BACKGROUND
winter rye  is an important cereal crop in central, eastern and northern europe, mainly due to its exceptional ability to thrive and to produce high yields in adverse environmental conditions.
nutrient efficiency and tolerance of diseases exhibited by rye, allowing for a reduced usage of pesticides and fertilizers during production, increase its attractiveness for farmers and consumers.
the recently better recognized dietary value of rye contributed to the noticeable growth of consumers' interest in rye products.
breeding progress in rye, however, is rather slow, as the traditional breeding is hampered by the outcrossing nature of this crop, self-incompatibility and occurrence of inbreeding depression.
implementation of molecular breeding in rye improvement programs depends on the availability of high-density molecular linkage maps.
several genetic maps of rye have been published so far  <cit> , but the possibilities of their practical application are rather limited, mainly due to an insufficient saturation.
the average density of the most saturated rye linkage map published to date is  <dig>  cm.
however, there are seven gaps greater than  <dig> cm on the map  <cit> .
the average map interval length on remaining rye maps exceeds  <dig>  cm  <cit> , in the majority of maps it is greater than  <dig> cm, i.e.
<dig>   <cit> ,  <dig>   <cit> ,  <dig>   <cit> ,  <dig>   <cit> .
on the other hand, as the number of sequence-specific, pcr-based markers  available for the species was until recently below  <dig>  <cit> , rye genetic maps were constructed predominantly with the use of usually poorly-transferable aflp and rapd markers, or labor intensive, time consuming and low-throughput rflp markers.
the highest number of sequence-specific, pcr-based markers on a rye linkage map equals  <dig>  <cit> .
lately, with the creation of bac library specific for 1rs  <cit>  and the development of  <dig> ssr markers for 1rs  <cit> , a significant advance took place in rye genomics.
however, the knowledge about the remaining part of the rye genome remains very limited.
the diversity arrays technology  - a microarray, hybridization-based platform - has a capacity to deliver several thousand of sequence-specific markers without relying on sequence information  <cit> .
to date, the performance of the method was validated in several species including cereals such as barley   <cit> , wheat   <cit>  and sorghum  moench)  <cit> .
the current list of species for which dart arrays are available commercially as service is at http://www.diversityarrays.com and the most comprehensive review of the technology was presented by kilian et al  <cit> .
the technology finds increasing use in creating high density genetic maps  <cit>  and association studies  <cit> , but it is also expanding into the area of plant and animal biodiversity and population genetics  <cit> .
the objective of this study was  to develop dart markers for rye,  to test their usefulness for assessing genetic similarity in rye inbred lines and varieties and  to use dart markers for constructing a high-density linkage map of the cross l <dig> × l <dig>  <cit> .
RESULTS
applicability of the psti/taqi complexity reduction method for the rye genome
complexity reduction is a process, which reproducibly selects a defined fraction of genomic fragments and is a critical step in dart.
the psti/taqi method is one of routinely used methods of genome complexity reduction in dart assays and was shown to be superior to other method tested in wheat  <cit>  and barley  <cit> .
consequently, this method was chosen for preparing targets form rye dna in the preliminary experiments with a wheat diversity panel.
the performance of psti/taqi generated rye targets during hybridizations was satisfactory, as demonstrated by good values of quality parameters, and for this reason the psti/taqi method of genome complexity reduction was used in all subsequent dart analyses performed.
additionally, the preliminary hybridizations revealed wheat dart markers that differentiated rye ils.
in total  <dig> candidate markers were identified on the wheat dart array as polymorphic among the rye accessions tested, when the quality criteria of q >77%, call rate > 80% and discordance < <dig>  were applied.
these clones  were included in microarrays used for genotyping in genetic diversity and mapping analyses along with the clones from rye libraries.
the utility of wheat dart markers for rye genotyping is consistent with the previous data on cross transferability of molecular markers between wheat and rye - it was proven that wheat rflps  <cit>  and ssrs  <cit>  can be successfully used for rye genome analyses.
the experiments conducted with the rye genotyping array confirmed the usefulness of the psti/taqi method for the analysis of the very large , highly methylated and composed predominantly of repetitive sequences rye genome.
it is clearly demonstrated by the proportion of clones displaying polymorphism in the materials genotyped.
