that interstitial telo-per. There were, h owever, seemingly random interrup-

meric rep eats colocalized with rearrangemen t break-tions in synten y. Th ese markers may have been whatpoints. Telomeric sequences have been mapped to theled Tanksl ey et al. (1988) to conclude that many ofcentromeric regions of eight tomato chromosomesthe pepper chromosomeswere comprised ofmanyinde-( Pr est ing et al. 1996), and all but one of the tran sloca-pendent tomato segments.

tion breakpoints between tomato/ potato and pepperOne observation emerging from other comparativeappear at the centromere o r pu tative centromere of thestudies is that th ese ro gue m arkers seem to be concen-respective chromosome. Tomato telomeric sequencestrated in centrom eric and telomeric regions ( Moo r e etappear at tomato centromeres, where we believe theal. 1997). This same result is man ifest in our com parisonchromosomes have been truncated in pepp er ( T4 andat the centromeres of P1, P2, P4, P7, P12, T4, T5, T9,T8); at th e cen trom eres of T5, T9, T11, and T12, whichand T12, and the telomeres of P2, P4, P5, T3, T8, andare breakpoints; and at the centromeres of T3 and T7,T11. This phenomenon may be a function of the con-which may or may not be sites of rearrangement. Nocentr ation of breaks at th ese sites; however, th e specifictelomeric sequences were mapped, however, to themechan isms that account for m arker accumulation an dbreakpoints that we con cluded were u nique to tomato,loss at these breakpoints remains unknown. AnotherT10 and T11, although this may result from lack ofgeneral mech anism that could p ossibly explain the ap-polymorphism or the pericentric inversion we believepearance of n onsynten ous m arkers is excision via in-occurred on either T11/ P11. These results, therefore,

trachromosomal recombination of direct rep eats, fol- support both the observation that centromeres are im-lowed by integration at distant sites. This process hasportant sites for chromosomal rearrangement and thebeen shown to move transgenes to distant sites in thehypoth esis that interstitial telomeric repeats m ay be a

genome of transformed tobacco ( Pet er h an s et al.critical if not a causal link between centromeres and

1990). If retrotransposons, which have been associatedthese events.

with duplications and rearrangements in the genomeThree interrelated lines of evidence imply that the

of Saccharomyces cerevisiae ( Kim et al. 1998b), acted asmajority of the u np laced chromosomal rearrangements

direct repeats in this process, it is not difficult to seeprobably occurred in the pepper lineage. (i) We have

how the present situation could h ave developed.observed at least five differences between the parental

Genome rearrangement: Our estimate of the minimumpepper species that are equal to the number of differ-

nu mber o f breaks that differentiate tomato and pepp erences between potato and tomato ( Tanksl ey et al.

(22) is 7 greater than that reported by Pr inc e et al.1992); therefore, propen sitytoward rearrangeme nt may

(1993), but 10 less than that reported by Tanksl ey et

be an inherent p ropertyof the pepper genome, a trendal. (1988). The probable cause of the differences innoticed earlier by Lant er i an d Picker sgil l (1993).

these estimates is the exten t of coverage of the tomato(ii) The increase in the size of the p epper genome,

genome in each study. By looking at th e en tire tomatowithout apparen t increases in gene content, implicates

genome as it is represented in pepper, we have beenexpansion of heterochromatin in this genome. Hetero-

able to both see the larger patterns of genome reorgani-chromatin has been positively correlated with the

zation and refine th e estimate of the overall num ber of amount of rearrangement in a genome ( Pr oko fi eva-events that have occurred since divergence. Bel govska ya 1986). (iii) Retrotransposons probably

