BACKGROUND
lettuce dieback disease is widespread in commercially grown romaine and leaf-type lettuces  <cit> .
the disease is caused by two closely related soilborne viruses from the family tombusviridae -- tomato bushy stunt virus  and lettuce necrotic stunt virus   <cit> .
symptoms of lettuce dieback include mottling and necrosis of older leaves, stunting, and plant death .
the characteristic symptoms usually appear after the plant has reached  <dig> to  <dig> weeks of age and render the plant unmarketable  <cit> .
tbsv and lnsv are extremely persistent viruses and they are likely to survive in soil and water for long periods of time  <cit> .
the virus has no known vector and it seems to move through infested soil and water  <cit> .
while fungal vectors are not necessary for transmission, studies have yet to be conducted to determine if such vectors can facilitate or increase rates of virus transmission to lettuce.
previous studies have provided no evidence that either chemical treatment or rotation with non-host crops can effectively reduce, remove, or destroy the virus in infested soil  <cit> .
since there are no known methods to prevent the disease in a lettuce crop grown in an infested field, genetic resistance remains the only option for disease control  <cit> .
although susceptibility to dieback is widespread in romaine and leaf lettuces, modern iceberg-type cultivars remain completely free of symptoms when grown in infested soil  <cit> .
it appears that the resistance observed in iceberg cultivars was originally introduced into the iceberg genepool from the cultivar imperial around  <dig> years ago  <cit> .
if true, this suggests that the resistance is effective and highly durable despite extensive cultivation of iceberg cultivars.
through use of molecular marker technology, the single dominant gene , which is responsible for the dieback resistance in iceberg lettuce, has been mapped to chromosomal linkage group  <dig>  <cit> .
position of the gene was inferred with aflp and rapd markers in a population originating from a cross between the resistant cultivar salinas and the susceptible cultivar iceberg .
another dieback resistance gene was discovered in the primitive romaine-like accession pi <dig>  <cit> .
analysis of resistance in offspring originating from a cross between the two resistant genotypes  indicates that the resistance locus in pi <dig> is either allelic or linked to tvr <dig>  <cit> .
because of the increased interest in non-iceberg types of lettuce, introgressing tvr <dig> into romaine, leaf, and other susceptible types is of high priority for the lettuce industry.
however, the breeding process is slow and labor intensive due to a need for extensive field-based testing.
application of marker-assisted selection  can reduce the need for field screening and accelerate development of dieback resistant material.
to pinpoint the location of the tvr <dig> gene and develop markers for marker-assisted selection, we employed a combination of classical linkage and association mapping techniques  <cit> .
the association mapping approach is based on the extent of linkage disequilibrium observed in a set of accessions that are not closely related.
in contrast to linkage mapping, association mapping is a method that detects relationships between phenotypic variation and genetic polymorphism in existing germplasm, without development of mapping populations.
this method incorporates the effects of recombination occurring in many past generations into a single analysis  <cit>  and is thus complementary to linkage analysis.
association mapping has been successfully applied in mapping resistance genes in several diploid and polyploid plant species .
the main drawback of association mapping is the possibility of false-positive results due to an unrecognized population structure.
when the trait of interest is more prevalent in one subpopulation  than others, the trait will be associated with any marker allele that is in high frequency in that subpopulation .
our previous analysis of population structure with molecular markers revealed that cultivated lettuce is divided into several well-defined subpopulations that correspond approximately to different horticultural types  <cit> .
consequently, traits that are strongly correlated with lettuce types display many false-positive results when population structure is ignored.
however, these spurious associations disappear when estimates of population structure are included in the statistical model  <cit> .
therefore, the best approach for avoiding spurious associations in lettuce association studies is to assess relatedness of accessions with molecular markers and to include this information into the statistical model  <cit> .
in the present study we mapped the tvr <dig> gene using a combination of linkage and association mapping.
high-resolution dna melting curve analysis  was used to assess polymorphism in mapping populations and to detect haplotypes associated with the disease resistance.
the potential for marker-assisted selection was then validated in the genetic backgrounds present in most common horticultural types of lettuce.
finally, we used snp markers to assess intra- and inter-locus linkage disequilibrium in the tvr <dig> region.
methods
linkage mapping population
recombinant-inbred lines  were derived from a cross between an f <dig> of cv.
valmaine  × cv.
salinas  <dig> and cv.
salinas.
both salinas and salinas  <dig> are iceberg type lettuces resistant to dieback whose appearance and performance is the same, except for reaction to lettuce mosaic virus .
two hundred and fifty three f <dig> rils were screened for resistance to dieback in multiple trials and  <dig> of these rils were randomly selected for genotyping with molecular markers.
association mapping set
a set of  <dig> cultivars, plant introductions , and breeding lines representing all predominant types of cultivated lettuce was used for association mapping.
the set includes  <dig> batavia types,  <dig> butterhead types,  <dig> iceberg types,  <dig> latin types,  <dig> leaf types,  <dig> romaine types, and  <dig> stem types .
the lettuce accessions were selected from material used in breeding programs, ancestors frequently observed in pedigrees, and newly developed breeding lines.
for each horticultural type both dieback resistant and susceptible accessions were selected, with the exception of iceberg lettuce, where only resistant cultivars were available, and the latin type, where only susceptible cultivars were available.
accessions that were sequenced are in bold; the remaining accessions were analyzed with the hrm approach only.
validation set
to validate the marker-trait association detected in the association mapping set, a validation set of  <dig> accessions was screened for disease resistance and genotyped with the marker, cntg <dig>  this set represents the spectrum of phenotypic and genotypic variability observed in cultivated lettuce and includes  <dig> batavia types,  <dig> butterhead types,  <dig> iceberg types,  <dig> latin type,  <dig> leaf types,  <dig> oil types,  <dig> romaine types, and  <dig> stem types .
assessment of dieback resistance
dieback resistance data were obtained from field observations as previously described  <cit> .
susceptibility was evaluated by seeding lettuce directly in the field in salinas, ca, from which tbsv and lnsv had previously been isolated from plants exhibiting characteristic dieback symptoms  <cit> .
the experiment was comprised of two complete blocks, with ~ <dig> plants per genotype per block.
plants were seeded in two rows on  <dig> m wide beds and were thinned to obtain spacing of  <dig> cm between plants.
standard commercial practices were used for irrigation, fertilization, and pest control.
plants were checked weekly for disease symptoms in order to discriminate between plants dying due to dieback and those due to unrelated causes.
the percentage of plants that showed typical dieback symptoms  was recorded at harvest maturity.
accessions with < 5% of symptomatic plants were considered to be resistant.
to minimize the possibility of inaccurate scoring, all accessions were tested in at least three independent field trials.
if results from all three trials were consistent, the material was not tested further.
in the case of inconsistent results, material was retested in another two independent trials, after which all accessions were classified into one of the two groups.
the resistance and susceptibility classification was subsequently used in statistical analyses.
dna isolation
tissue from young leaves of about one-month-old plants was collected and immediately lyophilized.
lyophilized samples were ground to fine powder using a tissuelyser mill , before extracting genomic dna with the nucleospin plant ii kit .
the dna concentration and quality was analyzed with an nd- <dig> spectrometer  and gel electrophoresis.
polymerase chain reaction, allele detection, and product sequencing
primer pairs were designed for each marker from est  sequence with the primer  <dig> software  <cit> .
the selection of ests from the cgpdb database  <cit>  was based on their position in the genome - only ests previously mapped to the linkage group  <dig> were considered for development of markers.
due to the presence of introns in genomic dna, primers for several markers had to be designed more than once to obtain an amplicon for the given marker.
the polymerase chain reaction  was performed in a  <dig> μl volume containing  <dig> ng of genomic dna as a template,  <dig> μmol/l of each dntp, 1× standard taq pcr buffer with  <dig>  mmol/l mgcl <dig>   <dig>  u taq polymerase , and forward and reverse primers at a concentration of  <dig>  μmol/l each.
the reaction conditions were as follows: 95° for  <dig> min, followed by  <dig> cycles of 95° for  <dig> s, annealing temperature  for  <dig> s, and 72° for  <dig> s, with final extension of 72° for  <dig> min.
amplification was performed in an mj research tetrad thermal cycler .
the pcr products were analyzed on gels composed of  <dig> % agarose  and  <dig> % synergel  run with  <dig> × tbe buffer.
pcr samples were stained prior to electrophoresis with 1× gelred .
alternatively, the pcr products were separated using an hda-gt <dig> dna analyzer and scored by biocalculator software .
if sequencing was needed, pcr products were first treated with exonuclease i and subsequently with antarctic phosphatase .
dna sequencing was performed using abi bigdye terminator  according to the manufacturer's protocol, except that 5-μl reactions were performed with  <dig>  μl of bigdye on an abi 3730xl dna sequencing machine with  <dig> cm arrays.
columns indicate marker name, est or contig information in the cgpdb database, forward and reverse primers, annealing temperature , magnesium concentration in pcr reaction, and size of amplicon.
marker qgg19e <dig> could not be successfully amplified from  <dig> accessions even though  <dig> primer combinations were tested.
dna sequences were analyzed with codoncode aligner v.  <dig> .