from the total of  <dig> clones that were polymorphic in the genotyped ils and varieties,  <dig> originated from the rye libraries, which corresponds to  <dig>  polymorphism rate.
the proportion of polymorphic clones in mapping experiments was slightly higher -  <dig>  .
however, those two numbers are not directly comparable as different marker selection criteria were used in diversity and mapping experiments.
moreover, the array extended with  <dig> dna clones from genetically diverse parental components of rye mapping populations was used for mapping.
those clones  constituted 40% of the rye genotyping array  <dig>  and  <dig> % of them  were polymorphic.
another 40% of the rye genotyping array  <dig>  originated form dna of parental lines of the population used in this study  and  <dig> % of them  segregated in the rils.
the percentage of polymorphic markers observed for the diversity array during mapping experiments was  <dig>  .
in the case of genetic diversity experiments the percentages of polymorphic markers were  <dig>   and  <dig>   for the arrays mapping  <dig>  and diversity, respectively.
the low number of polymorphic clones in the diversity array can be attributed to the low genetic diversity represented by the rye varieties used for library creation revealed in subsequent analyses.
in general, the proportion of polymorphic markers in rye is higher than those reported for other cereals analyzed using dart - wheat  <cit>  and barley  <cit>  -  <dig>  and  <dig>  respectively.
from  <dig> wheat dart markers identified in the preliminary experiments,  <dig> differentiated ils and varieties ,  <dig> were useful for mapping  at p > 80%, q>80% and a call rate of at least 90%.
genetic diversity analysis
an upgma dendrogram based on the jaccard's similarity matrix data obtained with  <dig> dart markers is shown in figure  <dig>  il  <dig> separated from the remaining lines and varieties at about 38% similarity level.
il  <dig> is very sensitive to preharvest sprouting and originated from the cross involving the rye variety smolickie and lines selected from the variety kazimierskie  <cit> .
while kazimierskie was included in the study, to our knowledge no other il analysed is related to smolickie.
in our opinion those are the two main factors that contributed to the observed outcome of the cluster analysis.
all the varieties analyzed were clustered together at ca.
94% similarity level.
very similar results were obtained by ma et al  <cit> , who analyzed spring and winter rye varieties using rapd markers and reported clustering of winter varieties at similarity level slightly lower than 90%.
rye varieties are highly heterozygous  <cit> .
since dart markers were scored in the described experiments as dominant markers , it was not possible to distinguish between markers contained in heterozygous state  and homozygous markers .
in addition, the genotypic and allelic frequencies are likely to vary among the varieties for a number of markers, and because dart assays measure the differences in allelic frequencies well  <cit> , the binarisation of signal intensity data by dartsoft was likely seriously compromised, resulting in reduced frequency of markers discriminating varieties.
genetic similarity  coefficients for all  <dig> possible pairs of genotypes calculated on the basis of the jaccard's coefficient ranged from  <dig>  in the pair of ils ot 1- <dig> and  <dig> to  <dig>  in each pair of varieties dańkowskie nowe and dańkowskie złote, dańkowskie nowe and tetra, dańkowskie nowe and włoszanowskie, dańkowskie nowe and petkus.
the ils included in the experiment were analyzed previously with respect to genetic similarity based on data from  <dig> pcr-based markers  <cit> .
the result of the 2-way mantel test used for the comparison of similarity matrices from both studies was not statistically significant.
this result is not surprising since dart markers exploit a different source of polymorphism then the pcr- based markers used earlier.
a poor correlation between estimates of similarity based on data derived using different markers systems was observed also in other studies  <cit> .
at this point, it is not possible to judge, which markers - dart or pcr-based - reflect the genetic relationships between rye genotypes more accurately, since only a small number of genotypes was common for both studies and for some of them a detailed prodigy information is not available.
moreover, pedigree information can be an insufficient criterion to conclude about genetic relationships between rye lines obtained using selfing.
since rye varieties are highly heterozygous, it can be expected that inbred lines selected from the same variety or cross will differ in a number of loci  <cit> .
to resolve this issue an additional study of a larger set of rye genotypes involving an analysis of phenotypic features is needed.
the average gs coefficient values were  <dig>  and  <dig>  for dart and pcr-based markers, respectively.
hence, in case of this study, the discriminating power of dart markers didn't differ significantly from that of pcr-based markers.