This study joins with others that begin to provide make up t he bulk of t he ext ra DN A in t he pepperglimpses into the complex nature and mechanisms of genome, and retroelements h ave been associated withgenome structural rearrangements. Similar to our re- chromosomal rearrangemen ts in plants (Robbins et al.sults, inversions were also a major contributor to the 1989; Bel zil e an d Yo d er 1994), yeast ( Kim et al. 1998b),extensive rearrangement of the Brassica nigra genome mosquitoes ( Mat h iopoul os et al. 1998), and Drosoph -

relative to Arabidopsis ( Lager cr ant z 1998). Clues to ila ( Engel s an d Pr est on 1984; Lim 1988; Lyt t l e an dthe biology underlying these rearrangements include Haymer 1992; Sheen et al. 1993; Eggl est on et al. 1996;this and oth er stud ies of intraspecific karyotype diversity Ladeveze et al. 1998; OHar e et al. 1998).( Gil l et al. 1980; Badaeva et al. 1994) and comparative Segregation distortion factors: Many of the markersmapping ( Moo r e et al. 1997) that have shown transloca- in our population displayed significant deviations fromtion breakpoints to occur more frequently at centro- the ir expe cted Men delian r atios. While th is observationmeres. Although to the best of our knowledge no com- has been made in man y interspecific plant pop ulationsparable st udy has been done for inver sions, t he ( e.g., Zamir an d Tadmor 1986), comparisons of the

analogous localization of inversion breakpoints to re- amoun t and direction of distortion across different gen-

gions of the genome would make similar independent era are limited. We have identified regions that display

consistent segregation distortion both within a genusinversions more likely, such as those we observed in the


18/20


and across genera. Understanding of the loci control- comparisons available across three genera, now stands

as the broadest and most thoroughlych aracterized com-ling this beh avior has impo rtant practical applications

for breeders and biological implications for the evolu- parative genetic system in dicotyledonous plants.

tion of these genera. The recent cloning of the Segrega- The auth ors acknowledge J. Prince, E.Radwanski, J. Jantz, M. Cadle,tion distorterlocus from Drosophila ( Mer r il l et al. 1999) L. Landry, and G. Moriarty for their assistance. We th ank Drs. S.

Tanksley for clones and access to unpu blished data; B.-D. Kim, U.shows that molecular stud y of th ese loci is feasible. LociBonas, M. Massoudi, K. Welch, A. Palloix, and V. Lefebvre for markerswith conserved distortion functionalityapparent in mul-and un pub lished data; and N. Weeden for isozyme an alyses. We than k

tiple genera would make approp riate initial targets forR. Grube, A. Matern, L. Landry, M. Sorrells, S. Tanksley, and two

molecular characterization in plants. anonymous reviewers for critical reading and suggestions that im-Genome size, genetic length, and implications for proved the manuscript. K.D.L. and J.R.B. were supported in part by

a Department of Energy/ National Science Foundation/ United Statesrecombination: The lengths of the tomato and pepperDepartment of Agriculture grant to the Research Training Groupgenetic maps are almost identical: 1275 cM in tomatoin Molecular Mechanisms of Plant Processes and in part by Marie

vs. 1246 cM in pepper. Figures 2 and 3 illustrate thatLavallard. Financial and material support was provided by Seminis

most of the intervals between adjacent syntenous mark- Vegetable Seeds, the California Pepper Commission/ California Pep-ers are approximately equal in pepper and tomato de- per Improvement Foundation, Gilroy Foods, Mr. C. Werly, USDA

NRICGP awards 91-37300-6564 an d 94-37300-0333, an d BARD awardspite comparisons of dual interspecific maps. The simi-IS-2389-94.lar lengths of the genetic maps, together with the

difference in DNA content, indicate that the average

recombination rate per un it of ph ysical distance is not

the same in pepper and tomato. This is what would be LITERATURE CITEDexpected if recombination was restricted on lyto h omol-

An, C. S., S. C. Kim an d S. L. Go, 1996 Analysis of red pepp erogous genes, as originally proposed by Thur ieaux ( Capsicum annuu m) genome. J. Plant Biol. 39: 5761.Ar umuganat han, K., an d E. D. Ear l e, 1991 Nuclear DNA content( 1977) and shown in maize ( Dooner et al. 1985;

of some importan t plant species. Plant Mol. Biol. Rep. 9: 208218.Dooner 1986; Br ow n an d Sund ar esan 1991; Civar diBadaeva, E. D., N. S. Badaev, B. S. Gil an d A. A. Fil at enko, 1994

et al. 1994; Eggl est on et al. 1995; Pat t er son et al. 1995; Intraspecific karyotype divergen ce in Triticum araraticum ( Poa-ceae). Plant Syst. Evol. 192: 117145.Dooner an d Mar t nez-Fer ez 1997).

