BACKGROUND
cultivated tetraploid wheat  is genetically differentiated from hexaploid wheat  by as little as ca.
<dig>  years of evolution.
both species derived from domesticated emmer  through a rather long human-driven selection process, including distinct and sequential domestication bottlenecks and continuous gene flow from wild emmer  schweinf)  <cit> .
in the past two decades, molecular genetics and genomics of durum wheat, including breeding applications such as marker-assisted selection , have largely relied on the molecular tools specifically developed for hexaploid wheat .
the restriction fragment length polymorphisms  and the pcr-based molecular markers such as the simple sequence repeats , amplified fragment length polymorphisms , and sequence tagged sites  developed for hexaploid wheat performed rather efficiently in tetraploid wheat based on the commonalities between the two shared a- and b-genomes .
however, marker’s polymorphism information content had to be re-assessed directly in the durum wheat germplasm  <cit> .
in the 2000’s, intra- and inter-specific durum wheat and durum wheat × wild emmer genetic linkage maps were developed mainly using ssr loci  <cit>  as well as the microarray-based diversity array technology  markers .
integration of the ssr-based linkage map data into consensus maps was first pursued in hexaploid wheat by somers et al.
<cit>  and crossa et al.
<cit> , and then in durum wheat by trebbi et al.
<cit> , marone et al.
<cit>  and letta et al.
<cit> .
in durum wheat, the limited number of maps available to these studies has not yet allowed for full coverage of the genome, an important prerequisite for genome-wide association mapping, meta-analysis and positional cloning.
the most recently published consensus map specific to tetraploid wheat  <cit>  is composed of  <dig>  loci arranged in  <dig> linkage groups, a number that exceeds the  <dig> nuclear chromosomes of this species.
the hexaploid wheat ssr-based consensus map  by somers et al.
<cit>  has been widely used as a reference for wheat genomics studies for more than a decade.
in hexaploid wheat, several mapping studies were published using ssr and dart technologies, revealing major genes and qtls for grain yield, yield components, adaptive traits, response to abiotic and biotic stresses and quality .
collectively, these studies laid the foundation for mas applications in wheat .
within this dynamic scenario, the availability of a high-quality consensus map more exhaustively covering the entire genome is a valuable asset for genetic studies and breeding applications.
furthermore, powerful association mapping  and meta-qtl analysis require reference genetic maps of a quality standard higher than that commonly adopted for coarse mapping in bi-parental populations.
am and meta-qtl analysis are being increasingly adopted in wheat genomics , including durum wheat .
the development of integrated maps were approached based on:  ‘consensus’ mapping, where de novo maps are produced by merging all the single segregation data-sets available to develop a novel unified map,  ‘interpolation’ mapping , where integrated maps are built by regressing the single component map marker positions on an initial reference map that provides the framework for sequential interpolation.
the latter method is computation-and-time efficient but relies on the availability of an accurate reference with strong prerequisites such as comprehensive genome coverage and proven representativeness.
consensus mapping has the potential to overcome the major limitations typical of mapping information based on single maps, such as local aberrations in crossover rates  <cit>  and presence of chromosome regions with locally low marker density/lack of polymorphism due to the occurrence of identity by descent  <cit> .
moreover, consensus mapping provides more accurate mapping information thanks to the higher number of progenies considered.
several software packages were developed for consensus mapping, from the early ones that pool single component segregation data and calculate consensus maps based on the assumption of homogeneity of marker order and recombination rate across populations, such as joinmap  <cit>  and carthagene  <cit> , to others that implement graph-theoretic models with marker removal in case of conflicting orders  or attempt to define the optimal consensus order of shared markers by a synchronous optimization of the local orders in single component maps .
in this study, segregation data from six core mapping populations of durum wheat were analysed based on a common procedure with stringent quality criteria.
following identification and removal from the global computation of chromosome regions showing local deviations from the homogeneity assumptions, mainly identified in single component maps only, the segregation data from markers shared among populations were pooled in carthagene to obtain a consensus framework map that proved to be highly robust compared to the single component maps.
the value of this consensus map, enriched in density by the interpolation of the unique markers, was assessed through the identification of signatures of genetic differentiations among sub-populations of the durum wheat germplasm and the identification of qtls controlling heading date in the mediterranean cultivation areas at the genome-wide scale.
RESULTS
linkage maps from the individual populations
the genotypic data of  <dig> mapping populations of tetraploid wheat , either recombinant inbred lines  or double haploids , were made available by collaborating institutions or were downloaded from the graingenes database.
the genotypic data were used to re-construct the maps of the original populations following a common mapping procedure.
the reconstructed maps are thereafter reported as component maps.
details of the parental accessions, cumulative genetic distances and marker composition for each of the component maps are reported in table  <dig> table  <dig>
component maps used for consensus mapping and map integration: markers and map features
2
mapping populations used for consensus framework mapping
mapping population used for marker interpolation only
mapping population used for marker interpolation only, no segregation data available
for each map, the cross, population type , number of mapped markers listed by marker type , number of linkage groups, total map length  and average inter-marker distance  are reported.
a core-set of six ril-based component maps was selected to obtain a robust framework map subsequently used for interpolation of unique markers.
all but one of these six ril populations were obtained from intraspecific t. durum crosses, with parental lines chosen among diverse groups of the elite durum germplasm .
one of the six populations included in the core set was obtained from the cross of langdon × t. dicoccoides , the wild progenitor of t. durum.
in total, the core set of ril populations included  <dig>  lines.
the single maps were constituted by  <dig> to  <dig> linkage groups, with total length ranging from  <dig>  to  <dig>  cm , with an average of  <dig>  cm, and inter-marker distance varying from  <dig>   to  <dig>   cm, with an average of  <dig>  cm/marker.
eight additional populations were used for marker interpolation.
four of the populations included in this second set were dhs obtained from agriculture and agrifood canada, university of saskatchewan and usda.
three additional populations were recombinant inbred and one was a population of f2: <dig> progenies .
for six out of these eight populations the original segregation data were available and thus the linkage maps were reconstructed according to the common procedure used for the common maps.
the two pdw233 × bhalegaon  <dig>  <cit>  and latino × primadur maps  <cit> , for which the original segregation data were not available, were inspected for their homogeneity in marker distribution and inter-marker distances as compared to the component maps before to integrate their map information data into the consensus map.
the marker density of all of these eight maps was inferior to that reached in the six core set ril populations , while retaining a good level of genome coverage .
consensus map features
the genotypes from the core set of six ril populations were used to build a reliable consensus framework map based on common markers only, including  <dig> and  <dig> anchor ssr and dart markers, respectively,  <dig> anchor snp/stss and one morphological locus.
these markers were grouped into  <dig> linkage groups .
representative estimates of recombination rate were obtained across mapping populations, yielding a framework map of common markers with total length of  <dig>  cm , with an average inter-marker distance of  <dig>  cm per common marker.
the consensus framework map was thus only  <dig> % longer than the longest among the six component maps , with the number of independent linkage groups decreased from  <dig> to  <dig> table  <dig>
consensus framework and interpolated map marker summary
number of mapped loci  included in the consensus framework map  and in the final interpolated map , number of linkage groups, total map length  and average inter-marker distance  for both maps.
the six core ril maps and the consensus framework map are reported in additional file 1: figure s <dig> and additional file 2: table s <dig>  with anchor markers reported in red font.
in the computation of the consensus map, portions of linkage groups from single maps were not included in the merged data-set due to either excessive heterogeneity of recombination rate  or low density of anchor markers .
frequency of common framework markers  and map length of each of the framework linkage groups are reported in table  <dig>  the  <dig> framework linkage groups covered most of the <dig> durum wheat chromosomes.
two separate linkage groups were obtained for chromosomes 1a, 2a and 3a.
a relatively low number of anchor markers was observed for chromosomes 1a, 4b and 5a  while up to  <dig> common markers were mapped on chromosome 7b, followed by  <dig> common markers on chromosome 6b.
the inter-marker distance between common markers ranged from  <dig>  cm/marker for linkage group 3a <dig> and  <dig>  cm/marker for 5b.
the two-point mapping lod score of framework markers averaged  <dig>  across all chromosomes and ranged from  <dig>  for 1a to  <dig>  for 4a .table  <dig>
consensus framework and interpolated map features summarized by linkage group
number of mapped loci  included in the consensus framework and in the final interpolated map, detailed by linkage group .
the subsequent interpolation of the unique loci allowed us to map  <dig>  loci in total, for a total map length of  <dig>  cm.
this final consensus interpolated map was  <dig> % longer  than the longest component maps mr × cl.
the category and number of markers mapped in the interpolated map are summarized in table  <dig> and detailed in table  <dig>  depending on the chromosome/linkage group, the interpolated map showed average inter-marker distances ranging from less than 1 cm/marker, e.g.