<dig> .
we detected three types of polymorphism in our sequences - single feature polymorphism , insertions and deletions  and variable number tandem repeats .
most of the sfps that had been detected using the affymetrix genechip  <cit>  were due to a single nucleotide polymorphism , but in five cases due to a single base indel.
since haploview cannot handle missing values, missing bases were substituted prior to data analysis with an appropriate single nucleotide.
because all single-base indels could be tagged with snps from the same marker locus , we use the term snp throughout the text.
both indels and vntrs were excluded from data analysis, unless otherwise noted in the text.
high-resolution dna melting curve  analysis
est-derived markers were screened for polymorphism using high-resolution melting curve analysis.
primer pairs for each marker were developed with the primer  <dig> software and tested for optimal amplification using a temperature gradient .
amplifications were performed in  <dig> μl reactions containing  <dig> ng dna,  <dig> μmol/l of each dntp,  <dig>  u taq polymerase, 1× standard taq buffer with  <dig>  mmol/l mgcl <dig> , 1× lcgreen plus melting dye ,  <dig>  μmol/l of each primer, and  <dig> μl of mineral oil .
pcr was performed on a mj research tetrad thermal cycler with an initial denaturation of 95° for  <dig> min, followed by  <dig> cycles of 95° for  <dig> s, annealing temperature  for  <dig> s, and 72° for  <dig> s, with final extension of 72° for  <dig> min.
to facilitate heteroduplex formation samples were subjected, after the final extension, to 95° for  <dig> s followed by cooling to 25° for  <dig> s. simulation of a heterozygote was achieved by mixing equal amounts of dna from the two parental homozygous cultivars before pcr amplification.
melting-curve analysis was performed in a 96-well plate  on a lightscanner system and with the lightscanner software v.  <dig> .
<dig>  .
melting curves were analyzed as described in the lightscanner software manual.
marker cntg <dig> was analyzed in combination with a probe.
polymorphisms for three markers that are not shown in the table were detected by electrophoresis.
all information for these is the same as in table  <dig>
linkage mapping
one hundred and ninety two rils derived from a cross between an f <dig> of cv.
valmaine × cv.
salinas  <dig> and cv.
salinas were genotyped with est-derived markers.
selection of markers for this first round of genotyping was based on the molecular linkage map developed from an interspecific cross between l. sativa cv.
salinas and lactuca serriola accession uc96us <dig>  <cit> .
twenty markers were selected to evenly cover linkage group  <dig> in intervals of approximately  <dig> to  <dig> cm.
after preliminary mapping of the resistance gene, the region containing tvr <dig> was saturated with markers originating from a microarray-based study also carried out on the salinas × uc96us <dig> population  <cit> .
marker polymorphism was tested with hrm analysis, unless the difference between segregating alleles could be visually observed using gel electrophoresis.
if polymorphism could not be observed with hrm analysis, pcr products from the two parental genotypes were sequenced and new primers were designed for hrm.
statistical analysis of the linkage between molecular markers and dieback resistance was performed by mapmanager qtx software  <cit> .
dieback resistance for each ril was considered as a bi-allelic qualitative trait  and used for linkage analysis.
association mapping and assessment of population structure
association mapping was performed on a set of  <dig> accessions from seven horticultural types of lettuce .
in the first step, markers closely linked to the tvr <dig> gene were amplified from each accession and sequenced.
in the second step, the sequenced amplicons were analyzed for polymorphism with the codoncode software and inputted into haploview v.  <dig>   <cit> .
intra-locus snps were tagged in haploview with the tagger function at r <dig> =  <dig>  untagged snps from all markers and a representative snp for each tag were then entered into tassel v.  <dig> .
<dig>  <cit> .
tassel was subsequently used to test for association between individual snps and resistance to dieback while accounting for the population structure.
both p-values for each snp and percent of phenotypic variation explained by the model  were calculated with tassel after  <dig>  permutations.
prior to association analysis, the population structure in the set of  <dig> accessions was assessed with thirty est-ssr markers distributed throughout the genome  <cit>  using the computer program structure  <dig>   <cit> .
ten runs of structure were done by setting the number of populations  from  <dig> to  <dig>  for each run, the number of iterations and burn-in period iterations were both set to  <dig> .
the ad hoc statistic  <cit>  was used to estimate the number of subpopulations.
the optimum number of subpopulations  was subsequently used to calculate the fraction of each individual's genome  that originates from each of the five subpopulations.
the qk values obtained from structure were used as covariates in the statistical model given by tassel.
genetic variation and a linkage disequilibrium estimate
the level of genetic variation at the nucleotide level was estimated as nucleotide polymorphism  and nucleotide diversity .
to test the neutrality of mutations, we employed tajima's d test  <cit> , which is based on differences between π and θ. analyses of genetic variation and estimates of haplotype diversity  were carried out using dnasp v.  <dig> .
<dig> software  <cit> .
linkage disequilibrium  between pairs of snp loci in the genome was calculated with haploview and the values were pooled over the entire data set.
decay of ld with distance was estimated using a logarithmic trend line that was fitted to the data.
distances between markers were calculated from their respective positions on the consensus molecular linkage map.
the consensus map was created with joinmap v.  <dig>   <cit>  from the salinas × uc96us <dig> map  <cit>  and the  × salinas map .
snps with frequency < 5% were excluded from the analysis.
RESULTS
linkage mapping
cv.
salinas was resistant, while cv.
valmaine was susceptible to dieback in seven trials over four years.
the disease index for cultivar salinas ranged from 0% to 2% and for cultivar valmaine from 69% to 100% among these field experiments.
we found highly significant correlations  between estimated percentages of symptomatic plants in independent trials .
from  <dig> rils tested in multiple experiments,  <dig> were resistant and  <dig> were susceptible.
this segregation is not significantly different from the expected 1: <dig> ratio, consistent with a single gene effect.
the segregation ratio in the  <dig> individuals that were used for mapping of the resistance gene was  <dig> resistant to  <dig> susceptible.
linkage mapping on the framework map with markers spaced about  <dig> cm to  <dig> cm apart indicated that the tvr <dig> gene is linked to the marker lk <dig>  when this genomic region was saturated with additional markers, the tvr <dig> locus co-segregated with two of them.
these two markers are based on ests cntg <dig> and cntg <dig>  besides the two co-segregating markers; another six markers were located within  <dig> cm of the resistance gene.
these markers are based on ests cntg <dig>  qgg19e <dig>  clsm <dig>  clsz <dig>  qgc11n <dig>  and cntg <dig> .
nucleotide polymorphism
the nine markers closely linked to tvr <dig> were amplified and sequenced from a set of  <dig> accessions.
this set included all major horticultural types of lettuce that had been previously screened for resistance to dieback.
thirty-six of the accessions showed resistance to the disease and  <dig> were susceptible.
five of the seven horticultural types included both resistant and susceptible genotypes.
the two exceptions were iceberg and latin types, where only resistant and susceptible accessions respectively were available.
sequencing of over  <dig> kb from nine markers in the  <dig> accessions revealed  <dig> snps, six indels , and two vntrs .
sequenced markers were between ~ <dig> bp to  <dig> kb long, having  <dig> to  <dig> polymorphic sites, and  <dig> to  <dig> haplotypes .
haplotype diversity  was similar in all markers and ranged from  <dig>  to  <dig> .
values for nucleotide diversity  ranged from  <dig>  × 10- <dig> to  <dig>  × 10- <dig>  with an exception of marker clsz <dig> that had a value of  <dig>  × 10- <dig>  nucleotide polymorphism  was in the range from  <dig>  × 10- <dig> to  <dig>  × 10- <dig>  however, two markers each had a level of polymorphism above  <dig> × 10-3; marker qgc11n <dig>  and marker clcz <dig> .
since the sequenced regions of markers lk <dig>  cntg <dig>  cntg <dig>  and cntg <dig> contain both introns and exons, it is possible to compare polymorphism between the two groups.
while there was no significant difference in haplotype diversity between introns and exons, both nucleotide diversity  and polymorphism  were approximately  <dig>  fold higher in introns  .
values of tajima's d ranged from - <dig>  to  <dig> .
significant values of this parameter were calculated for markers lk <dig>  cntg <dig>  and cntg <dig> when combined intron and exon data were considered and for markers cntg <dig>  clsm <dig>  and clsz <dig> that contain exons only.
five of the markers consist of exons only, while the remaining four markers consist of a combination of exons and introns.
analyzed fragments are shorter than amplified markers, because indels, vntrs, and some poor sequences were deleted prior to data analysis.