Bar akat , A., N. Car el s an d G. Ber nar di, 1997 The distributionConclusions: We have produced a moderate-densityof genes in th e gen omes of the Gramineae. Pro c. Natl. Acad. Sci.

map of the Capsicum genome using tomato-derived USA 94: 68576861.Bel zil e, F., an d J. I. Yod er , 1994 Unstable transmission and fre-clones distributed across the tomato genome. Compari-

quent rearrangements of two closely linked transposed Ac ele-son of this map with the tomato map shows that: (i)ments in transgenic tomato. Genome 37: 832839.

insofar as has been analyzed, the genic contents of to- Bennet zen, J. L., an d M. Fr eel ing , 1997 The unified grass genome:synergy in synteny. Genome Res. 7: 301306.mato and pepp er are equivalent; (ii) virtually all the

Bennet zen , J. L., P. San Miguel , M. Ch en, A. Tikhon ov, M. Fr an ckitomato an d pepp er gen omes are covered by conservedet al., 1998 Grass genomes. Proc. Natl. Acad. Sci. USA95: 1975

linkage blocks; (iii) the overall genetic lengths of pepp er 1978.and tomato are approximately equal despite at least a Ber nacch i, D., an d S. Tanksl ey, 1997 An interspecific backcross

ofLycopersicon esculentu m L. hirsutum:linkage analysisan d a Q TLtwofold increase in the 2C content of the pepper ge-studyof sexual compatibilityfactorsand floral traits. Genetics 147:

nom e; (iv) a typical nu mber of common types of chro- 861877.mosomal rearrangemen ts differentiate th ese genomes. Bl au t h , J. R., 1994 Genetic analysis of resistance to peppe r mottle

potyvirus and tobacco etch potyvirus in pep per, genu s Capsicum.This study unites the tomato-pepper comparison withPh.D. Th esis, Corn ell Un iversity, Ithaca, NY.

results from other dicotyledonous genera ( cf. Tanksl eyBoni er bal e, M. W., R. L. Pl aist ed an d S. D. Tanksl ey, 1988 RFLP

et al. 1992; Weeden et al. 1992; Menancio-Haut ea et al. maps based on a common set of clones reveal modes of chromo-somal evolution in tomato and potato. Genetics 120: 10951103.1993; Kowa l ski et al. 1994; Cheung et al. 1997; Lager -

Br own, J., an d V. Sund ar esan, 1991 A recombination h otspot incr ant z 1998) and the grasses ( reviewed recently in

the maize a1 intragenic region. Theor. Appl. Genet. 81: 185188.Bennet zen an d Fr eel in g 1997; Bennet zen et al. 1998; Bur nh am, C. R., 1991 Discussions in Cytogenetics. Burgess Publishing

Co., Minneapolis.Gal e an d Devos 1998a,b), which all sho w conservationCaccone, A., G.-S. Min an d J. R. Powel l , 1998 Multiple origins of

of content within large linkage blocks, but not associa-cytologically iden tical chrom osome inversions in the Anopheles

tions between blocks, as the primary consequences of gambiae complex. Genetics 150: 807814.Car ant a , C., V. Lefebvr e an d A. Pal l oix, 1997a Polygenic resis-chromosomal evolution.

tance of pepp er to potyvirusescon sistsof a combination of isolate-The ability to compare phenotypes geneticallyspecific and broad-spectrum quantitative trait loci. Mol. Plant-

mapped to orthologous positions of the different ge- Microbe Interact. 10: 872878.Car ant a, C., A. Pal l oix, V. Lefebvr e an d A. M. Da ub ez e, 1997bnom es will shed light on genes that op erate across the

QTLs for a component of partial resistance to cucumber mosaicSolanaceae. This map will also contribute to the under-virus in pepper: restriction of virus installation in host cells.