<dig> - <dig>  cm/marker for linkage groups 1b, 2a <dig>  3a <dig>  3b, 4a, 4b, 6a, 6b and 7b, to  <dig> - <dig>  cm/marker for linkage groups 1a <dig>  5a, 5b .
the number of markers mapped to the a genome  was considerably less than those mapped to the b genome  while the cumulative genetic distances of the linkage groups of the two genomes were balanced .
the degree of monotony of consensus marker order as compared to the original component maps  was checked by projection plots reported in additional file 3: figure s <dig>  few inconsistencies were observed for closely linked markers mapped on genetic intervals of less than 2 cm.
for most of the detected order conflicts, the original data of the component populations were re-inspected and, in most cases, it was found that the consensus marker order showed an overall lod score and probability close to the one present in the single discordant maps; therefore, the consensus marker order was retained.
pair-wise spearman rank correlations rho  of marker order between the consensus and the single component maps were generally very high across chromosomes.
out of  <dig> pair-wise comparisons,  <dig> showed ρ values higher than  <dig> , with  <dig> comprised between  <dig>  and  <dig>  when considering the regression r <dig> values, which highlight not only departure from colinearity but also local divergence in recombination frequency,  <dig> out of  <dig> pair-wise comparisons showed values ≥  <dig> ,  <dig> were comprised between  <dig>  and  <dig>  and  <dig> were <  <dig> .
overall the r <dig> values were thus slightly lower as compared to rank correlation values.
local deviations from colinearity were observed only for a few chromosomes and populations as follows: in chromosomes 1a , 2a , 3a  and 4a .
the projection plots clearly showed that  marker density of the single durum wheat maps differed markedly along the linkage groups and  the interpolated map effectively integrated the marker information from the component maps with improved marker density and genome coverage along the consensus chromosomes, with only a slight increase in linkage group total length.
the single component maps showed a high frequency of locally low marker density or even no marker coverage at all , particularly those derived from the elite × elite t. durum crosses.
these regions were irregularly scattered across maps on most of the chromosomes .
examples can be observed in the projection plots of chromosomes 1b , 2b , 3b , 5b , 6a , 7a  and 7b .
the linkage map obtained from t. durum langdon × t. dicoccoides g18- <dig> was much less affected by uneven marker density distribution as compared to the intra-specific t. durum maps.
in some cases, chromosome regions showing low marker density were observed consistently across the majority of the component maps and were thus considered as a constitutive feature.
examples were the centromeric portion of chromosome 1a, the proximal region of 2a, and the distal regions of 3a and 7a.
as a result, these four chromosome regions also showed a lower-than-average marker density in the consensus map.
the durum interpolated map was compared with the reference ssr consensus map of hexaploid wheat  .
the comparison was based on the ssr markers shared between the two maps, which varied from  <dig> to  <dig> depending on the linkage group.
spearman rank correlations rho  values were lower than those observed within the intra-specific maps of durum wheat; the average  value was  <dig> , ranging from  <dig> - <dig>   to  <dig>  .
coefficient of determination r <dig> values averaged  <dig>  and ranged from less than  <dig>   up to  <dig> - <dig>  .
as compared to the ta-ssr- <dig> map, the durum-specific map herein reported provided genome coverage of 100% for the majority of the chromosomes, with the exception of chromosomes 1b and 5b were genome coverage of the durum consensus was  <dig>  and  <dig> % less than ta-ssr- <dig> due to low coverage of common markers on the distal ends of short arms.
in chromosome 3a and 6b the durum consensus extended the genome coverage in the distal chromosome regions as compared to the ta-ssr- <dig> table  <dig>
comparison between the durum consensus interpolated map and the hexaploid consensus maps
ta-ssr-2004
chr.
3b consensus map
ta-ssr- <dig> reported in somers et al.
;  <cit> .
chr.
3b consensus map reported in paux et al.
2008;  <cit> .
noticeable differences in local recombination rate were observed between the hexaploid and the durum maps.
for instance, the strong decline in marker density found in the durum peri-centromeric regions of chromosomes 1a and 2a was not observed in the corresponding hexaploid regions.
as for chromosome 1a, the high recombination rate  observed in durum wheat between the peri-centromeric regions of the two distal linkage groups  was not observed in ta-ssr- <dig>  where the map distance between gwm <dig> and cfa <dig> was only  <dig>  cm and the marker density in the local centromeric region was not affected.
similarly, in chromosome 3a, the low-marker density, highly recombinogenic region detected between anchor markers gwm <dig>  and gwm <dig>  spanned only  <dig>  cm in the hexaploid wheat consensus map.
the updated consensus map for chromosome 3b published by paux et al.
<cit>  and derived from the analysis of  <dig> mapping populations was also considered.
sixty-six markers  were common to both the hexaploid and tetraploid 3b maps.
the correlation coefficient between our map and the paux et al.
<cit>  map was high .
the durum interpolated map was then compared with the most recent tetraploid consensus map  <cit>  obtained with different software .
in this case, while the number of mapped markers was only slightly lower than in our case , the results were different in terms of number of lg obtained , and total map length .
overall conservation of colinearity of the two durum consensus maps and ta-ssr- <dig> was better for our map  than for the marone et al.
<cit>  map .
ld decay rate and molecular diversity in elite durum wheat germplasm
a panel of  <dig> elite durum accessions representative of the major gene pool cultivated in the mediterranean region for which ld and population structure were previously investigated based on low-density genotyping with ssr markers  was re-investigated in depth based on the profiles of  <dig>  markers included in the consensus map.
of these  <dig>  markers,  <dig> showed minor allele frequency  equal or higher than  <dig>  and were thus considered informative for ld and am analysis.
this set of markers, including  <dig> ssr/stss and  <dig> dart, generated  <dig>  pairwise combinations of intra-chromosomal loci for which ld significance and r2/d’ estimates were calculated.
ld decay was investigated through fitted regression and box plot distribution, , with a focus on the short inter-marker distances .
non-linear modeling of ld decay reported in figure  <dig> showed an overall r <dig> fit value of 42%, an α value of  <dig>  and an effective population size  of  <dig> .
based on the fitted model, at 0 cm genetic distance the expected r <dig> value was equal to  <dig>  while the r <dig> half-value decline  was reached at  <dig>  cm.
the upper 95th percentile of the r2value distribution for unlinked marker pairs , widely considered as a threshold useful to separate the true linkage ld from the background ld due to population structure, was equal to  <dig>  .
this trend was confirmed by inspecting the ld statistics for discrete marker pairwise classes of incremental map distances .
the class of completely linked markers  showed mean r2 =  <dig> , median ld r2 =  <dig> , inter-quartile range from  <dig>  to  <dig>  and d’ =  <dig> .
the mean and median ld r <dig> decreased by half in the  <dig> -1 cm inter-marker distance class  and more than half in the 1-5 cm class, respectively; the median ld r <dig> values dropped below  <dig>  in the 5-10 cm class .
the ld estimates calculated for independent markers  showed mean r2 =  <dig>  and d’ =  <dig> .figure  <dig>
intra-chromosomal linkage disequilibrium  decay plot as a function of genetic distance .
ld decay assessed in a durum wheat panel of  <dig> elite  accessions adapted to the mediterranean environments.
ld estimates are reported as squared correlations of allele frequencies .
inter-marker genetic distances are from the durum wheat consensus map.
non-linear modeling of ld was performed using the sved  <cit>  equation.
boxplot charts of linkage disequilibrium  estimates for categorized inter-marker genetic map distances .
pairwise ld estimates are reported as squared correlations of allele frequencies.
inter-marker genetic distances are from the durum wheat consensus map.
linkage disequilibrium estimates for the elite durum wheat panel based on mapped ssr and dart markers
r
2
d
ld decay in a collection of  <dig> elite durum wheat accessions from the mediterranean, cimmyt and icarda germplasm included in the association mapping durum panel.
detailed pair-wise ld r <dig> values for all the consensus linkage groups are projected as heat-plot triangular matrices in additional file 6: figure s <dig>  together with the polymorphism index content plots along the chromosomes  and the distributions of markers with highly significant  genetic differentiation  among the main sub-populations represented in the panel.
when detectable, ld blocks with sizeable r <dig> values  were in most cases observed within a 5 cm window size; relatively small ld blocks were detectable across the full length of durum wheat chromosomes, from distal to proximal regions.
however, a large number of closely linked adjacent markers showed ld r <dig> values in the range of  <dig>  or less.
a few long-range ld blocks extending more than 10 cm were also observed, particularly in the proximal regions of chromosomes 1b, 6a and 7b.
the polymorphism information content  plots showed a trend for higher values in the distal regions of the chromosomes and lower values in the peri-centromeric regions .
chromosome 1a exhibited the most extended peri-centromeric region with both low marker density and diversity in the elite germplasm, causing a gap in the continuity of the chr.
1a consensus map in this region.
a similar phenomenon was observed for peri-centromeric regions of chromosomes 2a, 2b and in 3as.
none of the six core ril maps showed a marker density sufficiently high to guarantee the continuity of the consensus linkage groups in these four chromosomes.
additionally, numerous locally defined sharp decreases of pic values extending over stretches of  <dig> to  <dig> adjacent markers were commonly observed in both centromeric and distal regions of several chromosomes , even in chromosome regions where the marker density was not locally affected.
the population structure of the elite panel of accessions was previously investigated based on a non-redundant set of  <dig> highly informative ssr markers .
hierarchical and non-hierarchical model-based cluster analyses showed that the population structure could be described based on five main sub-populations corresponding to landraces- and breeding-derived germplasm founders that originated from the italian, cimmyt and icarda breeding programs distinct by time period  or target environment .
the founders were widely used in the national breeding programs of mediterranean countries and a high degree of admixture was detected among sub-populations  <cit> .
the increased density of genetically mapped markers based on the consensus map allowed for a more in-depth investigation of the patterns of genetic differentiation present within and among the five main sub-populations.
amova showed that the genetic variation within was higher than the variation among sub-groups , with the latter  reflecting known temporal, geographic and pedigree differences.
a medium level of genetic differentiation was observed between the two icarda sub-populations for dryland and temperate areas .
more differentiation was found between the icarda sub-population for dryland areas and the italian and early-period cimmyt germplasm .
lower-than-average differentiation was observed between the icarda-temperate and the italian-early cimmyt as well as the mid-cimmyt.