*, **, and *** indicate the significance of tajima's d test at p ≤  <dig> , p ≤  <dig> , and p ≤  <dig>  .
association mapping
evaluation of population structure in a set of  <dig> accessions revealed that the best estimate of the number of subpopulations was five  .
these subpopulations corresponded approximately with the horticultural types.
best separated were crisphead , romaine, butterhead plus latin, and stem-type lettuces.
leaf-type lettuce was not separated in a single sub-population.
from  <dig> snps that were identified in the nine markers closely linked to the tvr <dig> gene,  <dig> were non-redundant for discrimination of haplotypes.
these unique snps were included together with the estimates of population structure in the association analysis performed with tassel.
eighteen snps, one indel, and one vntr were significantly  associated with the resistance allele .
significant snps were detected on all markers with the exception of marker cntg <dig>  for which the best value was p =  <dig> .
the snp with the largest effect was found on marker cntg <dig> at position  <dig>  this snp matches perfectly with the observed resistance .
an additional snp from the same tag is located at position  <dig>  both of these snps have c ⇔ t base substitutions where t is associated with resistance and c with susceptibility to dieback.
although both mutations are located in the coding region, they are synonymous and do not lead to changes in amino acids.
columns indicate markers, snp position in the marker, the p-value of association, the percent of phenotypic variation explained by the snp , and snps from the same tag.
snps with a p-value of ≤  <dig>  are shown, but only those with p ≤  <dig>  are considered to be significant.
*, **, and *** denote indel, sfp, and variable number of tandem repeats .
linkage disequilibrium
intra- and inter-locus ld were analyzed on nine markers flanking the tvr <dig> gene.
intra-locus ld shows a gradual decline as a function of distance and was estimated to have a value of r2~ <dig>  at  <dig> bp .
to observe inter-locus ld, we calculated r <dig> between snps detected in different markers.
analysis showed progressive, but slow, decay of ld and snps separated by ~ <dig> cm had an r <dig> value of  <dig> .
since estimates of ld can be substantially affected by a population structure, we calculated ld decay in two well-defined subpopulations with sufficient numbers of individuals .
estimated values of r <dig> at  <dig> bp were  <dig>  and  <dig>  for romaine and crisphead types, respectively.
similarly, at a distance of ~ <dig> cm we observed a larger ld in both types  than in the whole set that combined multiple subpopulations.
development of markers for marker-assisted selection
the resistance-snp association observed in the set of  <dig> accessions was detected through sequencing of pcr amplicons from individual accessions.
in order to accelerate and simplify the test of association, we developed a primer pair that allowed detection of polymorphism in the marker cntg <dig> through high-resolution melting analysis.
these primers amplify a  <dig> bp product that contains all three snps detected in the marker cntg <dig> at the positions  <dig>   <dig>  and  <dig>  the first two snps match perfectly with the resistance allele, while the third snp explains  <dig> % of the trait variation.
as with the first two snps, the third snp has a c ⇔ t substitution.
all susceptible genotypes carry the t allele, while resistant genotypes have either the t or c alleles at the third snp.
it appears that the t allele in the resistant material is associated with the resistance present in cv.
salinas and most of the other iceberg cultivars, whereas the c allele is associated with the resistance present in the three lines  that originate from the romaine-like primitive accession pi <dig>  marker cntg <dig>  therefore, not only allows for the detection of alleles associated with dieback resistance, but also separates alleles of different origins.
to further investigate polymorphism in this genomic region we sequenced two accessions from l. serriola, a wild species closely related to cultivated lettuce.
one of the accessions  is resistant to the disease, while the other one  is susceptible.
the susceptible genotype has the same allele sequence as all susceptible l. sativa accessions.
the resistant accession has a haplotype similar to cv.
salinas but instead of the t allele at position  <dig>  it carries the c allele.
the three snps at the marker cntg <dig> can thus distinguish four different haplotypes; three resistant and one associated with susceptibility .
haplotype r <dig>  has the t-t-t allele combination at positions  <dig>   <dig>  and  <dig>  haplotype r <dig>  carries the t-t-c combination, while haplotype r <dig>  carries the c-t-t alleles.
disease susceptibility was always associated with the s <dig> haplotype  that carries the c-c-t combination.
all four haplotypes can easily be separated through high-resolution melting analysis .
marker validation
validation of the haplotype-resistance association detected in the set of  <dig> l. sativa accessions and two l. serriola genotypes was performed on an additional set consisting of  <dig> accessions of l. sativa.
this set also contained diverse material that represented a broad spectrum of the variability present in cultivated lettuce.
we used the hrm approach for marker cntg <dig> and, as before, all genotypes that were susceptible to the disease carried haplotype s <dig>  while resistant material had either the r <dig> or r <dig> haplotypes .
this association was independent from population structure and was observed across all horticultural types.
discussion
nucleotide polymorphism
nucleotide polymorphism was observed in all nine markers that were sequenced from the region flanking the tvr <dig> gene.
the rate of nucleotide substitutions in a set of  <dig> accessions translates into ~ <dig> snp per  <dig> bp  between pairs of randomly selected sequences.
this snp frequency was somewhat lower when only coding regions were considered .
these values are well within the range observed for other plant species.
for example, the average snp frequency is  <dig> bp in aspen   <cit> ,  <dig> bp in potato   <cit> ,  <dig> bp in maize   <cit> ,  <dig> bp in sugar beet   <cit> ,  <dig> bp in rice   <cit> ,  <dig> bp in sorghum   <cit> ,  <dig> bp in tomato   <cit> , and  <dig> bp in soybean   <cit> .
both nucleotide polymorphism  and nucleotide diversity  of lettuce are similar to that observed in maize , potato , and sugar beet , but larger than in tomato , and soybean   <cit> .
if results from the analyzed region correspond to those for the whole genome, sequence variation in lettuce is relatively high for a selfing species.
it was previously observed that selfing species have generally lower levels of sequence variation than outcrossing species because of smaller effective population sizes  <cit> .
although polymorphism in lettuce appears to be considerably larger than in selfing soybean and tomato, it is similar to that observed in rice, which is also a self-pollinating species.
the ratio of nucleotide diversity in coding  and non-coding  sequences was not analyzed in detail, since data from only four markers  are available.
however, the ratio  across these markers appears to be smaller than in arabidopsis  , soybean , maize , and potato .
this difference is likely due to a higher level of functional constraint on the perigenic sequence  <cit>  of lettuce.
measures of haplotype diversity  were based on estimated haplotype frequencies  <cit> , and calculated using the dnasp software.
this measure of diversity is analogous to the heterozygosity at a single locus, and is at its maximum when haplotypes observed in the sample occur at equal frequencies  <cit> .
diversity based on haplotypes ranged from  <dig>  in qgg19e <dig> to  <dig>  in marker cntg <dig>  with an average value of  <dig>  ±  <dig> .
these values are higher than in rice , soybean , and human .
it is possible that the high level of diversity is related to the way that selection of the  <dig> accessions was performed.
we included dieback resistant and susceptible material from all predominant horticultural types, thereby selecting haplotypes at similar frequencies.
it would be interesting to observe how haplotype diversity changes in different genomic regions and/or for a different set of accessions.
to test the neutrality of mutations, tajima's d was calculated for all surveyed markers.
the average d  was larger than in soybean , potato , and sorghum .
a positive d value indicates a deficit of low-frequency alleles relative to what is expected.
since large d values can be caused by a population subdivision  <cit> , it is possible that the presence of subpopulations in the analyzed set of lettuce accessions affects both haplotype diversity and the d values.
when neutrality of mutations was tested in individual markers, three markers closely linked to the tvr <dig> gene  had tajima's d values significantly higher  than expected .
again, the population structure or selection at the tvr <dig> locus or the marker itself could have caused departures from neutrality.
linkage disequilibrium
the decay of ld for the trv <dig> region was relatively slow when measured both within individual markers and between markers flanking tvr <dig>  estimated values of r <dig> were ~ <dig>  at  <dig> bp, and ~ <dig>  at  <dig> cm.
a fitted logarithmic curve shows that the r <dig> value of  <dig>   is reached somewhere between  <dig>  cm to  <dig> cm.
ld of snp markers observed in some other selfing species was similar; ld in arabidopsis was  <dig> kb or  <dig> cm  <cit> ) and in soybean was ~ <dig> kb  <cit> ).
intra-locus ld decayed very little in tomato, with the log trend showing r <dig> >  <dig>  at  <dig> bp  <cit> .
however, it is problematic to compare decay of ld across species due to the large variability in ld quantification.
ld depends on a combination of many factors, such as the origin of the population, selected set of accessions, analyzed genomic region, molecular marker system, and presence of unidentified subpopulations.
hyten  <cit>  compared four different soybean populations for levels of ld decline.
while in the domesticated asian g. max population ld did not decline along the  <dig> kb sequenced region, the wild glycine soja population had a large ld decline within the ld block size averaging  <dig> kb.