standing of pep per at the molecular level throu gh com- Theor. Appl. Genet. 94: 431438.Chen, M., P. SanMiguel , A. C. D. Ol iveir a, S.-S. Woo, H. Zhangparative genomics between pepper and tomato, an d

et al., 1997 Microcolinearity in sh-2-homologous regions of thebetween pep per and Arabidop sis via tomato-Arabidop sismaize, rice, and sorghum genomes. Proc. Natl. Acad. Sci. USA

comparisons now underway ( S. Tanksl ey, personal 94: 34313435.Cheu ng , W. Y., G. Champagne, N. Hu l ber t an d B. S. Land r y, 1997communication). The Solanaceae, with whole-genome


19/20


Comparison of the genetic maps of Brassica napus an d Brassica Ladeveze, V., S. Aul a r d, N. Ch aminade, G. Per iq uet an d F. Lemeu-nier , 1998 Hobo transposons causing chromosomal break-oleracea. Theor. Appl. Genet. 94: 569582.

Civar d i, L., Y. Xia, K. J. Edwa r ds, P. S. Sch na bl e an d B. J. Nikol au, points. Proc. R. Soc. Lond. Ser B 265: 11571159.Lager cr ant z, U., 1998 Comparative mapping between Arabidopsis1994 The r elationship between genetic and ph ysical distances

in the cloned a1-sh2 interval of the Zea mays L. genome. Proc. thaliana an d Brassica nigra indicates that Brassica genomes haveevolved through extensive genome replication accompanied byNatl. Acad. Sci. USA 91: 82688272.

Cl ou t ier , S., M. Cappad oc ia an d B. S. Land r y, 1997 Analysis of chromosome fusionsand frequent rearrangements. Genetics150:12171228.RFLP mapping inaccuracy in Brassica napus L. Theor. Appl.

Genet. 95: 8391. Lant er i, S., an d B. Picker sgil l , 1993 Chromosomal structuralchanges in Capsicum annuu m L. and C. chinense Jacq. Euphyticade Vicen t e, M. C., an d S. D. Tanksl ey, 1993 QTL analysis of trans-

gressive segregation in an interspecific tomato cross. Genetics 67: 155160.

Lefebv r e, V., an d A. Pal l oix, 1996 Both epistatic and add itive134: 585596.Dooner , H. K., 1986 Genetic fine structure of the bronze locus in effects of QTLs are involved in polygenic induced resistance to

disease: a case study, the interaction pepperPhytophthora capsicimaize. Genetics 113: 10211036.Dooner , H . K., an d I. M. Mar t nez-Fer ez, 1997 Re co mb in at io n Le on ian . T he or . Ap p l. Ge ne t. 93: 503511.

Lefebvr e, V., A. Pal l oix , C. Car an t a an d E. Poch ar d, 1995 Con-occursu niformlywithin the bronzegene, a meiotic recombinationhotspot in the maize genome. Plant Cell 9: 16331646. st ru ct io n o f a n in tr asp ecifi c in te gr at ed lin kage m ap o f p ep p er

using molecular markers and doubled-haploid p rogenies. Ge-Dooner , H. K., E. Weck, S. Adams, E. Ral st on, M. Favr eau et al.,1985 Amolecular genetic analysis of insertion mutations in the nome 38: 112121.

Lefebvr e, V., C. Car ant a, S. Pfl ieger , B. Mour y, A.-M. Daubezebronze locus in maize. Mol. Gen. Genet. 200: 240246.Egg l est o n, W. B., M. Al l eman an d J. L. Ker micl e , 1995 Molecular et al., 1997 Updated intraspecific maps of pepper. Capsicum

and Eggplant Newslett. 16: 3541.organ ization an d germ inal instabilityo f R-stippled maize. Genet-ics 141: 347360. Lim, J. K., 1988 Intrachromosomal rearrangements mediated by

hobo transposons in Drosophila melanogaster. Proc. Natl. Acad. Sci.Eggl est on, W. B., N. R. Rim an d J. K. Lim, 1996 Molecular charac-terization of ho bo-mediated inversions in Drosophila melanogaster. USA 85: 91539157.