dart markers, however, offer substantial advantages over pcr-based markers such as independence form gel electrophoresis and sequence information, transferability, reproducibility, automated scoring and high throughput, which allow obtaining more reliable results in a more cost effective way.
these advantages make dart a method of choice over serially produced low-plex markers for diversity studies  <cit> .
the principal correspondence plot generated from dart data is shown in figure  <dig>  the first principal axis, explaining  <dig>  9% of the variation, differentiates rye varieties from ils and resolves the differences within ils, the second principal axis, explaining  <dig> % of the variation, differentiates il  <dig> from the remaining ils and varieties.
chromosomal location of dart markers
genotyping of wheat-rye addition lines on the rye genotyping array  <dig>  revealed  <dig>  dart markers that were present in genomic representation of only one of the addition lines , and therefore their chromosomal location could be determined.
proportions of dart markers localized on individual chromosomes were not uniform and varied from  <dig> % for the chromosome 1r  to  <dig> % for the chromosome 6r .
the result of the spearman rank correlation analysis of these proportions with physical lengths of rye chromosomes  <cit>   was not statistically significant.
from the dart marker with determined chromosomal location,  <dig>  displayed polymorphism in parental lines of mapping population and could be used as anchor loci during map construction.
genetic mapping of dart markers
the mendelian nature of dart markers was demonstrated previously by jacccoud at al.
<cit> , wenzl et al.
<cit>  and akbari et al.
<cit> .
darts turned out to be highly efficient also in genetic mapping of rye.
in total  <dig>  dart markers differentiated ils l <dig> and l <dig> and segregated in the rils .
record separated them into  <dig> linkage groups with marker number ranging from  <dig>  to  <dig> .
based on the presence of anchor loci  the linkage groups were assembled using joinmap  <dig> into  <dig> larger linkage groups representing rye chromosomes .
the resulting map contains  <dig> markers.
among them  <dig> loci  were unique, non co-segregating with other markers.
number of markers per chromosome ranged from  <dig>  for 3r to  <dig>  for 4r with an average of  <dig> markers  per chromosome.
the map spans  <dig>  cm, providing an average density of one unique marker every  <dig>  cm .
markers were not evenly distributed along the chromosomes - clustering of markers was apparent in certain chromosome regions, on the other hand,  <dig> intervals that are longer than  <dig> cm long can be found on the map on the chromosomes 2r , 4r , 6r  and 7r .
a consensus map of rye based on data from five mapping populations was published recently by gustafson et al.
<cit> .
the existence of five gaps of  <dig> cm or longer in the map was reported: four at the telomeric ends of the chromosomes - 1r , 4r and 5r - and one in the middle of the short arm of the chromosome 6r.
the complete lack of common markers between the l <dig> × l <dig> and the consensus map makes the comparison of gap locations impossible.
we expect, however, that the ongoing creation of a dart-based integrated map of several rye mapping population, including the ds <dig> × rxl <dig> cross , will deliver the information necessary to answer, whether the particular gaps are population specific, result from limitation of the marker system used, or are conserved in rye.
the length of the newly constructed l <dig> × l <dig> linkage map exceeded more than twice the length of the most saturated rye linkage map published to date, created by bednarek et al.
<cit> , based on analysis of a f <dig> population, which spanned  <dig> cm and comprised  <dig> loci.
this can be explained by map expansion due to the use of rils, resulting from the multiple rounds of meiosis undergone  <cit> .
a similar length relation between f <dig> and ril-based genetic maps was observed earlier in maize  <cit> .
as shown by knox and ellis  <cit> , another factor that contributes to genetic map expansion is excess heterozygosity.
an overrepresentation of heterozygots in l <dig> × l <dig> rils was revealed in the earlier study of the population employing a larger number of ssr markers  <cit> .
of  <dig> polymorphic markers,  <dig>  deviated from the expected segregation ratio at the 1% level.
consistently with the results of previous mapping experiments conducted in rye on the same  <cit>  and a different mapping population  <cit> , the highest proportion of distorted unique markers was found on the chromosome 7r .
the percentage of distorted markers on remaining chromosomes varied from  <dig>   to  <dig>  .
hackauf and wehling  <cit>  attributed the high percentage of distorted markers on the rye chromosome 7r maps to the existence of a locus governing zygotic selection on that chromosome.