comparable observations were not only made in the selfing arabidopsis  <cit> , but also in the outcrossing maize  <cit>  and aspen  <cit> .
our results show a large difference between estimates of ld when analyses were performed across all horticultural types or within each individual type.
while the estimate of r <dig> at a distance of  <dig> cm was  <dig>  for the whole set, it was  <dig>  for romaine type and  <dig>  for crisphead lettuce.
because only a relatively small part of the genome was analyzed in the present work, it is not possible to calculate ld at distances over  <dig> cm.
however, the trend for the logarithmic curve suggests that ld could reach more than  <dig> cm in romaine and probably more than  <dig> cm in crisphead types before declining to the value of r <dig> <  <dig> .
when only iceberg types  were included in the analysis, ld was still at its maximum  at a distance of  <dig> cm .
although these observations come from a limited number of individuals, they are supported by the fact that the modern iceberg-type lettuce has an extremely limited genetic diversity  <cit>  that is frequently associated with extensive ld.
linkage mapping
a previous study on the salinas × iceberg mapping population showed that the single, dominant gene  located on linkage group  <dig> confers resistance to lettuce dieback  <cit> .
we confirmed that the gene is located on linkage group  <dig> and pinpointed its position with markers cntg <dig> and cntg <dig>  both of these markers co-segregated with the resistance allele in  <dig> rils derived from the  × salinas cross.
the molecular linkage map based on the  × salinas cross showed good colinearity in order of the markers with the map based on the interspecific cross between cv.
salinas and l. serriola accessions uc96us <dig>  <cit> .
however, the interval from lk <dig> to cntg <dig> is more than twice the size when estimated from the interspecific cross .
similarly, while markers cntg <dig> and cntg <dig> co-segregate in the intraspecific map, they are separated by  <dig> cm on the interspecific map, despite the latter being based on fewer rils.
these values are within the range of other observations on intra- and interspecific maps of lettuce  <cit> .
colinearity between the two maps allows for development of a consensus map that places markers cntg <dig> and cntg <dig>  <dig>  cm apart.
association mapping
we identified the genomic region carrying resistance against dieback and nine markers closely linked with the tvr <dig> gene through linkage analysis.
we subsequently used this information to test the linked markers for association with the disease resistance on a set of  <dig> diverse accessions.
eight of the nine markers showed highly significant association with dieback resistance, consistent with the tvr <dig> gene being located in this region.
although the threshold for declaring association significant was set at p <  <dig> , most of the associations were significant at p ≤  <dig> .
the only exception was marker cntg <dig>  where the most significant association reached only p =  <dig> .
the low association between snps at this marker and dieback resistance was somewhat unexpected, since cntg <dig> co-segregated with the resistance allele in the  × salinas mapping population.
while unexpected, it is not uncommon that markers closely linked with a trait in a mapping population do not show association when tested on a set of diverse accessions.
this problem is well documented in potato, where markers linked to the gro <dig> and h <dig> resistance genes in the mapping population were tested on  <dig> unrelated cultivars.
the gro1-specific marker was not correlated with the resistance phenotype, while h1-specific marker was indicative of resistance in only four cultivars  <cit> .
a similar example can be shown for lettuce, where markers most tightly linked to the cor resistance gene were the least useful for diagnostic when tested in a large collection of cultivars  <cit> .
there are several other examples of markers tightly linked to resistance genes, but whose use present problems in material different from the original in which they were identified  <cit> .
therefore, an important requirement for any molecular marker used in mas is not just its applicability in a specific cross, but its association in a wide gene pool.
from snps that were significantly associated with dieback resistance, the best fit was observed for those located in marker cntg <dig>  this is the second of two markers, the other being cntg <dig>  that co-segregated with the resistance allele in the mapping population.
it is intriguing that one of the two markers co-segregating with the tvr <dig> allele in the mapping population showed no significant association in a set of diverse accessions, while the other showed a perfect match.
although these two markers were not separated in the intraspecific population, the linkage map developed from the salinas × uc96us <dig> cross indicates that they are  <dig> cm apart.
therefore it is possible that testing more rils from the intraspecific population would separate the two markers and tvr <dig>  association of snps from marker cntg <dig> with the resistance allele was validated in a larger set of  <dig> diverse accessions from several horticultural types.
the marker-trait association was observed not only in l. sativa, but also in two l. serriola accessions included in the study.
however, while the susceptible haplotype is identical in both species , the resistant haplotypes are different .
to investigate the relationship between tvr <dig> and the resistance observed in l. serriola, we screened  <dig> f <dig> rils from the salinas × uc96us <dig> population for resistance to dieback.
if tvr <dig> and the resistance locus from uc96us <dig> were distinct and unlinked, approximately 25% susceptible offspring would be observed.
however, since all rils were resistant to the disease , we concluded that the resistance locus in uc96us <dig> is either allelic or linked to tvr <dig>  the same conclusion was reached for the resistance locus in the primitive romaine-type accession pi <dig>  <cit> .
the three resistance loci are associated with three distinct haplotypes; resistance in cv.
salinas with r <dig>  in pi <dig> with r <dig>  and in uc96us <dig> with r <dig>
even though all  <dig> l. sativa accessions from the two testing sets showed the same haplotype-resistance association, it is unlikely that the est from which this marker was derived is directly involved in dieback resistance.
a search for protein similarity in the ncbi database  <cit>  indicates that cntg <dig> is similar to the copper ion binding protein from castorbean  and the plastocyanin-like domain-containing protein from arabidopsis .
the annotated functions of these two proteins do not imply an obvious role in plant-pathogen interactions  <cit> .
moreover, the two substitutions  at marker cntg <dig> that are the most significantly associated with dieback resistance are synonymous, coding the same amino acid.
assuming that marker cntg <dig> is not directly involved in the resistance, it is probable that a recombinant genotype will eventually be identified.
on the other hand, marker-trait associations can be very strong between some tightly linked alleles.
for example, rick and forbes  <cit>  documented linkage between allozyme aps <dig> and tomato resistance gene mi that did not break in as many as  <dig> backcross generations.
chromosomal linkage group  <dig> contains a large cluster of resistance genes that confer resistance to downy mildew   and lettuce root aphid   <cit> .
however, the cntg <dig> marker is well separated  from this cluster on the salinas × uc96us <dig> map.
moreover, tvr <dig> is one of the few resistance genes that was not at a genetic position coincident with any type of candidate resistance gene so far mapped in lettuce  <cit> .
thus, it is possible that tvr <dig> is different from the common types of pathogen recognition genes.
using high-resolution dna melting analysis for marker-assisted selection
we used hrm to directly detect sequence variations in pcr amplicons.
high-resolution melting curves were recorded by the slow and steady heating of pcr products in a lightscanner instrument.
changes in the shape of the melting curve were then used to identify mutations and variations.
the method worked well for most of the analyzed markers, however, in a few cases, alleles could not be distinguished.
when this occurred, we applied two alternative approaches to increase sensitivity through heteroduplex formation.
in one approach, the heteroduplex formation was facilitated through mixing of samples prior to pcr.
for example, if one sample contained dna from cv.
salinas only, the other one would contain a mix of dna  from both cv.
salinas and valmaine.
the second alternative used an unlabeled probe  <dig> bp to  <dig> bp long that was designed for the region carrying the snp.
the probe was included in the pcr mix prior to cycling but was not consumed during amplification due to 3' block.
genotyping was accomplished by monitoring the melting of probe-target duplexes post-pcr as described in lightscanner manual.
both of the above alternatives improved allele detection; however, the probe-target duplex approach appeared to be more sensitive.
CONCLUSIONS
lettuce dieback is a soil-borne viral disease that is one of the limiting factors for romaine and leaf-type lettuce production in california.
currently, there is no method that effectively reduces, removes, or destroys the virus in infested soil.
thus the best control of lettuce dieback is accomplished by using resistant cultivars.
however, development of resistant cultivars up to now has required extensive field-based testing.
our identification of a molecular marker that is tightly linked to the tvr <dig> gene conferring durable resistance will reduce the need for field-based screening and accelerate development of resistant cultivars.
a combination of classical linkage mapping and association mapping allowed us to pinpoint the location of the resistance gene on chromosomal linkage group  <dig>  examination of the tvr <dig> region revealed a relatively high level of nucleotide polymorphism  and extensive linkage disequilibrium.
one of the markers  flanking the tvr <dig> gene showed 100% accuracy in detecting resistant and susceptible phenotypes in a set of  <dig> l. sativa accessions from all horticultural types of lettuce and two accessions from l. serriola.
a combination of three snps in this est-based marker identified four haplotypes.
three of the haplotypes are related to dieback resistance, while a single haplotype is always associated with susceptibility to the disease.
application of high-resolution dna melting analysis allowed us to distinguish all four haplotypes of the cntg <dig> marker in a single assay.
since heterozygous state is also easily distinguishable by the hrm analysis , we can identify and select homozygous individuals whose offspring do not segregate for resistance in the following generation.
screening for dieback resistance with this molecular marker is now part of our breeding program.
marker-assisted selection with cntg <dig> is being used to develop improved romaine and leaf-type cultivars resistant to the disease.
in addition, we are employing the molecular markers to prevent inadvertent introgression of the susceptible haplotype into the iceberg lettuce gene pool.
data access
described sequences have been submitted to genbank under accession numbers gq <dig> to gq <dig>
list of abbreviations
aflp: amplified fragment length polymorphism; cgpdb: compositae genome project database; cntg : contig; cv.