Lincol n, S. E., M. J. Dal y an d E. S. Lander , 1993 ConstructingGenetics 144: 647656.Eng el s, W. R., an d C. R. Pr est on , 1984 Formation of chromosome genetic linkage map with MAPMAKER/ EXP v3.0: a tutorial and

reference man ual. Whitehead Institute Technical Report, Cam-rearrangements by P factors in Drosophila. Genetics 107: 657

678. bridge, MA.Livingst one, K., 1999 Comparative mapping in the Solanaceae.Feinber g, A. P., an d B. Vog el st ein, 1983 A technique for radiola-

belling DNArestriction fragments to a high specific activity. Anal. Ph.D. Thesis, Cornell University, Ithaca, NY.Loaiza-Figuer oa, F., K. Rit l and , J. A. Labor de-Canc ino an dBiochem. 132: 613.

Fl avel l , R. B., M. D. Bennet t , J. B. Smit h an d D. B. Smit h , 1974 S. D. Tanksl ey, 1989 Patterns of genetic variation of the genusCapsicum (Solanaceae) in Mexico. Plant Syst. Evol. 165: 159188.Genome size and the proportion ofrepeated nucleotide sequence

DNA in plants. Biochem. Genet. 12: 257269. Lor ieux, M., X. Per r ier , B. Gof fi net , C. Lana ud an d D. Go n za l ezd e Leo n, 1995 Maximum-likelihood m odels for mapp ing ge-Fl avel l , A. J., D. B. Smit h an d A. Kumar , 1992 Extreme heteroge-

neity of Ty1-copia group retrotransposons in plants. Mol. Gen. netic markers showing segregation distortion. 2. F2 populations.Theor. Appl. Genet. 90: 8190.Genet. 231: 233242.

Gal e, M. D., an d K. M. Devos, 1998a Comparative genetics in the Lyt t l e, T. W., an d D. S. Hay mer , 1992 The role of the transposableelement h obo in the origin of endem ic inversions in wild popula-grasses. Proc. Natl. Acad. Sci. USA 95: 19711974.

Gal e, M. D., an d K. M. Devos, 1998b Plan t co mp ar at ive ge n et ics t io n s o f Drosophila melanogaster. Genetica 86: 113126.Massoudi, M., 1995 Genetic mapping of pepper, Capsicum annuumafter 10 years. Science 282: 656658.

Gan al , M. W., N. L. V. Lapit a n an d S. Tanksl ey, 1988 Amolecular L., and identification of markers l inked to phytophthora root rotresistance ( Phytophthora capsici). Ph.D. Th esis, New Mexico Stateand cytogenetic survey of m ajor repeated DNA sequences in

tomato (Lycopersicon esculentum). Mol. Gen. Genet. 213: 2 62 2 68 . U n ive r sit y, La s Cr u ce s, N M.Mat hio poul os, K. D., A. del l a Tor r e, V. Pr eda zzi, V. Pet r ar caGebha r dt , C., E. Rit t er , A. Bar one, T. Debener , B. Wal kemeier

et al., 1 991 RFLP m ap s o f p o ta to a n d t h eir a lig nm e n t wit h t h e a n d M. Col uzzi, 1998 Cloning of inversion breakpoints in theAn opheles gambiae complex traces a transposable element at thehomologous tomato genome. Theor. Appl. Genet. 83: 4957.

Gil l , B. S., C. R. Bur nham, G. R. St r ingham, J. T. St out and inversion junction. Proc. Natl. Acad. Sci. USA 95: 1244412449.Menan cio-Hau t ea, D., C. A. Fat okun, L. Kumar , D. Danesh an dW. H. Wein h eimer , 1980 Cytogene tic analysis of chrom osomal

translocations in the tomato: preferential breakage in hetero- N. D. You ng , 1993 Comparative genome analysis of mungbean( Vigna radiata L. Wilczek) and cowpea ( V. unguiculata L. Walpers)chromatin. Can. J. Genet. Cyto. 22: 333341.