a high proportion of markers with segregation distortion observed on the chromosome 1r can be explained in a similar way as the self-incompability locus s is located there  <cit> .
the segregation distortion is very likely to occur in a population of an out crossing crop suffering from inbreeding depression due to several cycles of selfing.
segregation distortion is a common phenomenon in rye  <cit>  and in other plant species  <cit> .
importantly, it was shown not to influence the quality of mapping results both with simulated  <cit>  and experimental data  <cit> , even in the case of a ril-based map with a higher proportion of distorted markers that reported in this study  <cit> .
the dart based l <dig> × l <dig> linkage map is the most saturated of the rye maps based solely on transferable markers available at the moment.
in our opinion, the potential for its practical application is increased by the kind of the population used.
rils allow for repeated measurements and therefore for identifying loci influencing various traits of interest for breeders and researchers, but are relatively rarely used in rye genetics.
the extent and uniformity of the genome coverage are still not sufficient for map based cloning and alignment of the  physical map.
however, using the same array as used in this study for genotyping several other mapping populations, we identified over  <dig>  markers segregating in at least one of these populations .
integrating the information from several populations typed on the commercially available dart array resulted in the construction of a high density consensus map of barley  <cit>  and a similar strategy will be deployed to construct a  <dig> + dart marker map of the rye genome.
having such a resource combined with a bac anchoring strategy using dart arrays , there is an opportunity to rapidly integrate genetic and physical mapping information for rye.
importantly, the relatively low level of marker redundancy observed in the mapping data points clearly to a potential for further array expansion using more candidate clones from additional varieties representing different germplasm pools.
as some of the apparent marker redundancy in mapping data is likely to be due to genetic linkage  rather than sequence redundancy, we can anticipate doubling the number of markers on the next generation array for the psti/taqi representation.
an even larger increase in dart marker density can be achieved by deploying other methods of complexity reduction opening opportunities for rapid identification of tightly linked markers and providing a platform for positional cloning of rye genes.
CONCLUSIONS
the presented study has demonstrated that the diversity arrays technology can be efficiently and effectively used for the rye genome analyses - assessment of genetic similarity and linkage mapping.
the 11520-clone rye genotyping panel, including  <dig> dart markers with chromosomal location determined using wheat-rye addition lines, and the dart based genetic linkage map of the population l <dig> × l <dig> can be a valuable resource for studies on rye genome organization and in molecular breeding of the species.
the array developed in the course of this study has been already applied with success to type a number of rye mapping populations.

 winter rye is an important cereal crop in central, eastern and northern europe, mainly due to its exceptional ability to thrive and to produce high yields in adverse environmental conditions. nutrient efficiency and tolerance of diseases exhibited by rye, allowing for a reduced usage of pesticides and fertilizers during production, increase its attractiveness for farmers and consumers. the recently better recognized dietary value of rye contributed to the noticeable growth of consumers' interest in rye products. breeding progress in rye, however, is rather slow, as the traditional breeding is hampered by the outcrossing nature of this crop, self-incompatibility and occurrence of inbreeding depression. implementation of molecular breeding in rye improvement programs depends on the availability of high-density molecular linkage maps. several genetic maps of rye have been published so far, but the possibilities of their practical application are rather limited, mainly due to an insufficient saturation. the average density of the most saturated rye linkage map published to date is cm. however, there are seven gaps greater than cm on the map. the average map interval length on remaining rye maps exceeds cm, in the majority of maps it is greater than cm, i.e.,,,. on the other hand, as the number of sequence-specific, pcr-based markers available for the species was until recently below, rye genetic maps were constructed predominantly with the use of usually poorly-transferable aflp and rapd markers, or labor intensive, time consuming and low-throughput rflp markers. the highest number of sequence-specific, pcr-based markers on a rye linkage map equals. lately, with the creation of bac library specific for 1rs and the development of ssr markers for 1rs, a significant advance took place in rye genomics. however, the knowledge about the remaining part of the rye genome remains very limited. the diversity arrays technology - a microarray, hybridization-based platform - has a capacity to deliver several thousand of sequence-specific markers without relying on sequence information. to date, the performance of the method was validated in several species including cereals such as barley, wheat and sorghum moench). the current list of species for which dart arrays are available commercially as service is at