: cultivar; est: expressed sequence tag; hrm: high-resolution dna melting curve analysis; indel: insertion or deletion; ld: linkage disequilibrium; ncbi: national center for biotechnology information; pcr: polymerase chain reaction; rapd: random amplification of polymorphic dna; ril: recombinant-inbred line; sfp: single-feature polymorphism; snp: single-nucleotide polymorphism; vntr: variable number tandem repeat.
authors' contributions
is designed and coordinated the study, performed phenotypic evaluations, carried out statistical analyses of the data, and prepared the manuscript.
dap developed primers, performed marker and sequence analysis, and assisted in drafting the manuscript.
lkm, mjt, oeo and rwm developed mapping populations, provided est data, and revised the manuscript.
bes carried out sequencing and revised the manuscript.
all authors read and approved the final manuscript.

 lettuce dieback disease is widespread in commercially grown romaine and leaf-type lettuces. the disease is caused by two closely related soilborne viruses from the family tombusviridae -- tomato bushy stunt virus and lettuce necrotic stunt virus. symptoms of lettuce dieback include mottling and necrosis of older leaves, stunting, and plant death. the characteristic symptoms usually appear after the plant has reached to weeks of age and render the plant unmarketable. tbsv and lnsv are extremely persistent viruses and they are likely to survive in soil and water for long periods of time. the virus has no known vector and it seems to move through infested soil and water. while fungal vectors are not necessary for transmission, studies have yet to be conducted to determine if such vectors can facilitate or increase rates of virus transmission to lettuce. previous studies have provided no evidence that either chemical treatment or rotation with non-host crops can effectively reduce, remove, or destroy the virus in infested soil. since there are no known methods to prevent the disease in a lettuce crop grown in an infested field, genetic resistance remains the only option for disease control. although susceptibility to dieback is widespread in romaine and leaf lettuces, modern iceberg-type cultivars remain completely free of symptoms when grown in infested soil. it appears that the resistance observed in iceberg cultivars was originally introduced into the iceberg genepool from the cultivar imperial around years ago. if true, this suggests that the resistance is effective and highly durable despite extensive cultivation of iceberg cultivars. through use of molecular marker technology, the single dominant gene, which is responsible for the dieback resistance in iceberg lettuce, has been mapped to chromosomal linkage group. position of the gene was inferred with aflp and rapd markers in a population originating from a cross between the resistant cultivar salinas and the susceptible cultivar iceberg. another dieback resistance gene was discovered in the primitive romaine-like accession pi. analysis of resistance in offspring originating from a cross between the two resistant genotypes indicates that the resistance locus in pi is either allelic or linked to tvr. because of the increased interest in non-iceberg types of lettuce, introgressing tvr into romaine, leaf, and other susceptible types is of high priority for the lettuce industry. however, the breeding process is slow and labor intensive due to a need for extensive field-based testing. application of marker-assisted selection can reduce the need for field screening and accelerate development of dieback resistant material. to pinpoint the location of the tvr gene and develop markers for marker-assisted selection, we employed a combination of classical linkage and association mapping techniques. the association mapping approach is based on the extent of linkage disequilibrium observed in a set of accessions that are not closely related. in contrast to linkage mapping, association mapping is a method that detects relationships between phenotypic variation and genetic polymorphism in existing germplasm, without development of mapping populations. this method incorporates the effects of recombination occurring in many past generations into a single analysis and is thus complementary to linkage analysis. association mapping has been successfully applied in mapping resistance genes in several diploid and polyploid plant species. the main drawback of association mapping is the possibility of false-positive results due to an unrecognized population structure. when the trait of interest is more prevalent in one subpopulation than others, the trait will be associated with any marker allele that is in high frequency in that subpopulation. our previous analysis of population structure with molecular markers revealed that cultivated lettuce is divided into several well-defined subpopulations that correspond approximately to different horticultural types. consequently, traits that are strongly correlated with lettuce types display many false-positive results when population structure is ignored. however, these spurious associations disappear when estimates of population structure are included in the statistical model. therefore, the best approach for avoiding spurious associations in lettuce association studies is to assess relatedness of accessions with molecular markers and to include this information into the statistical model. in the present study we mapped the tvr gene using a combination of linkage and association mapping. high-resolution dna melting curve analysis was used to assess polymorphism in mapping populations and to detect haplotypes associated with the disease resistance. the potential for marker-assisted selection was then validated in the genetic backgrounds present in most common horticultural types of lettuce. finally, we used snp markers to assess intra- and inter-locus linkage disequilibrium in the tvr region. methods linkage mapping population recombinant-inbred lines were derived from a cross between an f of cv. valmaine × cv. salinas and cv. salinas. both salinas and salinas are iceberg type lettuces resistant to dieback whose appearance and performance is the same, except for reaction to lettuce mosaic virus. two hundred and fifty three f rils were screened for resistance to dieback in multiple trials and of these rils were randomly selected for genotyping with molecular markers. association mapping set a set of cultivars, plant introductions, and breeding lines representing all predominant types of cultivated lettuce was used for association mapping. the set includes batavia types, butterhead types, iceberg types, latin types, leaf types, romaine types, and stem types. the lettuce accessions were selected from material used in breeding programs, ancestors frequently observed in pedigrees, and newly developed breeding lines. for each horticultural type both dieback resistant and susceptible accessions were selected, with the exception of iceberg lettuce, where only resistant cultivars were available, and the latin type, where only susceptible cultivars were available. accessions that were sequenced are in bold; the remaining accessions were analyzed with the hrm approach only. validation set to validate the marker-trait association detected in the association mapping set, a validation set of accessions was screened for disease resistance and genotyped with the marker, cntg this set represents the spectrum of phenotypic and genotypic variability observed in cultivated lettuce and includes batavia types, butterhead types, iceberg types, latin type, leaf types, oil types, romaine types, and stem types. assessment of dieback resistance dieback resistance data were obtained from field observations as previously described. susceptibility was evaluated by seeding lettuce directly in the field in salinas, ca, from which tbsv and lnsv had previously been isolated from plants exhibiting characteristic dieback symptoms. the experiment was comprised of two complete blocks, with ~ plants per genotype per block. plants were seeded in two rows on m wide beds and were thinned to obtain spacing of cm between plants. standard commercial practices were used for irrigation, fertilization, and pest control. plants were checked weekly for disease symptoms in order to discriminate between plants dying due to dieback and those due to unrelated causes. the percentage of plants that showed typical dieback symptoms was recorded at harvest maturity. accessions with < 5% of symptomatic plants were considered to be resistant. to minimize the possibility of inaccurate scoring, all accessions were tested in at least three independent field trials. if results from all three trials were consistent, the material was not tested further. in the case of inconsistent results, material was retested in another two independent trials, after which all accessions were classified into one of the two groups. the resistance and susceptibility classification was subsequently used in statistical analyses. dna isolation tissue from young leaves of about one-month-old plants was collected and immediately lyophilized. lyophilized samples were ground to fine powder using a tissuelyser mill, before extracting genomic dna with the nucleospin plant ii kit. the dna concentration and quality was analyzed with an nd- spectrometer and gel electrophoresis. polymerase chain reaction, allele detection, and product sequencing primer pairs were designed for each marker from est sequence with the primer software. the selection of ests from the cgpdb database was based on their position in the genome - only ests previously mapped to the linkage group were considered for development of markers. due to the presence of introns in genomic dna, primers for several markers had to be designed more than once to obtain an amplicon for the given marker. the polymerase chain reaction was performed in a μl volume containing ng of genomic dna as a template, μmol/l of each dntp, 1× standard taq pcr buffer with mmol/l mgcl u taq polymerase, and forward and reverse primers at a concentration of μmol/l each. the reaction conditions were as follows: 95° for min, followed by cycles of 95° for s, annealing temperature for s, and 72° for s, with final extension of 72° for min. amplification was performed in an mj research tetrad thermal cycler. the pcr products were analyzed on gels composed of % agarose and % synergel run with × tbe buffer. pcr samples were stained prior to electrophoresis with 1× gelred. alternatively, the pcr products were separated using an hda-gt dna analyzer and scored by biocalculator software. if sequencing was needed, pcr products were first treated with exonuclease i and subsequently with antarctic phosphatase. dna sequencing was performed using abi bigdye terminator according to the manufacturer's protocol, except that 5-μl reactions were performed with μl of bigdye on an abi 3730xl dna sequencing machine with cm arrays. columns indicate marker name, est or contig information in the cgpdb database, forward and reverse primers, annealing temperature, magnesium concentration in pcr reaction, and size of amplicon. marker qgg19e could not be successfully amplified from accessions even though primer combinations were tested. dna sequences were analyzed with codoncode aligner v... we detected three types of polymorphism in our sequences - single feature polymorphism, insertions and deletions and variable number