Hu l ber t , S. H ., T. E. Rich t er , J. D. Axt el l an d J. L. Bennet zen, using RFLP mapping data. Theor. Appl. Genet. 86: 797810.Mer r il l , C., L. Bayr akt ar ogl u, A. Kusano an d B. Gan et zky, 19991990 Genetic mapping and characterization of sorghum and

related crops by means of maize DNA probes. Proc. Natl. Acad. Truncated RanGAP encoded by the Segregation distorter locus ofDrosophila. Science 283: 17421745.Sci. USA 87: 42514255.

Kim, B.-D., B. C. Kan g, S. H. Na h m, J. H. H uh , H . S. Yoo et al., 1998a Moor e, G., M. Rober t s, L. Ar agon-Al caide an d T. Foot e, 1997Centromeric sites and cereal chromosome evolution. Chro-Construction of m olecular linkage m ap an d development of flu-

orescence in situ h yb rid izat io n t ech n iq ue in h o t p ep p er , p p . m oso ma 105: 321323.Mosco ne, E. A., M. Lambr ou , A. T. Hun ziker an d F. Eh r endo r fer ,227230 in Xth Meeting on Genetics an d Breeding of Capsicum and

Eggplant, edited by A. Pal l oix an d M. C. Daunay. I n st it u t N a- 1 99 3 Gie m sa C-b an d e d k ar yo typ e s in Capsicum (Solanaceae).

Plant Syst. Evol. 186: 213229.tional de la Recherche Agronomique, Avignon, France.Kim, J. M., S. Vangur i, J. D. Boeke, A. Gabr iel an d D . F. Vo y t a s , N a ka y a ma , R. M. , an d F. B. Mat t a, 1985 NuMex R Naky chilepepper. HortScience 20: 961962.1998b Transposable elementsand genome organization: a com-

prehensive survey of retrotransposons revealed by the complete OHar e, K., J. L. Y. Tam, J. K. Lim, N. N. Yur chen ko an d I. K.Zakh ar ov, 1998 Rearrangements at H obo element insertedSaccharomyces cerevisiae genome sequence. Genome Res. 8: 464

478. in to the first intron of th e singedgene in the un stable sn49 systemof Drosophila melanogaster. Mol. Gen. Genet. 257: 452460.Kosambi, D. D., 1944 The estimation of map distances from recom-

bination values. Ann. Eugen. 12: 172175. Panst r uga , R., R. Busch ges, P. Piffa nel l i an d P. Sch ul ze-Lefer t ,1998 A contiguous 60 kb genomic stretch from barley revealsKowal ski, S. P., T.-H. Lan, K. A. Fel dmann an d A. H . Pat er son,

1994 Comparative mapping ofArabidopsis thaliana an d Brassica molecular evidence for gene islands in a monocot gen ome. Nu-cleic Acids Res. 26: 10561062.oleracea chromosomes reveals islands of conserved organization.

Genetics 138: 499510. Pat t er so n, G. I., K. M. Kubo , T. Sh r oyer an d V. L. Chan dl er , 1995Sequences required for paramutation of the maize b gene mapKumar , O. A., R. C. Panda an d K. G. R. Rao, 1987 Cytogenetic

studies of the F1 hybrids of Capsicum annuum with C. chinense to a region containing the promoter and upstream sequences.Genetics 140: 13891406.an d C. baccatum. Theor. Appl. Genet. 74: 242246.


20/20


Pau l , E., M. Got o an d S. D. Tanksl ey, 1994 Solgenes: a Solanaceae SanMiguel , P., A. Tikh on ov, Y.-K. Jin, N. Mot ch ou l skaia, D. Zak-h a r o v et al., 1996 Nested retrotransposons in the intergenicdatabase. Eup hytica 79: 181186.

Pet er h ans, A., H. Sch l upmann, C. Basse an d J. Paszkowski, 1990 r egio n s o f t he m aize ge n om e. Scie nce 274: 765768.Sh een , F. M., J. K. Lim an d M. J. Simmon s, 1993 Genetic instabilityinIntrachromosomal recombination in plants. EMBO J. 9: 3437

3445. Drosophila melanogaster mediated b y hobo transposable elements.Genetics 133: 315334.Pil l en, K., O. Pineda, C. B. Lewis an d S. D. Tan ksl ey, 1996 Status

of genome mapping tools in th e taxon Solanaceae, pp. 281307 Spoo ner , D. M., G. J. And er son an d R. K. Janse n, 1993 ChloroplastDNAevidence for the interre lationships with tomatoes, potatoes,in Genome Mapping in Plants, edited by A. H. Pat er son. R. G.