the late-cimmyt germplasm  was the most differentiated from the icarda-dryland and italian-early cimmyt sub-populations.table  <dig>
analysis of molecular variance  for the elite durum wheat panel based on mapped ssr and dart markers
sub-population pairwise f
st
sub-population
founder
pairwise differences
<dig>
<dig>
<dig>
<dig>
<dig>
analysis of molecular variance for the elite durum wheat panel of  <dig> accessions adapted to mediterranean areas based on the sub-population subdivision as from a previous population genetic structure analysis  <cit> .
overall fst index among sub-populations and specific sub-population pairwise fst indexes are reported.
average population pairwise differences are reported as follows:  above diagonal: average number of pairwise differences between populations ,  diagonal elements : average number of pairwise differences within population ,  below diagonal: corrected average pairwise difference  /2).
the improved marker density of the consensus map allowed us to search genome-wide for chromosome regions showing evidence of high genetic differentiation among sub-populations .
single markers or chromosome regions  with sub-population pair-wises fst values greater than the fst thresholds set at p  <dig>  were observed in most of the chromosome arms and projected on the consensus map .
three main genetic differentiation patterns were observed as follows:  fst differentiation “pattern 1”: significant differentiation across the majority of sub-populations indicating differentiation by time and by target environments  fst differentiation “pattern 2”: significant differentiation between icarda-dryland vs. all the other subpopulations ,  fst differentiation “pattern 3”: significant differentiation of either or both icarda-temperate and italian, early-cimmyt subpopulations vs. the mid- and late-cimmyt subpopulations .
there were  <dig>   <dig> and  <dig> single markers/chromosome regions in the durum wheat genome that showed genetic differentiation pattern  <dig>   <dig> and  <dig>  respectively .
fst differentiation pattern  <dig> was mainly found on chromosomes 1b, 2a, 2b, 4b, 5a, 5b and 6b.
high frequency of both pattern  <dig> and  <dig> were observed in chromosomes 3a and 7b.
pattern  <dig> was also frequently found in chromosomes 1b, 3b and 7a.
in chromosome 2a, ppd-a <dig> and four closely associated flanking markers showed highly significant fst differences for all sub-population pair-wises .
in chromosome 2b, coincident with ppd-b <dig>   a strong differentiation was observed between the italian and icarda populations  vs. the cimmyt sub-populations bred at sub-tropical latitudes .
as expected, rht-b <dig> on chromosome 4b showed a type  <dig> fst differentiation pattern with peaks of fst values for the pair-wise comparisons including the icarda dryland population  vs. all the other populations .
gwas for heading date
the consensus map was used for a genome-wide association scan  to detect association of the  <dig> mapped ssr and dart markers with maf >  <dig>  with time to heading in the durum wheat association panel.
time to heading data were available for  <dig> field trials carried out in the mediterranean region and in mexico.
the ammi biplot analysis showed that the heading date phenotypes from the  <dig> environments could be grouped according to five macro-environments: southern europe , north africa-tunisia, north africa-morocco, west-asia  and mexico .
the association scan was performed for each environment as well as for the adjusted means of each of the five macro-environments.
broad-sense heritability  values of heading date calculated across environments were high for southern european , asian  and mexican macro-areas , including  <dig>   <dig> and  <dig> environments, respectively, but lower for the north african moroccan  and tunisian  macro-environments, each with two environments.
the phenotypic data of six genotypes known to carry the vernalization-sensitive vrn- <dig> allele at vrn-a <dig> were excluded from the analysis.
the initial gwas analysis showed strong experiment-wise significant associations at the two chromosome regions corresponding to the location of ppd-a <dig> and ppd-b <dig> loci and numerous chromosome regions with highly significant  marker-wise associations across environments.
detailed results are reported in table  <dig> table  <dig>
association results for heading date in the elite durum panel at the two major photoperiod-response homeologous
ppd-1
loci
ppd-a1
ppd-b1
macro-environmental area
r
2
r
2
southern europe
north africa – tunisia
west asia
north africa – morocco
mexico
association analysis based on  <dig> accessions from the durum panel, evaluated for heading date across  <dig> environments grouped in five macro-environmental areas in the mediterranean basin and mexico.
the ppd-a <dig> specific assay  <cit>  and wpt- <dig> dart marker tightly associated to ppd-b <dig> have been used.
significance of p ≤ <dig> e- <dig> refers to the experiment-wise significance threshold of p ≤  <dig> .
results are reported for single environments and for the adjusted means across macro-environmental areas.
at ppd-a <dig>  association peaks were detected in coincidence of the diagnostic marker developed from the causal locus.
considering the adjusted means of macro-environmental areas, p-values of association ranged from a minimum of p =  <dig> e- <dig>  for the southern european area , to a maximum significance of p =  <dig> e- <dig>  in mexico .
among the four markers wmc <dig>  cfa2201-2a, gwm1198-2a and wpt- <dig> located within  <dig>  cm from the ppd-a <dig> locus and with ld r <dig> values between  <dig>  and  <dig> , significant associations with heading date were observed for cfa2201-2a only .
for the region harboring ppd-b <dig>  highly significant marker- and experiment-wise associations with heading date were detected for  <dig> dart and one ssr markers mapped within an interval of  <dig>  cm .
the majority of these markers formed a unique linkage block with strong inter-marker ld r <dig> values .
peaks of association to heading date across environments were observed for wpt- <dig>  the qtl-representative marker, at position  <dig>  cm.
this marker showed a range of p-values from a minimum of p =  <dig>   in mexico to a maximum association of p =  <dig> e- <dig>  in southern europe.
according to hanocq et al.
and bennett et al.
<cit> , the small linkage block includes markers associated with the predicted position of ppd-b <dig>
as expected, the level of significance and magnitude of effects associated with the ppd loci were strongly influenced by latitude.
the genotypic to phenotypic proportion of variance of ppd-qtls, as estimated by r <dig> values on a single-environment basis, was significantly correlated with latitude  as presented in figure  <dig>  ppd-a <dig> showed a strong trend towards increased r <dig> values at latitudes lower than 40°  while the markers tagging ppd-b <dig> showed an opposite trend.figure  <dig>
scatterplot of the relationship between latitude and genotypic to phenotypic variance coefficient of determination  values for
ppd-a1
and
ppd-b1
in  <dig> mediterranean and mexican environments.
the gwas was repeated after including ppd-a <dig> and ppd-b <dig> representative markers as covariates in the mlm association model.
based on this analysis,  <dig> unique chromosome regions showed highly significant  association to the heading date adjusted means of at least one or more of the five macro-environmental areas.
marker-features of these regions are summarized in additional file 7: table s <dig> and figure  <dig>  none of these qtl-harboring regions reached the experiment-wise adjusted bonferroni significance threshold based on the number of independent ld blocks .
however, the reported associations were all supported by marker-wise significances  over multiple environments , as detailed in additional file 7: table s <dig>  out of the 50 am-qtls,  <dig> consisted of single-marker associations  while  <dig> consisted of small blocks of multiple adjacent markers all associated to the phenotype as well as to each other with ld r <dig> values ≥  <dig> .
from the consensus map, these qtls included markers that were either coincident  or closely linked within a 3-4 cm interval.
there were only three qtls with a significance interval of 5 cm or more on chromosomes 2b  and 3b .
based on the predicted ld decay in the collection, confidence interval boundaries of  <dig>  cm, corresponding to the genetic distance over which the ld decays to r2 =  <dig> , were attributed to both sides of the marker’s blocks significantly associated with the phenotype.
thus, a confidence interval of  <dig>  cm was attributed to the single markers associated with the phenotype.
the r <dig> values of the associations on a macro-environmental basis were mostly between  <dig>  and  <dig> % .
the proportion of phenotypic variance explained by simultaneously considering all the reported qtl-representative markers  ranged from a minimum of  <dig> % for the tunisian macro-area to a maximum of  <dig> % for mexico, with r <dig> values of  <dig> ,  <dig>  and  <dig> % for the southern-european, asian and moroccan macro-areas, respectively.figure  <dig>
association mapping qtls  for time to heading in the mediterranean regions reported on the tetraploid ssr and dart
®
marker consensus map.
am-qtls are reported as red bars  on the left side of the chromosomes.
red thin wiskers extending the red bars corresponds to the confidence intervals  of am-qtls.
projected qtl confidence intervals from previous studies are reported as vertical bars of various colors other than red.
am-qtls were distributed in both distal and pericentromeric regions of the chromosomes.
out of 50 am-qtls,  <dig> were identified in regions within 20 cm from the centromeres while  <dig> were positioned in the very distal telomeric chromosome regions.
thirty-two am-qtls were positioned within the cis of the hexaploid wheat meta-qtls or the kofa × svevo qtls, although in many cases the cis of hexaploid wheat meta-qtls were excessively wide  to support qtl coincidence.
the map location of the ppd- <dig> homeologs and 50 am-qtls  on the consensus map is reported on figure  <dig>  along with the projections of the ci of the meta-qtls and am-qtls found in hexaploid wheat  <cit>  and the qtls from the durum wheat ril population kofa × svevo  <cit> .
co-locations between am-qtls and hexaploid wheat meta-qtls with cis shorter than 20 cm or kf × sv qtls were observed for 16 am-qtls .
apart from ppd-a <dig> and ppd-b <dig>  homoelogous effects between a- and b-genome qtls could be hypothesized for qtl <dig> and qtl <dig> as shown by significant effects at both of the homeologous copies tagged by the ssr marker cfd <dig>  qtl <dig>  has been positioned very close  to the location of taft <dig> in chromosome 7a of hexaploid wheat reported by bonnin et al.
<cit> .
the homeolog of taft <dig> in the b-genome, mapped by yan et al.