tandem repeats. most of the sfps that had been detected using the affymetrix genechip were due to a single nucleotide polymorphism, but in five cases due to a single base indel. since haploview cannot handle missing values, missing bases were substituted prior to data analysis with an appropriate single nucleotide. because all single-base indels could be tagged with snps from the same marker locus, we use the term snp throughout the text. both indels and vntrs were excluded from data analysis, unless otherwise noted in the text. high-resolution dna melting curve analysis est-derived markers were screened for polymorphism using high-resolution melting curve analysis. primer pairs for each marker were developed with the primer software and tested for optimal amplification using a temperature gradient. amplifications were performed in μl reactions containing ng dna, μmol/l of each dntp, u taq polymerase, 1× standard taq buffer with mmol/l mgcl, 1× lcgreen plus melting dye, μmol/l of each primer, and μl of mineral oil. pcr was performed on a mj research tetrad thermal cycler with an initial denaturation of 95° for min, followed by cycles of 95° for s, annealing temperature for s, and 72° for s, with final extension of 72° for min. to facilitate heteroduplex formation samples were subjected, after the final extension, to 95° for s followed by cooling to 25° for s. simulation of a heterozygote was achieved by mixing equal amounts of dna from the two parental homozygous cultivars before pcr amplification. melting-curve analysis was performed in a 96-well plate on a lightscanner system and with the lightscanner software v... melting curves were analyzed as described in the lightscanner software manual. marker cntg was analyzed in combination with a probe. polymorphisms for three markers that are not shown in the table were detected by electrophoresis. all information for these is the same as in table linkage mapping one hundred and ninety two rils derived from a cross between an f of cv. valmaine × cv. salinas and cv. salinas were genotyped with est-derived markers. selection of markers for this first round of genotyping was based on the molecular linkage map developed from an interspecific cross between l. sativa cv. salinas and lactuca serriola accession uc96us. twenty markers were selected to evenly cover linkage group in intervals of approximately to cm. after preliminary mapping of the resistance gene, the region containing tvr was saturated with markers originating from a microarray-based study also carried out on the salinas × uc96us population. marker polymorphism was tested with hrm analysis, unless the difference between segregating alleles could be visually observed using gel electrophoresis. if polymorphism could not be observed with hrm analysis, pcr products from the two parental genotypes were sequenced and new primers were designed for hrm. statistical analysis of the linkage between molecular markers and dieback resistance was performed by mapmanager qtx software. dieback resistance for each ril was considered as a bi-allelic qualitative trait and used for linkage analysis. association mapping and assessment of population structure association mapping was performed on a set of accessions from seven horticultural types of lettuce. in the first step, markers closely linked to the tvr gene were amplified from each accession and sequenced. in the second step, the sequenced amplicons were analyzed for polymorphism with the codoncode software and inputted into haploview v.. intra-locus snps were tagged in haploview with the tagger function at r = untagged snps from all markers and a representative snp for each tag were then entered into tassel v... tassel was subsequently used to test for association between individual snps and resistance to dieback while accounting for the population structure. both p-values for each snp and percent of phenotypic variation explained by the model were calculated with tassel after permutations. prior to association analysis, the population structure in the set of accessions was assessed with thirty est-ssr markers distributed throughout the genome using the computer program structure. ten runs of structure were done by setting the number of populations from to for each run, the number of iterations and burn-in period iterations were both set to. the ad hoc statistic was used to estimate the number of subpopulations. the optimum number of subpopulations was subsequently used to calculate the fraction of each individual's genome that originates from each of the five subpopulations. the qk values obtained from structure were used as covariates in the statistical model given by tassel. genetic variation and a linkage disequilibrium estimate the level of genetic variation at the nucleotide level was estimated as nucleotide polymorphism and nucleotide diversity. to test the neutrality of mutations, we employed tajima's d test, which is based on differences between π and θ. analyses of genetic variation and estimates of haplotype diversity were carried out using dnasp v.. software. linkage disequilibrium between pairs of snp loci in the genome was calculated with haploview and the values were pooled over the entire data set. decay of ld with distance was estimated using a logarithmic trend line that was fitted to the data. distances between markers were calculated from their respective positions on the consensus molecular linkage map. the consensus map was created with joinmap v. from the salinas × uc96us map and the × salinas map. snps with frequency < 5% were excluded from the analysis.  linkage mapping cv. salinas was resistant, while cv. valmaine was susceptible to dieback in seven trials over four years. the disease index for cultivar salinas ranged from 0% to 2% and for cultivar valmaine from 69% to 100% among these field experiments. we found highly significant correlations between estimated percentages of symptomatic plants in independent trials. from rils tested in multiple experiments, were resistant and were susceptible. this segregation is not significantly different from the expected 1: ratio, consistent with a single gene effect. the segregation ratio in the individuals that were used for mapping of the resistance gene was resistant to susceptible. linkage mapping on the framework map with markers spaced about cm to cm apart indicated that the tvr gene is linked to the marker lk when this genomic region was saturated with additional markers, the tvr locus co-segregated with two of them. these two markers are based on ests cntg and cntg besides the two co-segregating markers; another six markers were located within cm of the resistance gene. these markers are based on ests cntg qgg19e clsm clsz qgc11n and cntg. nucleotide polymorphism the nine markers closely linked to tvr were amplified and sequenced from a set of accessions. this set included all major horticultural types of lettuce that had been previously screened for resistance to dieback. thirty-six of the accessions showed resistance to the disease and were susceptible. five of the seven horticultural types included both resistant and susceptible genotypes. the two exceptions were iceberg and latin types, where only resistant and susceptible accessions respectively were available. sequencing of over kb from nine markers in the accessions revealed snps, six indels, and two vntrs. sequenced markers were between ~ bp to kb long, having to polymorphic sites, and to haplotypes. haplotype diversity was similar in all markers and ranged from to. values for nucleotide diversity ranged from × 10- to × 10- with an exception of marker clsz that had a value of × 10- nucleotide polymorphism was in the range from × 10- to × 10- however, two markers each had a level of polymorphism above × 10-3; marker qgc11n and marker clcz. since the sequenced regions of markers lk cntg cntg and cntg contain both introns and exons, it is possible to compare polymorphism between the two groups. while there was no significant difference in haplotype diversity between introns and exons, both nucleotide diversity and polymorphism were approximately fold higher in introns. values of tajima's d ranged from - to. significant values of this parameter were calculated for markers lk cntg and cntg when combined intron and exon data were considered and for markers cntg clsm and clsz that contain exons only. five of the markers consist of exons only, while the remaining four markers consist of a combination of exons and introns. analyzed fragments are shorter than amplified markers, because indels, vntrs, and some poor sequences were deleted prior to data analysis. *, **, and *** indicate the significance of tajima's d test at p ≤, p ≤, and p ≤. association mapping evaluation of population structure in a set of accessions revealed that the best estimate of the number of subpopulations was five. these subpopulations corresponded approximately with the horticultural types. best separated were crisphead, romaine, butterhead plus latin, and stem-type lettuces. leaf-type lettuce was not separated in a single sub-population. from snps that were identified in the nine markers closely linked to the tvr gene, were non-redundant for discrimination of haplotypes. these unique snps were included together with the estimates of population structure in the association analysis performed with tassel. eighteen snps, one indel, and one vntr were significantly associated with the resistance allele. significant snps were detected on all markers with the exception of marker cntg for which the best value was p =. the snp with the largest effect was found on marker cntg at position this snp matches perfectly with the observed resistance. an additional snp from the same tag is located at position both of these snps have c ⇔ t base substitutions where t is associated with resistance and c with susceptibility to dieback. although both mutations are located in the coding region, they are synonymous and do not lead to changes in amino acids. columns indicate markers, snp position in the marker, the p-value of association, the percent of phenotypic variation explained by the snp, and snps from the same tag. snps with a p-value of ≤ are shown, but only those with p ≤ are considered to be significant. *, **, and *** denote indel, sfp, and variable number of tandem repeats. linkage disequilibrium intra- and inter-locus ld were analyzed on nine markers flanking the tvr gene. intra-locus ld shows a gradual decline as a function of distance and was estimated to have a value of r2~ at bp. to observe inter-locus ld, we calculated r between snps detected in different markers. analysis showed progressive, but slow, decay of ld and snps separated by ~ cm had an r value of. since estimates of ld can be substantially affected by a population structure, we calculated ld decay in two well-defined subpopulations with sufficient numbers of individuals. estimated values of r at bp were and for romaine and crisphead types, respectively. similarly, at a distance of ~ cm we observed a larger ld in both types than in the whole set that combined multiple subpopulations. development of markers for marker-assisted selection the resistance-snp association observed in the set of accessions was detected through sequencing of pcr amplicons from individual accessions. in order to accelerate and simplify the test of association, we developed a primer pair that allowed detection of polymorphism in the