Landes, Austin, TX. an d pepinos ( Solan aceae) . Am. J. Bot. 80: 676688.Tanksl ey, S. D., 1984 Linkage relationships and chromosomal loca-Poch ar d, E., 1977 Localization of genes in Capsicum annuum L. by

trisomic analysis. Ann. Amelior. Plantes 27: 255266. tion s of e nzym e-cod in g gen es in p ep per, Capsicum annuum. Chro-

mosoma 89: 352360.Pozuet a-Romer o, J.,M. Kl ein, G. Ho ul ne, M.-L. Scha nt z, B.Meyeret al., 1995 Characterization of a family of genes encoding a Tanksl ey, S. D., R. Ber nat zky, N. L. Lapit an an d J. P. Pr ince, 1988

Conservation of gene repertoire but n ot gene order in pepperfruit-specific wound-stimulated protein of bell pepper ( Capsicumannuum): identification of a newfamilyof transposable elements. and tomato. Proc. Natl. Acad. Sci. USA 85: 64196423.

Tanksl ey, S. D., M. W. Ganal , J. P. Pr ince, M. C. de Vicent e,Plant Mol. Biol. 28: 10111025.Pr est ing, G.G.,A.Fr ar y,K.Pil l en an d S. D.Tan ksl ey, 1996 Telo- M. W. Bonier bal e et al., 1992 High density molecular linkage

maps of the tomato and potato genomes. Genetics 132: 1141mere-homologous sequences occur near the centromeres ofmany tomato chromosomes. Mol. Gen. Genet. 251: 526531. 1160.

Thu r ieaux , P., 1977 Is recombination confined to structural genesPr ince, J. P., E. Poch ar d an d S. D. Tanksl ey, 1993 Constructionof a molecular linkage map of pepper and a comparison of on the eukaryotic chromosome? Nature 268: 460462.

Vos, P., R. Hoger s, M. Bl eeker , M. Rel jans, T. van de Lee et al.,synteny with tomato. Genome 36: 404417.Pr ince, J. P., V. K. Lackney, C. Angel es, J. R. Bl aut h an d M. M. 1995 AFLP: a new techn ique for DNA fingerprinting. Nucleic

Acids Res. 23: 44074414.Kyl e, 1995 A survey of DNA polymorph ism within the genusCapsicum and the fingerprinting of pepper cultivars. Genome Weeden,N.F.,F.J.Muehl bauer an d G.Ladizinsky, 1992 Extensive38: 224231. conservation of linkage relationships between pea and lentil ge-

Pr ince, J. P., Y. Zha ng , E. R. Radwa nski an d M. M. Kyl e, 1997 A netic maps. J. Hered. 83: 123129.high-yielding and versatile DNAextraction p rotocol for Capsicum. Zamir , D., an d Y. Tad mor , 1986 Unequal segregation of nuclear

HortScience 32: 937939. genes in plants. Bot. Gaz. 147: 355358.Pr oko fi eva-Bel go vskaya , A. A., 1986 Heterochromatic Regions in Zha ng , Y., 1997 Detection of restriction fragment length polymor-

Chromosomes. Nauka, Moscow (in Russian). phism, construction of a molecular linkage map, and mappingRobbins, T. P., R. Car pent er an d E. S. Coen, 1989 A chromosome and tagging cucumber mosaic virus resistance loci in Capsicum.

rearrangement suggests that donor and recipient sites are associ- Ph.D. Th esis, Corn ell Un iversity, Ithaca, NY.ated during Tam3 transposition in Antirrhinum majus. EMBO J.8: 513. Commun icatin g editor: J. A. Bir ch l er

Capsicum Genome Maping

Documents

Transcript of Capsicum Genome Maping