<cit>  at 5 cm away from gwm <dig> in the distal portion of 7bs, was not identified with this survey, although in this region a major qtl for heading date was reported in the kofa × svevo mapping population .
discussion
integration of ssr and dart in a common framework
the consensus framework and the final interpolated map reported here integrates a large portion of the mapping efforts carried out in durum wheat.
our integrated data of  <dig> maps is based on a combination of segregation- and interpolation -based methods.
efficient projection-based integrations requires a pre-existing reference  framework map with a large number of high-quality markers and nearly complete genome coverage that serves as a backbone for marker projection from the component maps.
for durum wheat, this resource was not available.
the reference maps initially assembled with rflp and ssr markers  <cit>  were limited either in the number of progenies or markers used.
here, a core of six maps with adequate number of progenies, medium-to-high number of ssr and dart mapped loci, homogeneous genetic constitution  and complete genotype datasets available were identified as the best resource for assembling a robust framework.
all but one of these maps had parents derived from the cultivated durum wheat germplasm.
based on these commonalities, this segregation data-set was considered as the most suitable to produce a consensus framework based on actual genetic map distances calculated from a data-set of lines with relatively homogeneous constitutions that well represents the durum germplasm.
as compared to the projection-based method, building de novo consensus maps from a pooled set of segregation data was recently criticized  <cit> .
however, in our case it proved to be the best solution for obtaining a reference map with nearly complete genome coverage because none of the elite × elite durum wheat maps showed complete genome coverage, likely due to the scattered occurrence of identity by descent  in the genomes of parental genotypes.
the detection of shared long-range haplotypes in components of cultivated durum wheat germplasm was previously reported based on multi-allelic mapped ssr markers  <cit> .
on the other hand, the presence of locally strong differences in recombination rate among populations, which can affect the precision of marker ordering in de novo consensus maps from pooled segregation data, was monitored and was not considered as a main perturbing factor as could be the case when using populations derived from crosses between more distantly-related materials  <cit> .
the quality of the consensus framework map was checked based on the overall high two-point linkage lod values for common markers throughout all chromosomes.
interpolation was then effectively used to project all the markers that were uniquely mapped in each of the  <dig> maps available.
despite the integration of six core maps, gaps in the consensus framework map were observed for four regions on chromosomes 1a, 2a, 3a and 7a.
at least for chromosomes 1a and 2a, the presence of gaps of marker coverage was reported in the consensus map of marone et al.
<cit>  and was found to correspond to the centromeric deletion-bins of wheat.
the biological reasons at the basis of this molecular evidence deserves further work based on comparative genomics diversity studies among t. aestivum, t. durum, t. dicoccum and particularly the wild emmer t. dicoccoides.
this would allow one to test the hypothesis of occurrence of local severe speciation and domestication-related bottlenecks/selective sweeps  <cit> , or, alternatively, the presence of strong local differences in genomic constitution and/or alterations of the genetic to physical distance ratio among the triticum species .
the robustness of the marker order obtained in our final interpolated map is demonstrated by the overall high rank correlations  between the marker order of linkage groups from single component maps and the marker order of the consensus linkage groups.
correlation coefficients this high have rarely been observed in similar studies  <cit> .
comparison with the ta-ssr- <dig> map of somers et al.
<cit>  in hexaploid wheat revealed good but less conserved overall collinearity and low conservation of relative genetic distances.
this could in part be due to the different algorithms used to produce the consensus maps.
joinmap software calculates consensus map by a regression algorithm only, while carthagene allows one to work with the maximum likelihood even for integrated datasets, coupled with effective marker order refining procedures.
this could also account for the lower-than-expected performance of the durum consensus map reported here compared with that of marone et al.
<cit> , as well as more obvious differences such as the raw data quality assessment and mapping procedures.
application of the consensus map for linkage disequilibrium and germplasm diversity analysis
the final interpolated map was used to investigate at relatively high level of genetic resolution important genomics and breeding applications in t. durum such as:  describing the ld pattern and ld decay rate in elite germplasm,  exploring the pattern of genetic diversity among sub-populations of germplasm at the chromosome level, and  performing gwas.
to these ends, the durum wheat elite accession panel previously assembled for am studies was used as reference.
the pattern of ld present in the panel was re-estimated after maccaferri et al.
<cit> , where only low-density ssr markers were used.
the higher ssr and dart marker density in the present map provided a more detailed and accurate picture of ld decay in the crucial  <dig> - 5 cm interval.
in particular, ld in the elite mediterranean panel decays below the r <dig> reference threshold of  <dig>  within  <dig>  cm.
this r <dig> threshold is considered as a reference as regards to the power of gwas to detect association to qtls with medium to high effect  <cit> .
interestingly, the inferred average ld r <dig> value is  <dig>  at 0 cm inter-marker distance, i.e.
at the maximum resolution provided by the linkage studies, is far below the reference threshold of r2 =  <dig>  currently accepted as the r <dig> value to select representative snps for gwas  in those species where this resource is available.
these data indicate that actually the genetic resolution of am in this elite germplasm might be higher than expected based on previous assumptions and that, based on these results and on the length of the durum consensus map, exhaustive gwas in elite t. durum germplasm will require a marker density in the order of tens of thousands markers.
the reported results indicate that am had a mapping resolution of approximately  <dig> times higher in magnitude as compared to that obtained with conventional linkage mapping, even in the elite germplasm of an autogamous species such as durum wheat.
the ld decay pattern of this elite mediterranean germplasm panel compares favorably with that of populations with a more restricted genetic basis of elite durums from other areas.
somers et al.
<cit>  for a global panel with north american, european, cimmyt and argentinian germplasm reported similar genetic distances of 2-3 cm for the ld decay in such germplasm  <cit> .
as a comparison, ld decay to 50% in us elite hexaploid winter and spring wheat was observed at larger genetic intervals .
another interesting feature of the ld decay pattern observed along the chromosome is that, with only a few exceptions, the genetic resolution did not markedly decline in the peri-centromeric regions.
the interpolated map proved useful also for a first in-depth investigation of the distribution of the chromosome regions characterized by peaks of differentiation  among the durum sub-populations represented in the am panel.
evidence of differentiation was found for chromosome regions identified by three or more adjacent markers , and not only at the single-marker level.
the approach performed effectively, because high differentiation was detected near the major rhtb- <dig> and ppd-a <dig> loci, as expected.
in hexaploid wheat, this approach was used based on snps at medium mapping density  <cit> .
with the durum panel, the three patterns of genetic differentiation among sub-populations that were most frequently found along the chromosomes might correspond to regions harboring genes governing the morpho-physiological, adaptive and qualitative traits that were differentiated among sub-populations, as demonstrated for the ppd homeologs.
interestingly, a relatively high number of chromosome regions were found to differentiate the more recently developed cimmyt elite durum breeding lineages from the others , suggesting that the breeding innovation process of adding new valuable genetic diversity to the existing ones operated successfully.
application of the consensus interpolated map for mapping qtls controlling heading date
the evidence for an average ld decay in the cultivated durum wheat germplasm within less than 5 cm prompted us to assess the potential of gwas analysis for an important adaptive trait such as heading date and to use the consensus map as a framework for positioning am-qtls.
the mapping resolution of am-qtls reported here  appeared to be similar or higher to that observed for the same trait in the cultivated germplasm of hexaploid wheat  investigated by le gouis et al.
<cit> .
mapping resolution estimated at the whole-genome level using the average ld decay rate was confirmed by the association results obtained for the markers closely mapped to the major effector loci ppd-a <dig> and ppd-b <dig>  the marker density used in the present study  appeared adequate for medium-density genome-wide scans, as shown by the medium to high overall r <dig> values obtained by fitting the multiple-qtl model with all the highly significant qtl effects  <cit> .
the potential of gwas as an effective tool for qtl discovery, when coupled with sufficient marker density and reliable genetic map information, was evident from the high number of qtls  that were mapped consistently across environments.
heading date in the spring elite durum wheat germplasm was confirmed to be controlled by a few major loci  as well as by a wide range of small-effect qtls with r <dig> values below 5%, according to the ‘l-shaped’ distribution of qtl effects previously observed in most crop germplasm qtl analyses .
although the number of mapped markers used here for gwas  is among the highest reported for similar studies in wheat, it is also evident that reaching higher mapping precision and complete genome coverage  will require a marker density at least ten times higher, even in cultivated germplasm.
currently the marker technology in wheat is changing to single nucleotide polymorphisms , which hold great promise for high-throughput multiplex assays  <cit> .
until now, the ssr markers generally deployed in wheat genomics were mainly obtained from genomic libraries, and only a limited number of dart markers  have been sequenced in wheat .
therefore, comparative mapping across species with these two marker classes has limited resolution in wheat.
this notwithstanding, attempts to use new marker technologies such as snps have already been carried out  <cit> .
the use of transcript-derived snps will greatly facilitate the investigation of the putative gene content in the qtl-harboring regions, eventually leading to a more rapid identification of candidate genes at least for those cases where direct links between the putative gene function and the phenotype can be established.
as shown from the comparison between the cis of am-qtls and the projections of the cis from previous meta-qtl analysis carried out in hexaploid wheat, it was evident that the meta-qtl cis from bi-parental ril studies were substantially wider than those of the am-qtls, in the magnitude of  <dig>  to 30 cm  thus making it difficult to accurately infer qtl co-locations.
it is expected that in the near future the increasing number of qtl mapping results will allow for higher mapping resolution of meta-qtl analysis  <cit> .
additionally, the adoption of common high-density snp genotyping assays will also greatly facilitate the comparison of qtl regions across studies, germplasm and laboratories.
from the comparison between the mapping locations of am-qtls and the qtls for heading date found in the intra-specific kofa × svevo durum mapping population, it was also evident that the bi-parental population permitted mapping of several  qtls that were not identified in the am study.
this result underlines the concept that the compilation of the qtls present in the cultivated germplasm is far from being complete by relying on a single am study.
in particular, linkage analysis has the advantage over am of being more efficient in detecting alleles that are present in rare frequencies in the target germplasm, as could be the case for the qtls detected in the kofa × svevo durum mapping population, and alleles whose distribution correlates to the genetic population structure.
on the contrary, am studies carried out with the necessary marker density and population size show a favorable trade-off between the phenotyping cost and the output in terms of qtl identification.