marker cntg through high-resolution melting analysis. these primers amplify a bp product that contains all three snps detected in the marker cntg at the positions and the first two snps match perfectly with the resistance allele, while the third snp explains % of the trait variation. as with the first two snps, the third snp has a c ⇔ t substitution. all susceptible genotypes carry the t allele, while resistant genotypes have either the t or c alleles at the third snp. it appears that the t allele in the resistant material is associated with the resistance present in cv. salinas and most of the other iceberg cultivars, whereas the c allele is associated with the resistance present in the three lines that originate from the romaine-like primitive accession pi marker cntg therefore, not only allows for the detection of alleles associated with dieback resistance, but also separates alleles of different origins. to further investigate polymorphism in this genomic region we sequenced two accessions from l. serriola, a wild species closely related to cultivated lettuce. one of the accessions is resistant to the disease, while the other one is susceptible. the susceptible genotype has the same allele sequence as all susceptible l. sativa accessions. the resistant accession has a haplotype similar to cv. salinas but instead of the t allele at position it carries the c allele. the three snps at the marker cntg can thus distinguish four different haplotypes; three resistant and one associated with susceptibility. haplotype r has the t-t-t allele combination at positions and haplotype r carries the t-t-c combination, while haplotype r carries the c-t-t alleles. disease susceptibility was always associated with the s haplotype that carries the c-c-t combination. all four haplotypes can easily be separated through high-resolution melting analysis. marker validation validation of the haplotype-resistance association detected in the set of l. sativa accessions and two l. serriola genotypes was performed on an additional set consisting of accessions of l. sativa. this set also contained diverse material that represented a broad spectrum of the variability present in cultivated lettuce. we used the hrm approach for marker cntg and, as before, all genotypes that were susceptible to the disease carried haplotype s while resistant material had either the r or r haplotypes. this association was independent from population structure and was observed across all horticultural types. discussion nucleotide polymorphism nucleotide polymorphism was observed in all nine markers that were sequenced from the region flanking the tvr gene. the rate of nucleotide substitutions in a set of accessions translates into ~ snp per bp between pairs of randomly selected sequences. this snp frequency was somewhat lower when only coding regions were considered. these values are well within the range observed for other plant species. for example, the average snp frequency is bp in aspen, bp in potato, bp in maize, bp in sugar beet, bp in rice, bp in sorghum, bp in tomato, and bp in soybean. both nucleotide polymorphism and nucleotide diversity of lettuce are similar to that observed in maize, potato, and sugar beet, but larger than in tomato, and soybean. if results from the analyzed region correspond to those for the whole genome, sequence variation in lettuce is relatively high for a selfing species. it was previously observed that selfing species have generally lower levels of sequence variation than outcrossing species because of smaller effective population sizes. although polymorphism in lettuce appears to be considerably larger than in selfing soybean and tomato, it is similar to that observed in rice, which is also a self-pollinating species. the ratio of nucleotide diversity in coding and non-coding sequences was not analyzed in detail, since data from only four markers are available. however, the ratio across these markers appears to be smaller than in arabidopsis, soybean, maize, and potato. this difference is likely due to a higher level of functional constraint on the perigenic sequence of lettuce. measures of haplotype diversity were based on estimated haplotype frequencies, and calculated using the dnasp software. this measure of diversity is analogous to the heterozygosity at a single locus, and is at its maximum when haplotypes observed in the sample occur at equal frequencies. diversity based on haplotypes ranged from in qgg19e to in marker cntg with an average value of ±. these values are higher than in rice, soybean, and human. it is possible that the high level of diversity is related to the way that selection of the accessions was performed. we included dieback resistant and susceptible material from all predominant horticultural types, thereby selecting haplotypes at similar frequencies. it would be interesting to observe how haplotype diversity changes in different genomic regions and/or for a different set of accessions. to test the neutrality of mutations, tajima's d was calculated for all surveyed markers. the average d was larger than in soybean, potato, and sorghum. a positive d value indicates a deficit of low-frequency alleles relative to what is expected. since large d values can be caused by a population subdivision, it is possible that the presence of subpopulations in the analyzed set of lettuce accessions affects both haplotype diversity and the d values. when neutrality of mutations was tested in individual markers, three markers closely linked to the tvr gene had tajima's d values significantly higher than expected. again, the population structure or selection at the tvr locus or the marker itself could have caused departures from neutrality. linkage disequilibrium the decay of ld for the trv region was relatively slow when measured both within individual markers and between markers flanking tvr estimated values of r were ~ at bp, and ~ at cm. a fitted logarithmic curve shows that the r value of is reached somewhere between cm to cm. ld of snp markers observed in some other selfing species was similar; ld in arabidopsis was kb or cm ) and in soybean was ~ kb ). intra-locus ld decayed very little in tomato, with the log trend showing r > at bp. however, it is problematic to compare decay of ld across species due to the large variability in ld quantification. ld depends on a combination of many factors, such as the origin of the population, selected set of accessions, analyzed genomic region, molecular marker system, and presence of unidentified subpopulations. hyten compared four different soybean populations for levels of ld decline. while in the domesticated asian g. max population ld did not decline along the kb sequenced region, the wild glycine soja population had a large ld decline within the ld block size averaging kb. comparable observations were not only made in the selfing arabidopsis, but also in the outcrossing maize and aspen. our results show a large difference between estimates of ld when analyses were performed across all horticultural types or within each individual type. while the estimate of r at a distance of cm was for the whole set, it was for romaine type and for crisphead lettuce. because only a relatively small part of the genome was analyzed in the present work, it is not possible to calculate ld at distances over cm. however, the trend for the logarithmic curve suggests that ld could reach more than cm in romaine and probably more than cm in crisphead types before declining to the value of r <. when only iceberg types were included in the analysis, ld was still at its maximum at a distance of cm. although these observations come from a limited number of individuals, they are supported by the fact that the modern iceberg-type lettuce has an extremely limited genetic diversity that is frequently associated with extensive ld. linkage mapping a previous study on the salinas × iceberg mapping population showed that the single, dominant gene located on linkage group confers resistance to lettuce dieback. we confirmed that the gene is located on linkage group and pinpointed its position with markers cntg and cntg both of these markers co-segregated with the resistance allele in rils derived from the × salinas cross. the molecular linkage map based on the × salinas cross showed good colinearity in order of the markers with the map based on the interspecific cross between cv. salinas and l. serriola accessions uc96us. however, the interval from lk to cntg is more than twice the size when estimated from the interspecific cross. similarly, while markers cntg and cntg co-segregate in the intraspecific map, they are separated by cm on the interspecific map, despite the latter being based on fewer rils. these values are within the range of other observations on intra- and interspecific maps of lettuce. colinearity between the two maps allows for development of a consensus map that places markers cntg and cntg cm apart. association mapping we identified the genomic region carrying resistance against dieback and nine markers closely linked with the tvr gene through linkage analysis. we subsequently used this information to test the linked markers for association with the disease resistance on a set of diverse accessions. eight of the nine markers showed highly significant association with dieback resistance, consistent with the tvr gene being located in this region. although the threshold for declaring association significant was set at p <, most of the associations were significant at p ≤. the only exception was marker cntg where the most significant association reached only p =. the low association between snps at this marker and dieback resistance was somewhat unexpected, since cntg co-segregated with the resistance allele in the × salinas mapping population. while unexpected, it is not uncommon that markers closely linked with a trait in a mapping population do not show association when tested on a set of diverse accessions. this problem is well documented in potato, where markers linked to the gro and h resistance genes in the mapping population were tested on unrelated cultivars. the gro1-specific marker was not correlated with the resistance phenotype, while h1-specific marker was indicative of resistance in only four cultivars. a similar example can be shown for lettuce, where markers most tightly linked to the cor resistance gene were the least useful for diagnostic when tested in a large collection of cultivars. there are several other examples of markers tightly linked to resistance genes, but whose use present problems in material different from the original in which they were identified. therefore, an important requirement for any molecular marker used in mas is not just its applicability in a specific cross, but its association in a wide gene pool. from snps that were significantly associated with dieback resistance, the best fit was observed for those located in marker cntg this is the second of two markers, the other being cntg that co-segregated with the resistance allele in the mapping population. it is intriguing that one of the two markers co-segregating with the tvr allele in the mapping population showed no significant association in a set of diverse accessions, while the other showed a perfect match. although these two markers were not separated in the intraspecific population, the linkage map developed from the salinas × uc96us cross indicates that they are cm