CONCLUSIONS
overall, results from this study provide an exhaustive consensus framework map of ssr and dart markers for the durum wheat genome that was used to assess the genetic structure of cultivated durum wheat germplasm at the level of single chromosome regions and to assess the potential of gwas to dissect the genetic basis of heading date.
the reported results showed that the marker density provided by the consensus map was sufficient to identify chromosome regions harboring numerous small effect qtls for heading date, at a resolution level not possible with traditional bi-parental mapping studies.
more importantly, the results showed that there is scope for further refinement and expansion of these results as high-density and high-throughput genotyping snp platforms become available.
in view of this impending change in the commonly-applied genotyping technology, framework mapping data-sets that fit commonly accepted quality thresholds are valuable to provide a link between the qtl mapping results obtained in the last decade by means of ssr and dart technology and the up incoming snp-based technology.

 cultivated tetraploid wheat is genetically differentiated from hexaploid wheat by as little as ca.  years of evolution. both species derived from domesticated emmer through a rather long human-driven selection process, including distinct and sequential domestication bottlenecks and continuous gene flow from wild emmer schweinf). in the past two decades, molecular genetics and genomics of durum wheat, including breeding applications such as marker-assisted selection, have largely relied on the molecular tools specifically developed for hexaploid wheat. the restriction fragment length polymorphisms and the pcr-based molecular markers such as the simple sequence repeats, amplified fragment length polymorphisms, and sequence tagged sites developed for hexaploid wheat performed rather efficiently in tetraploid wheat based on the commonalities between the two shared a- and b-genomes. however, marker’s polymorphism information content had to be re-assessed directly in the durum wheat germplasm. in the 2000’s, intra- and inter-specific durum wheat and durum wheat × wild emmer genetic linkage maps were developed mainly using ssr loci as well as the microarray-based diversity array technology markers. integration of the ssr-based linkage map data into consensus maps was first pursued in hexaploid wheat by somers et al. and crossa et al., and then in durum wheat by trebbi et al., marone et al. and letta et al.. in durum wheat, the limited number of maps available to these studies has not yet allowed for full coverage of the genome, an important prerequisite for genome-wide association mapping, meta-analysis and positional cloning. the most recently published consensus map specific to tetraploid wheat is composed of loci arranged in linkage groups, a number that exceeds the nuclear chromosomes of this species. the hexaploid wheat ssr-based consensus map by somers et al. has been widely used as a reference for wheat genomics studies for more than a decade. in hexaploid wheat, several mapping studies were published using ssr and dart technologies, revealing major genes and qtls for grain yield, yield components, adaptive traits, response to abiotic and biotic stresses and quality. collectively, these studies laid the foundation for mas applications in wheat. within this dynamic scenario, the availability of a high-quality consensus map more exhaustively covering the entire genome is a valuable asset for genetic studies and breeding applications. furthermore, powerful association mapping and meta-qtl analysis require reference genetic maps of a quality standard higher than that commonly adopted for coarse mapping in bi-parental populations. am and meta-qtl analysis are being increasingly adopted in wheat genomics, including durum wheat. the development of integrated maps were approached based on: ‘consensus’ mapping, where de novo maps are produced by merging all the single segregation data-sets available to develop a novel unified map, ‘interpolation’ mapping, where integrated maps are built by regressing the single component map marker positions on an initial reference map that provides the framework for sequential interpolation. the latter method is computation-and-time efficient but relies on the availability of an accurate reference with strong prerequisites such as comprehensive genome coverage and proven representativeness. consensus mapping has the potential to overcome the major limitations typical of mapping information based on single maps, such as local aberrations in crossover rates and presence of chromosome regions with locally low marker density/lack of polymorphism due to the occurrence of identity by descent. moreover, consensus mapping provides more accurate mapping information thanks to the higher number of progenies considered. several software packages were developed for consensus mapping, from the early ones that pool single component segregation data and calculate consensus maps based on the assumption of homogeneity of marker order and recombination rate across populations, such as joinmap and carthagene, to others that implement graph-theoretic models with marker removal in case of conflicting orders or attempt to define the optimal consensus order of shared markers by a synchronous optimization of the local orders in single component maps. in this study, segregation data from six core mapping populations of durum wheat were analysed based on a common procedure with stringent quality criteria. following identification and removal from the global computation of chromosome regions showing local deviations from the homogeneity assumptions, mainly identified in single component maps only, the segregation data from markers shared among populations were pooled in carthagene to obtain a consensus framework map that proved to be highly robust compared to the single component maps. the value of this consensus map, enriched in density by the interpolation of the unique markers, was assessed through the identification of signatures of genetic differentiations among sub-populations of the durum wheat germplasm and the identification of qtls controlling heading date in the mediterranean cultivation areas at the genome-wide scale.  linkage maps from the individual populations the genotypic data of mapping populations of tetraploid wheat, either recombinant inbred lines or double haploids, were made available by collaborating institutions or were downloaded from the graingenes database. the genotypic data were used to re-construct the maps of the original populations following a common mapping procedure. the reconstructed maps are thereafter reported as component maps. details of the parental accessions, cumulative genetic distances and marker composition for each of the component maps are reported in table  table component maps used for consensus mapping and map integration: markers and map features 2 mapping populations used for consensus framework mapping mapping population used for marker interpolation only mapping population used for marker interpolation only, no segregation data available for each map, the cross, population type, number of mapped markers listed by marker type, number of linkage groups, total map length and average inter-marker distance are reported. a core-set of six ril-based component maps was selected to obtain a robust framework map subsequently used for interpolation of unique markers. all but one of these six ril populations were obtained from intraspecific t. durum crosses, with parental lines chosen among diverse groups of the elite durum germplasm. one of the six populations included in the core set was obtained from the cross of langdon × t. dicoccoides, the wild progenitor of t. durum. in total, the core set of ril populations included lines. the single maps were constituted by to linkage groups, with total length ranging from to  cm, with an average of  cm, and inter-marker distance varying from to cm, with an average of  cm/marker. eight additional populations were used for marker interpolation. four of the populations included in this second set were dhs obtained from agriculture and agrifood canada, university of saskatchewan and usda. three additional populations were recombinant inbred and one was a population of f2: progenies. for six out of these eight populations the original segregation data were available and thus the linkage maps were reconstructed according to the common procedure used for the common maps. the two pdw233 × bhalegaon and latino × primadur maps, for which the original segregation data were not available, were inspected for their homogeneity in marker distribution and inter-marker distances as compared to the component maps before to integrate their map information data into the consensus map. the marker density of all of these eight maps was inferior to that reached in the six core set ril populations, while retaining a good level of genome coverage. consensus map features the genotypes from the core set of six ril populations were used to build a reliable consensus framework map based on common markers only, including and anchor ssr and dart markers, respectively, anchor snp/stss and one morphological locus. these markers were grouped into linkage groups. representative estimates of recombination rate were obtained across mapping populations, yielding a framework map of common markers with total length of  cm, with an average inter-marker distance of  cm per common marker. the consensus framework map was thus only % longer than the longest among the six component maps, with the number of independent linkage groups decreased from to table consensus framework and interpolated map marker summary number of mapped loci included in the consensus framework map and in the final interpolated map, number of linkage groups, total map length and average inter-marker distance for both maps. the six core ril maps and the consensus framework map are reported in additional file 1: figure s and additional file 2: table s with anchor markers reported in red font. in the computation of the consensus map, portions of linkage groups from single maps were not included in the merged data-set due to either excessive heterogeneity of recombination rate or low density of anchor markers. frequency of common framework markers and map length of each of the framework linkage groups are reported in table  the framework linkage groups covered most of the durum wheat chromosomes. two separate linkage groups were obtained for chromosomes 1a, 2a and 3a. a relatively low number of anchor markers was observed for chromosomes 1a, 4b and 5a while up to common markers were mapped on chromosome 7b, followed by common markers on chromosome 6b. the inter-marker distance between common markers ranged from  cm/marker for linkage group 3a and  cm/marker for 5b. the two-point mapping lod score of framework markers averaged across all chromosomes and ranged from for 1a to for 4a.table consensus framework and interpolated map features summarized by linkage group number of mapped loci included in the consensus framework and in the final interpolated map, detailed by linkage group. the subsequent interpolation of the unique loci allowed us to map loci in total, for a total map length of  cm. this final consensus interpolated map was % longer than the longest component maps mr × cl. the category and number of markers mapped in the interpolated map are summarized in table  and detailed in table  depending on the chromosome/linkage group, the interpolated map showed average inter-marker distances ranging from less than 1 cm/marker, e.g. -  cm/marker for linkage groups 1b, 2a 3a 3b, 4a, 4b, 6a, 6b and 7b, to -  cm/marker for linkage groups 1a 5a, 5b. the number of markers mapped to the a genome was considerably less than those mapped to the b genome while the cumulative genetic distances of the linkage groups of the two genomes were balanced. the degree of monotony of consensus marker order as compared to the original component maps was checked by projection plots reported in additional file 3: figure s few inconsistencies were observed for closely linked markers mapped on genetic intervals of less than 2 cm. for most of the detected order conflicts, the original data of the component populations were re-inspected and, in most cases, it was found that the consensus marker order showed an overall lod score and probability close to the one present in the single discordant maps; therefore, the consensus marker order was retained. pair-wise spearman rank correlations rho of marker order between the consensus and the single component maps were generally very high across chromosomes. out of pair-wise comparisons, showed ρ values higher than, with comprised between and when considering the regression r values, which highlight not only departure from colinearity but also local divergence in recombination frequency, out of pair-wise comparisons showed values ≥ , were comprised between and and were < . overall the r values were thus slightly lower as compared to rank correlation values. local deviations from colinearity were observed only for a few chromosomes and populations as follows: in chromosomes 1a, 2a, 3a and 4a. the projection plots clearly showed that marker density of the single durum wheat maps differed markedly along the linkage groups and the interpolated map effectively integrated the marker information from the component maps with improved marker density and genome coverage along the consensus chromosomes, with only a slight increase in linkage group total length. the single component maps showed a high frequency of locally low marker density or even no marker coverage at all, particularly those derived from the elite × elite t. durum crosses. these regions were irregularly scattered across maps on most of the chromosomes. examples can be observed in the projection plots of chromosomes 1b, 2b, 3b, 5b, 6a, 7a and 7b. the linkage map obtained from t. durum langdon × t. dicoccoides g18- was much less affected by uneven marker density distribution as compared to the intra-specific t. durum maps. in some cases, chromosome regions showing low marker density were observed consistently across the majority of the component maps and were thus considered as a constitutive feature. examples were the centromeric portion of chromosome 1a, the proximal region of 2a, and the distal regions of 3a and 7a. as a result, these four chromosome regions also showed a lower-than-average marker density in the consensus map. the durum interpolated map was compared with the reference ssr consensus map of hexaploid wheat. the comparison was based on the ssr markers shared between the two maps, which varied from to depending on the linkage group. spearman rank correlations rho values were lower than those observed within the intra-specific maps of durum wheat; the average value was, ranging from - to. coefficient of determination r values averaged and ranged from less than up to -. as compared to the ta-ssr- map, the durum-specific map herein reported provided genome coverage of 100% for the majority of the chromosomes, with the exception of chromosomes 1b and 5b were genome coverage of the durum consensus was and % less than ta-ssr- due to low coverage of common markers on the distal ends of short arms. in chromosome 3a and 6b the durum consensus extended the genome coverage in the distal chromosome regions as compared to the ta-ssr- table comparison between the durum consensus interpolated map and the hexaploid consensus maps ta-ssr-2004 chr. 3b consensus map ta-ssr- reported in somers et al.;. chr. 3b consensus map reported in paux et al. 2008;. noticeable differences in local recombination rate were observed between the hexaploid and the durum maps. for instance, the strong decline in marker density found in the durum peri-centromeric regions of chromosomes 1a and 2a was not observed in the corresponding hexaploid regions. as for chromosome 1a, the high recombination rate observed in durum wheat between the peri-centromeric regions of the two distal linkage groups was not observed in ta-ssr- where the map distance between gwm and cfa was only  cm and the marker density in the local centromeric region was not affected. similarly, in chromosome 3a, the low-marker density, highly recombinogenic region detected between anchor markers gwm and gwm spanned only  cm in the hexaploid wheat consensus map. the updated consensus map for chromosome 3b published by paux et al. and derived from the analysis of mapping populations was also considered. sixty-six markers were common to both the hexaploid and tetraploid 3b maps. the correlation coefficient between our map and the paux et al. map was high. the durum interpolated map was then compared with the most recent tetraploid consensus map obtained with different software. in this case, while the number of mapped markers was only slightly lower than in our case, the results were different in terms of number of lg obtained, and total map length. overall conservation of colinearity of the two durum consensus maps and ta-ssr- was better for our map than for the marone et al. map. ld decay rate and molecular diversity in elite durum wheat germplasm a panel of elite durum accessions representative of the major gene pool cultivated in the mediterranean region for which ld and population structure were previously investigated based on low-density genotyping with ssr markers was re-investigated in depth based on the profiles of markers included in the consensus map. of these markers, showed minor allele frequency equal or higher than and were thus considered informative for ld and am analysis. this set of markers, including ssr/stss and dart, generated pairwise combinations of intra-chromosomal loci for which ld significance and r2/d’ estimates were calculated. ld decay was investigated through fitted regression and box plot distribution,, with a focus on the short inter-marker distances. non-linear modeling of ld decay reported in figure  showed an overall r fit value of 42%, an α value of and an effective population size of. based on the fitted model, at 0 cm genetic distance the expected r value was equal to while the r half-value decline was reached at  cm. the upper 95th percentile of the r2value distribution for unlinked marker pairs, widely considered as a threshold useful to separate the true linkage ld from the background ld due to population structure, was equal to. this trend was confirmed by inspecting the ld statistics for discrete marker pairwise classes of incremental map distances. the class of completely linked markers showed mean r2 = , median ld r2 = , inter-quartile range from to and d’ = . the mean and median ld r decreased by half in the -1 cm inter-marker distance class and more than half in the 1-5 cm class, respectively; the median ld r values dropped below in the 5-10 cm class. the ld estimates calculated for independent markers showed mean r2 =  and d’ = .figure intra-chromosomal linkage disequilibrium decay plot as a function of genetic distance. ld decay assessed in a durum wheat panel of elite accessions adapted to the mediterranean environments. ld estimates are reported as squared correlations of allele frequencies. inter-marker genetic distances are from the durum wheat consensus map. non-linear modeling of ld was performed using the sved equation. boxplot charts of linkage disequilibrium estimates for categorized inter-marker genetic map distances. pairwise ld estimates are reported as squared correlations of allele frequencies. inter-marker genetic distances are from the durum wheat consensus map. linkage disequilibrium estimates for the elite durum wheat panel based on mapped ssr and dart markers r 2 d ld decay in a collection of elite durum wheat accessions from the mediterranean, cimmyt and icarda germplasm included in the association mapping durum panel. detailed pair-wise ld r values for all the consensus linkage groups are projected as heat-plot triangular matrices in additional file 6: figure s together with the polymorphism index content plots along the chromosomes and the distributions of markers with highly significant genetic differentiation among the main sub-populations represented in the panel. when detectable, ld blocks with sizeable r values were in most cases observed within a 5 cm window size; relatively small ld blocks were detectable across the full length of durum wheat chromosomes, from distal to proximal regions. however, a large number of closely linked adjacent markers showed ld r values in the range of or less. a few long-range ld blocks extending more than 10 cm were also observed, particularly in the proximal regions of chromosomes 1b, 6a and 7b. the polymorphism information content plots showed a trend for higher values in the distal regions of the chromosomes and lower values in the peri-centromeric regions. chromosome 1a exhibited the most extended peri-centromeric region with both low marker density and diversity in the elite germplasm, causing a gap in the continuity of the chr. 1a consensus map in this region. a similar phenomenon was observed for peri-centromeric regions of chromosomes 2a, 2b and in 3as. none of the six core ril maps showed a marker density sufficiently high to guarantee the continuity of the consensus linkage groups in these four chromosomes. additionally, numerous locally defined sharp decreases of pic values extending over stretches of to adjacent markers were commonly observed in both centromeric and distal regions of several chromosomes, even in chromosome regions where the marker density was not locally affected. the population structure of the elite panel of accessions was previously investigated based on a non-redundant set of highly informative ssr markers. hierarchical and non-hierarchical model-based cluster analyses showed that the population structure could be described based on five main sub-populations corresponding to landraces- and breeding-derived germplasm founders that originated from the italian, cimmyt and icarda breeding programs distinct by time period or target environment. the founders were widely used in the national breeding programs of mediterranean countries and a high degree of admixture was detected among sub-populations. the increased density of genetically mapped markers based on the consensus map allowed for a more in-depth investigation of the patterns of genetic differentiation present within and among the five main sub-populations. amova showed that the genetic variation within was higher than the variation among sub-groups, with the latter reflecting known temporal, geographic and pedigree differences. a medium level of genetic differentiation was observed between the two icarda sub-populations for dryland and temperate areas. more differentiation was found between the icarda sub-population for dryland areas and the italian and early-period cimmyt germplasm. lower-than-average differentiation was observed between the icarda-temperate and the italian-early cimmyt as well as the mid-cimmyt. the late-cimmyt germplasm was the most differentiated from the icarda-dryland and italian-early cimmyt sub-populations.table analysis of molecular variance for the elite durum wheat panel based on mapped ssr and dart markers sub-population pairwise f st sub-population founder pairwise differences analysis of molecular variance for the elite durum wheat panel of accessions adapted to mediterranean areas based on the sub-population subdivision as from a previous population genetic structure analysis. overall fst index among sub-populations and specific sub-population pairwise fst indexes are reported. average population pairwise differences are reported as follows: above diagonal: average number of pairwise differences between populations, diagonal elements: average number of pairwise differences within population, below diagonal: corrected average pairwise difference /2). the improved marker density of the consensus map allowed us to search genome-wide for chromosome regions showing evidence of high genetic differentiation among sub-populations. single markers or chromosome regions with sub-population pair-wises fst values greater than the fst thresholds set at p were observed in most of the chromosome arms and projected on the consensus map. three main genetic differentiation patterns were observed as follows: fst differentiation “pattern 1”: significant differentiation across the majority of sub-populations indicating differentiation by time and by target environments fst differentiation “pattern 2”: significant differentiation between icarda-dryland vs. all the other subpopulations, fst differentiation “pattern 3”: significant differentiation of either or both icarda-temperate and italian, early-cimmyt subpopulations vs. the mid- and late-cimmyt subpopulations. there were and single markers/chromosome regions in the durum wheat genome that showed genetic differentiation pattern and respectively. fst differentiation pattern was mainly found on chromosomes 1b, 2a, 2b, 4b, 5a, 5b and 6b. high frequency of both pattern and were observed in chromosomes 3a and 7b. pattern was also frequently found in chromosomes 1b, 3b and 7a. in chromosome 2a, ppd-a and four closely associated flanking markers showed highly significant fst differences for all sub-population pair-wises. in chromosome 2b, coincident