apart. therefore it is possible that testing more rils from the intraspecific population would separate the two markers and tvr association of snps from marker cntg with the resistance allele was validated in a larger set of diverse accessions from several horticultural types. the marker-trait association was observed not only in l. sativa, but also in two l. serriola accessions included in the study. however, while the susceptible haplotype is identical in both species, the resistant haplotypes are different. to investigate the relationship between tvr and the resistance observed in l. serriola, we screened f rils from the salinas × uc96us population for resistance to dieback. if tvr and the resistance locus from uc96us were distinct and unlinked, approximately 25% susceptible offspring would be observed. however, since all rils were resistant to the disease, we concluded that the resistance locus in uc96us is either allelic or linked to tvr the same conclusion was reached for the resistance locus in the primitive romaine-type accession pi. the three resistance loci are associated with three distinct haplotypes; resistance in cv. salinas with r in pi with r and in uc96us with r even though all l. sativa accessions from the two testing sets showed the same haplotype-resistance association, it is unlikely that the est from which this marker was derived is directly involved in dieback resistance. a search for protein similarity in the ncbi database indicates that cntg is similar to the copper ion binding protein from castorbean and the plastocyanin-like domain-containing protein from arabidopsis. the annotated functions of these two proteins do not imply an obvious role in plant-pathogen interactions. moreover, the two substitutions at marker cntg that are the most significantly associated with dieback resistance are synonymous, coding the same amino acid. assuming that marker cntg is not directly involved in the resistance, it is probable that a recombinant genotype will eventually be identified. on the other hand, marker-trait associations can be very strong between some tightly linked alleles. for example, rick and forbes documented linkage between allozyme aps and tomato resistance gene mi that did not break in as many as backcross generations. chromosomal linkage group contains a large cluster of resistance genes that confer resistance to downy mildew and lettuce root aphid. however, the cntg marker is well separated from this cluster on the salinas × uc96us map. moreover, tvr is one of the few resistance genes that was not at a genetic position coincident with any type of candidate resistance gene so far mapped in lettuce. thus, it is possible that tvr is different from the common types of pathogen recognition genes. using high-resolution dna melting analysis for marker-assisted selection we used hrm to directly detect sequence variations in pcr amplicons. high-resolution melting curves were recorded by the slow and steady heating of pcr products in a lightscanner instrument. changes in the shape of the melting curve were then used to identify mutations and variations. the method worked well for most of the analyzed markers, however, in a few cases, alleles could not be distinguished. when this occurred, we applied two alternative approaches to increase sensitivity through heteroduplex formation. in one approach, the heteroduplex formation was facilitated through mixing of samples prior to pcr. for example, if one sample contained dna from cv. salinas only, the other one would contain a mix of dna from both cv. salinas and valmaine. the second alternative used an unlabeled probe bp to bp long that was designed for the region carrying the snp. the probe was included in the pcr mix prior to cycling but was not consumed during amplification due to 3' block. genotyping was accomplished by monitoring the melting of probe-target duplexes post-pcr as described in lightscanner manual. both of the above alternatives improved allele detection; however, the probe-target duplex approach appeared to be more sensitive.  lettuce dieback is a soil-borne viral disease that is one of the limiting factors for romaine and leaf-type lettuce production in california. currently, there is no method that effectively reduces, removes, or destroys the virus in infested soil. thus the best control of lettuce dieback is accomplished by using resistant cultivars. however, development of resistant cultivars up to now has required extensive field-based testing. our identification of a molecular marker that is tightly linked to the tvr gene conferring durable resistance will reduce the need for field-based screening and accelerate development of resistant cultivars. a combination of classical linkage mapping and association mapping allowed us to pinpoint the location of the resistance gene on chromosomal linkage group examination of the tvr region revealed a relatively high level of nucleotide polymorphism and extensive linkage disequilibrium. one of the markers flanking the tvr gene showed 100% accuracy in detecting resistant and susceptible phenotypes in a set of l. sativa accessions from all horticultural types of lettuce and two accessions from l. serriola. a combination of three snps in this est-based marker identified four haplotypes. three of the haplotypes are related to dieback resistance, while a single haplotype is always associated with susceptibility to the disease. application of high-resolution dna melting analysis allowed us to distinguish all four haplotypes of the cntg marker in a single assay. since heterozygous state is also easily distinguishable by the hrm analysis, we can identify and select homozygous individuals whose offspring do not segregate for resistance in the following generation. screening for dieback resistance with this molecular marker is now part of our breeding program. marker-assisted selection with cntg is being used to develop improved romaine and leaf-type cultivars resistant to the disease. in addition, we are employing the molecular markers to prevent inadvertent introgression of the susceptible haplotype into the iceberg lettuce gene pool. data access described sequences have been submitted to genbank under accession numbers gq to gq list of abbreviations aflp: amplified fragment length polymorphism; cgpdb: compositae genome project database; cntg: contig; cv.: cultivar; est: expressed sequence tag; hrm: high-resolution dna melting curve analysis; indel: insertion or deletion; ld: linkage disequilibrium; ncbi: national center for biotechnology information; pcr: polymerase chain reaction; rapd: random amplification of polymorphic dna; ril: recombinant-inbred line; sfp: single-feature polymorphism; snp: single-nucleotide polymorphism; vntr: variable number tandem repeat. authors' contributions is designed and coordinated the study, performed phenotypic evaluations, carried out statistical analyses of the data, and prepared the manuscript. dap developed primers, performed marker and sequence analysis, and assisted in drafting the manuscript. lkm, mjt, oeo and rwm developed mapping populations, provided est data, and revised the manuscript. bes carried out sequencing and revised the manuscript. all authors read and approved the final manuscript. 
lettuce is susceptible to dieback, a soilborne disease caused by two viruses from the family tombusviridae. sequencing of these markers from a set of cultivars revealed a relatively high level of nucleotide polymorphism and extensive linkage disequilibrium in this region. the association mapping approach revealed that one of the nine markers in the tvr region matched exactly with resistant and susceptible phenotypes when tested on a set of l. sativa accessions from all horticultural types of lettuce. susceptibility to dieback is widespread in romaine and leaf-type lettuce, while modern iceberg cultivars are resistant to this disease. a combination of classical linkage mapping and association mapping allowed us to pinpoint the location of the tvr resistance gene on chromosomal linkage group nine molecular markers, based on expressed sequence tags, were closely linked to tvr in the mapping population, developed from crosses between resistant and susceptible cultivars. this study describes fine mapping of the resistance gene, analysis of nucleotide polymorphism and linkage disequilibrium in the tvr region, and development of molecular markers for marker-assisted selection. the combination of three single-nucleotide polymorphisms at the cntg marker identified four haplotypes. we have successfully applied high-resolution dna melting analysis to distinguish all four haplotypes of the cntg marker in a single analysis. resistance in iceberg cultivars is conferred by tvr - a single, dominant gene that provides durable resistance. however, the extent of linkage disequilibrium was affected by population structure and the values were substantially larger when the analysis was performed only for romaine and crisphead accessions. the marker-trait association was also confirmed on two accessions of lactuca serriola - a wild relative of cultivated lettuce. marker-assisted selection for dieback resistance with hrm is now an integral part of our breeding program that is focused on the development of improved lettuce cultivars.
 lettuce is susceptible to dieback, a soilborne disease caused by two viruses from the family tombusviridae. susceptibility to dieback is widespread in romaine and leaf-type lettuce, while modern iceberg cultivars are resistant to this disease. resistance in iceberg cultivars is conferred by tvr - a single, dominant gene that provides durable resistance. this study describes fine mapping of the resistance gene, analysis of nucleotide polymorphism and linkage disequilibrium in the tvr region, and development of molecular markers for marker-assisted selection.  a combination of classical linkage mapping and association mapping allowed us to pinpoint the location of the tvr resistance gene on chromosomal linkage group nine molecular markers, based on expressed sequence tags, were closely linked to tvr in the mapping population, developed from crosses between resistant and susceptible cultivars. sequencing of these markers from a set of cultivars revealed a relatively high level of nucleotide polymorphism and extensive linkage disequilibrium in this region. however, the extent of linkage disequilibrium was affected by population structure and the values were substantially larger when the analysis was performed only for romaine and crisphead accessions. the association mapping approach revealed that one of the nine markers in the tvr region matched exactly with resistant and susceptible phenotypes when tested on a set of l. sativa accessions from all horticultural types of lettuce. the marker-trait association was also confirmed on two accessions of lactuca serriola - a wild relative of cultivated lettuce. the combination of three single-nucleotide polymorphisms at the cntg marker identified four haplotypes. three of the haplotypes were associated with resistance and one of them was always associated with susceptibility to the disease.  we have successfully applied high-resolution dna melting analysis to distinguish all four haplotypes of the cntg marker in a single analysis. marker-assisted selection for dieback resistance with hrm is now an integral part of our breeding program that is focused on the development of improved lettuce cultivars. 