with ppd-b a strong differentiation was observed between the italian and icarda populations vs. the cimmyt sub-populations bred at sub-tropical latitudes. as expected, rht-b on chromosome 4b showed a type fst differentiation pattern with peaks of fst values for the pair-wise comparisons including the icarda dryland population vs. all the other populations. gwas for heading date the consensus map was used for a genome-wide association scan to detect association of the mapped ssr and dart markers with maf >  with time to heading in the durum wheat association panel. time to heading data were available for field trials carried out in the mediterranean region and in mexico. the ammi biplot analysis showed that the heading date phenotypes from the environments could be grouped according to five macro-environments: southern europe, north africa-tunisia, north africa-morocco, west-asia and mexico. the association scan was performed for each environment as well as for the adjusted means of each of the five macro-environments. broad-sense heritability values of heading date calculated across environments were high for southern european, asian and mexican macro-areas, including and environments, respectively, but lower for the north african moroccan and tunisian macro-environments, each with two environments. the phenotypic data of six genotypes known to carry the vernalization-sensitive vrn- allele at vrn-a were excluded from the analysis. the initial gwas analysis showed strong experiment-wise significant associations at the two chromosome regions corresponding to the location of ppd-a and ppd-b loci and numerous chromosome regions with highly significant marker-wise associations across environments. detailed results are reported in table  table association results for heading date in the elite durum panel at the two major photoperiod-response homeologous ppd-1 loci ppd-a1 ppd-b1 macro-environmental area r 2 r 2 southern europe north africa – tunisia west asia north africa – morocco mexico association analysis based on accessions from the durum panel, evaluated for heading date across environments grouped in five macro-environmental areas in the mediterranean basin and mexico. the ppd-a specific assay and wpt- dart marker tightly associated to ppd-b have been used. significance of p ≤ e- refers to the experiment-wise significance threshold of p ≤ . results are reported for single environments and for the adjusted means across macro-environmental areas. at ppd-a association peaks were detected in coincidence of the diagnostic marker developed from the causal locus. considering the adjusted means of macro-environmental areas, p-values of association ranged from a minimum of p =  e- for the southern european area, to a maximum significance of p =  e- in mexico. among the four markers wmc cfa2201-2a, gwm1198-2a and wpt- located within  cm from the ppd-a locus and with ld r values between and, significant associations with heading date were observed for cfa2201-2a only. for the region harboring ppd-b highly significant marker- and experiment-wise associations with heading date were detected for dart and one ssr markers mapped within an interval of  cm. the majority of these markers formed a unique linkage block with strong inter-marker ld r values. peaks of association to heading date across environments were observed for wpt- the qtl-representative marker, at position  cm. this marker showed a range of p-values from a minimum of p =  in mexico to a maximum association of p =  e- in southern europe. according to hanocq et al. and bennett et al., the small linkage block includes markers associated with the predicted position of ppd-b as expected, the level of significance and magnitude of effects associated with the ppd loci were strongly influenced by latitude. the genotypic to phenotypic proportion of variance of ppd-qtls, as estimated by r values on a single-environment basis, was significantly correlated with latitude as presented in figure  ppd-a showed a strong trend towards increased r values at latitudes lower than 40° while the markers tagging ppd-b showed an opposite trend.figure scatterplot of the relationship between latitude and genotypic to phenotypic variance coefficient of determination values for ppd-a1 and ppd-b1 in mediterranean and mexican environments. the gwas was repeated after including ppd-a and ppd-b representative markers as covariates in the mlm association model. based on this analysis, unique chromosome regions showed highly significant association to the heading date adjusted means of at least one or more of the five macro-environmental areas. marker-features of these regions are summarized in additional file 7: table s and figure  none of these qtl-harboring regions reached the experiment-wise adjusted bonferroni significance threshold based on the number of independent ld blocks. however, the reported associations were all supported by marker-wise significances over multiple environments, as detailed in additional file 7: table s out of the 50 am-qtls, consisted of single-marker associations while consisted of small blocks of multiple adjacent markers all associated to the phenotype as well as to each other with ld r values ≥ . from the consensus map, these qtls included markers that were either coincident or closely linked within a 3-4 cm interval. there were only three qtls with a significance interval of 5 cm or more on chromosomes 2b and 3b. based on the predicted ld decay in the collection, confidence interval boundaries of  cm, corresponding to the genetic distance over which the ld decays to r2 = , were attributed to both sides of the marker’s blocks significantly associated with the phenotype. thus, a confidence interval of  cm was attributed to the single markers associated with the phenotype. the r values of the associations on a macro-environmental basis were mostly between and %. the proportion of phenotypic variance explained by simultaneously considering all the reported qtl-representative markers ranged from a minimum of % for the tunisian macro-area to a maximum of % for mexico, with r values of, and % for the southern-european, asian and moroccan macro-areas, respectively.figure association mapping qtls for time to heading in the mediterranean regions reported on the tetraploid ssr and dart ® marker consensus map. am-qtls are reported as red bars on the left side of the chromosomes. red thin wiskers extending the red bars corresponds to the confidence intervals of am-qtls. projected qtl confidence intervals from previous studies are reported as vertical bars of various colors other than red. am-qtls were distributed in both distal and pericentromeric regions of the chromosomes. out of 50 am-qtls, were identified in regions within 20 cm from the centromeres while were positioned in the very distal telomeric chromosome regions. thirty-two am-qtls were positioned within the cis of the hexaploid wheat meta-qtls or the kofa × svevo qtls, although in many cases the cis of hexaploid wheat meta-qtls were excessively wide to support qtl coincidence. the map location of the ppd- homeologs and 50 am-qtls on the consensus map is reported on figure  along with the projections of the ci of the meta-qtls and am-qtls found in hexaploid wheat and the qtls from the durum wheat ril population kofa × svevo. co-locations between am-qtls and hexaploid wheat meta-qtls with cis shorter than 20 cm or kf × sv qtls were observed for 16 am-qtls. apart from ppd-a and ppd-b homoelogous effects between a- and b-genome qtls could be hypothesized for qtl and qtl as shown by significant effects at both of the homeologous copies tagged by the ssr marker cfd qtl has been positioned very close to the location of taft in chromosome 7a of hexaploid wheat reported by bonnin et al.. the homeolog of taft in the b-genome, mapped by yan et al. at 5 cm away from gwm in the distal portion of 7bs, was not identified with this survey, although in this region a major qtl for heading date was reported in the kofa × svevo mapping population. discussion integration of ssr and dart in a common framework the consensus framework and the final interpolated map reported here integrates a large portion of the mapping efforts carried out in durum wheat. our integrated data of maps is based on a combination of segregation- and interpolation -based methods. efficient projection-based integrations requires a pre-existing reference framework map with a large number of high-quality markers and nearly complete genome coverage that serves as a backbone for marker projection from the component maps. for durum wheat, this resource was not available. the reference maps initially assembled with rflp and ssr markers were limited either in the number of progenies or markers used. here, a core of six maps with adequate number of progenies, medium-to-high number of ssr and dart mapped loci, homogeneous genetic constitution and complete genotype datasets available were identified as the best resource for assembling a robust framework. all but one of these maps had parents derived from the cultivated durum wheat germplasm. based on these commonalities, this segregation data-set was considered as the most suitable to produce a consensus framework based on actual genetic map distances calculated from a data-set of lines with relatively homogeneous constitutions that well represents the durum germplasm. as compared to the projection-based method, building de novo consensus maps from a pooled set of segregation data was recently criticized. however, in our case it proved to be the best solution for obtaining a reference map with nearly complete genome coverage because none of the elite × elite durum wheat maps showed complete genome coverage, likely due to the scattered occurrence of identity by descent in the genomes of parental genotypes. the detection of shared long-range haplotypes in components of cultivated durum wheat germplasm was previously reported based on multi-allelic mapped ssr markers. on the other hand, the presence of locally strong differences in recombination rate among populations, which can affect the precision of marker ordering in de novo consensus maps from pooled segregation data, was monitored and was not considered as a main perturbing factor as could be the case when using populations derived from crosses between more distantly-related materials. the quality of the consensus framework map was checked based on the overall high two-point linkage lod values for common markers throughout all chromosomes. interpolation was then effectively used to project all the markers that were uniquely mapped in each of the maps available. despite the integration of six core maps, gaps in the consensus framework map were observed for four regions on chromosomes 1a, 2a, 3a and 7a. at least for chromosomes 1a and 2a, the presence of gaps of marker coverage was reported in the consensus map of marone et al. and was found to correspond to the centromeric deletion-bins of wheat. the biological reasons at the basis of this molecular evidence deserves further work based on comparative genomics diversity studies among t. aestivum, t. durum, t. dicoccum and particularly the wild emmer t. dicoccoides. this would allow one to test the hypothesis of occurrence of local severe speciation and domestication-related bottlenecks/selective sweeps, or, alternatively, the presence of strong local differences in genomic constitution and/or alterations of the genetic to physical distance ratio among the triticum species. the robustness of the marker order obtained in our final interpolated map is demonstrated by the overall high rank correlations between the marker order of linkage groups from single component maps and the marker order of the consensus linkage groups. correlation coefficients this high have rarely been observed in similar studies. comparison with the ta-ssr- map of somers et al. in hexaploid wheat revealed good but less conserved overall collinearity and low conservation of relative genetic distances. this could in part be due to the different algorithms used to produce the consensus maps. joinmap software calculates consensus map by a regression algorithm only, while carthagene allows one to work with the maximum likelihood even for integrated datasets, coupled with effective marker order refining procedures. this could also account for the lower-than-expected performance of the durum consensus map reported here compared with that of marone et al., as well as more obvious differences such as the raw data quality assessment and mapping procedures. application of the consensus map for linkage disequilibrium and germplasm diversity analysis the final interpolated map was used to investigate at relatively high level of genetic resolution important genomics and breeding applications in t. durum such as: describing the ld pattern and ld decay rate in elite germplasm, exploring the pattern of genetic diversity among sub-populations of germplasm at the chromosome level, and performing gwas. to these ends, the durum wheat elite accession panel previously assembled for am studies was used as reference. the pattern of ld present in the panel was re-estimated after maccaferri et al., where only low-density ssr markers were used. the higher ssr and dart marker density in the present map provided a more detailed and accurate picture of ld decay in the crucial - 5 cm interval. in particular, ld in the elite mediterranean panel decays below the r reference threshold of within  cm. this r threshold is considered as a reference as regards to the power of gwas to detect association to qtls with medium to high effect. interestingly, the inferred average ld r value is at 0 cm inter-marker distance, i.e. at the maximum resolution provided by the linkage studies, is far below the reference threshold of r2 =  currently accepted as the r value to select representative snps for gwas in those species where this resource is available. these data indicate that actually the genetic resolution of am in this elite germplasm might be higher than expected based on previous assumptions and that, based on these results and on the length of the durum consensus map, exhaustive gwas in elite t. durum germplasm will require a marker density in the order of tens of thousands markers. the reported results indicate that am had a mapping resolution of approximately times higher in magnitude as compared to that obtained with conventional linkage mapping, even in the elite germplasm of an autogamous species such as durum wheat. the ld decay pattern of this elite mediterranean germplasm panel compares favorably with that of populations with a more restricted genetic basis of elite durums from other areas. somers et al. for a global panel with north american, european, cimmyt and argentinian germplasm reported similar genetic distances of 2-3 cm for the ld decay in such germplasm. as a comparison, ld decay to 50% in us elite hexaploid winter and spring wheat was observed at larger genetic intervals. another interesting feature of the ld decay pattern observed along the chromosome is that, with only a few exceptions, the genetic resolution did not markedly decline in the peri-centromeric regions. the interpolated map proved useful also for a first in-depth investigation of the distribution of the chromosome regions characterized by peaks of differentiation among the durum sub-populations represented in the am panel. evidence of differentiation was found for chromosome regions identified by three or more adjacent markers, and not only at the single-marker level. the approach performed effectively, because high differentiation was detected near the major rhtb- and ppd-a loci, as expected. in hexaploid wheat, this approach was used based on snps at medium mapping density. with the durum panel, the three patterns of genetic differentiation among sub-populations that were most frequently found along the chromosomes might correspond to regions harboring genes governing the morpho-physiological, adaptive and qualitative traits that were differentiated among sub-populations, as demonstrated for the ppd homeologs. interestingly, a relatively high number of chromosome regions were found to differentiate the more recently developed cimmyt elite durum breeding lineages from the others, suggesting that the breeding innovation process of adding new valuable genetic diversity to the existing ones operated successfully. application of the consensus interpolated map for mapping qtls controlling heading date the evidence for an average ld decay in the cultivated durum wheat germplasm within less than 5 cm prompted us to assess the potential of gwas analysis for an important adaptive trait such as heading date and to use the consensus map as a framework for positioning am-qtls. the mapping resolution of am-qtls reported here appeared to be similar or higher to that observed for the same trait in the cultivated germplasm of hexaploid wheat investigated by le gouis et al.. mapping resolution estimated at the whole-genome level using the average ld decay rate was confirmed by the association results obtained for the markers closely mapped to the major effector loci ppd-a and ppd-b the marker density used in the present study appeared adequate for medium-density genome-wide scans, as shown by the medium to high overall r values obtained by fitting the multiple-qtl model with all the highly significant qtl effects. the potential of gwas as an effective tool for qtl discovery, when coupled with sufficient marker density and reliable genetic map information, was evident from the high number of qtls that were mapped consistently across environments. heading date in the spring elite durum wheat germplasm was confirmed to be controlled by a few major loci as well as by a wide range of small-effect qtls with r values below 5%, according to the ‘l-shaped’ distribution of qtl effects previously observed in most crop germplasm qtl analyses. although the number of mapped markers used here for gwas is among the highest reported for similar studies in wheat, it is also evident that reaching higher mapping precision and complete genome coverage will require a marker density at least ten times higher, even in cultivated germplasm. currently the marker technology in wheat is changing to single nucleotide polymorphisms, which hold great promise for high-throughput multiplex assays. until now, the ssr markers generally deployed in wheat genomics were mainly obtained from genomic libraries, and only a limited number of dart markers have been sequenced in wheat. therefore, comparative mapping across species with these two marker classes has limited resolution in wheat. this notwithstanding, attempts to use new marker technologies such as snps have already been carried out. the use of transcript-derived snps will greatly facilitate the investigation of the putative gene content in the qtl-harboring regions, eventually leading to a more rapid identification of candidate genes at least for those cases where direct links between the putative gene function and the phenotype can be established. as shown from the comparison between the cis of am-qtls and the projections of the cis from previous meta-qtl analysis carried out in hexaploid wheat, it was evident that the meta-qtl cis from bi-parental ril studies were substantially wider than those of the am-qtls, in the magnitude of to 30 cm thus making it difficult to accurately infer qtl co-locations. it is expected that in the near future the increasing number of qtl mapping results will allow for higher mapping resolution of meta-qtl analysis. additionally, the adoption of common high-density snp genotyping assays will also greatly facilitate the comparison of qtl regions across studies, germplasm and laboratories. from the comparison between the mapping locations of am-qtls and the qtls for heading date found in the intra-specific kofa × svevo durum mapping population, it was also evident that the bi-parental population permitted mapping of several qtls that were not identified in the am study. this result underlines the concept that the compilation of the qtls present in the cultivated germplasm is far from being complete by relying on a single am study. in particular, linkage analysis has the advantage over am of being more efficient in detecting alleles that are present in rare frequencies in the target germplasm, as could be the case for the qtls detected in the kofa × svevo durum mapping population, and alleles whose distribution correlates to the genetic population structure. on the contrary, am studies carried out with the necessary marker density and population size show a favorable trade-off between the phenotyping cost and the output in terms of qtl identification.  overall, results from this study provide an exhaustive consensus framework map of ssr and dart markers for the durum wheat genome that was used to assess the genetic structure of cultivated durum wheat germplasm at the level of single chromosome regions and to assess the potential of gwas to dissect the genetic basis of heading date. the reported results showed that the marker density provided by the consensus map was sufficient to identify chromosome regions harboring numerous small effect qtls for heading date, at a resolution level not possible with traditional bi-parental mapping studies. more importantly, the results showed that there is scope for further refinement and expansion of these results as high-density and high-throughput genotyping snp platforms become available. in view of this impending change in the commonly-applied genotyping technology, framework mapping data-sets that fit commonly accepted quality thresholds are valuable to provide a link between the qtl mapping results obtained in the last decade by means of ssr and dart technology and the up incoming snp-based technology. 
a dense and accurate consensus map specific for t. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement. the t. durum a and b genomes were covered in their near totality based on the reference ssr hexaploid wheat map. the consensus map presented here was used as a reference for genetic diversity and mapping analyses in t. durum, providing nearly complete genome coverage and even marker density. a genome-wide association scan for heading date from field trials in the mediterranean basin and in mexico yielded chromosome regions with evidences of association in multiple environments. the consensus locus order compared to those of the single component maps showed good correspondence,. high quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of simple sequence repeats and diversity array technology® anchor markers. durum wheat is a tetraploid cereal grown in the medium to low-precipitation areas of the mediterranean basin, north america and south-west asia. interpolation of unique markers from maps allowed us to position a total of markers in a consensus map of  cm. genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits. the consensus map provides the basis for high-density single nucleotide polymorphic marker implementation in durum wheat. linkage disequilibrium was found to decay below the r threshold =  within  cm, on average. triticum durum desfconsensus maplinkage disequilibriumgenome-wide association mappingheading dateqtlissue-copyright-statement© the author 2014 the consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of accessions adapted to the mediterranean areas. differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps.
 durum wheat is a tetraploid cereal grown in the medium to low-precipitation areas of the mediterranean basin, north america and south-west asia. genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits. a dense and accurate consensus map specific for t. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.  high quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of simple sequence repeats and diversity array technology® anchor markers. interpolation of unique markers from maps allowed us to position a total of markers in a consensus map of  cm. the t. durum a and b genomes were covered in their near totality based on the reference ssr hexaploid wheat map. the consensus locus order compared to those of the single component maps showed good correspondence,. differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. the consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of accessions adapted to the mediterranean areas. linkage disequilibrium was found to decay below the r threshold =  within  cm, on average. strong molecular differentiations among sub-populations were mapped to chromosome regions. a genome-wide association scan for heading date from field trials in the mediterranean basin and in mexico yielded chromosome regions with evidences of association in multiple environments.  the consensus map presented here was used as a reference for genetic diversity and mapping analyses in t. durum, providing nearly complete genome coverage and even marker density. markers previously mapped in hexaploid wheat constitute a strong link between the two species. the consensus map provides the basis for high-density single nucleotide polymorphic marker implementation in durum wheat. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords triticum durum desfconsensus maplinkage disequilibriumgenome-wide association mappingheading dateqtlissue-copyright-statement© the author 2014 