http://www.diversityarrays.com and the most comprehensive review of the technology was presented by kilian et al. the technology finds increasing use in creating high density genetic maps and association studies, but it is also expanding into the area of plant and animal biodiversity and population genetics. the objective of this study was to develop dart markers for rye, to test their usefulness for assessing genetic similarity in rye inbred lines and varieties and to use dart markers for constructing a high-density linkage map of the cross l × l.  applicability of the psti/taqi complexity reduction method for the rye genome complexity reduction is a process, which reproducibly selects a defined fraction of genomic fragments and is a critical step in dart. the psti/taqi method is one of routinely used methods of genome complexity reduction in dart assays and was shown to be superior to other method tested in wheat and barley. consequently, this method was chosen for preparing targets form rye dna in the preliminary experiments with a wheat diversity panel. the performance of psti/taqi generated rye targets during hybridizations was satisfactory, as demonstrated by good values of quality parameters, and for this reason the psti/taqi method of genome complexity reduction was used in all subsequent dart analyses performed. additionally, the preliminary hybridizations revealed wheat dart markers that differentiated rye ils. in total candidate markers were identified on the wheat dart array as polymorphic among the rye accessions tested, when the quality criteria of q >77%, call rate > 80% and discordance < were applied. these clones were included in microarrays used for genotyping in genetic diversity and mapping analyses along with the clones from rye libraries. the utility of wheat dart markers for rye genotyping is consistent with the previous data on cross transferability of molecular markers between wheat and rye - it was proven that wheat rflps and ssrs can be successfully used for rye genome analyses. the experiments conducted with the rye genotyping array confirmed the usefulness of the psti/taqi method for the analysis of the very large, highly methylated and composed predominantly of repetitive sequences rye genome. it is clearly demonstrated by the proportion of clones displaying polymorphism in the materials genotyped. from the total of clones that were polymorphic in the genotyped ils and varieties, originated from the rye libraries, which corresponds to polymorphism rate. the proportion of polymorphic clones in mapping experiments was slightly higher -. however, those two numbers are not directly comparable as different marker selection criteria were used in diversity and mapping experiments. moreover, the array extended with dna clones from genetically diverse parental components of rye mapping populations was used for mapping. those clones constituted 40% of the rye genotyping array and % of them were polymorphic. another 40% of the rye genotyping array originated form dna of parental lines of the population used in this study and % of them segregated in the rils. the percentage of polymorphic markers observed for the diversity array during mapping experiments was. in the case of genetic diversity experiments the percentages of polymorphic markers were and for the arrays mapping and diversity, respectively. the low number of polymorphic clones in the diversity array can be attributed to the low genetic diversity represented by the rye varieties used for library creation revealed in subsequent analyses. in general, the proportion of polymorphic markers in rye is higher than those reported for other cereals analyzed using dart - wheat and barley - and respectively. from wheat dart markers identified in the preliminary experiments, differentiated ils and varieties, were useful for mapping at p > 80%, q>80% and a call rate of at least 90%. genetic diversity analysis an upgma dendrogram based on the jaccard's similarity matrix data obtained with dart markers is shown in figure il separated from the remaining lines and varieties at about 38% similarity level. il is very sensitive to preharvest sprouting and originated from the cross involving the rye variety smolickie and lines selected from the variety kazimierskie. while kazimierskie was included in the study, to our knowledge no other il analysed is related to smolickie. in our opinion those are the two main factors that contributed to the observed outcome of the cluster analysis. all the varieties analyzed were clustered together at ca. 94% similarity level. very similar results were obtained by ma et al, who analyzed spring and winter rye varieties using rapd markers and reported clustering of winter varieties at similarity level slightly lower than 90%. rye varieties are highly heterozygous. since dart markers were scored in the described experiments as dominant markers, it was not possible to distinguish between markers contained in heterozygous state and homozygous markers. in addition, the genotypic and allelic frequencies are likely to vary among the varieties for a number of markers, and because dart assays measure the differences in allelic frequencies well, the binarisation of signal intensity data by dartsoft was likely seriously compromised, resulting in reduced frequency of markers discriminating varieties. genetic similarity coefficients for all possible pairs of genotypes calculated on the basis of the jaccard's coefficient ranged from in the pair of ils ot 1- and to in each pair of varieties dańkowskie nowe and dańkowskie złote, dańkowskie nowe and tetra, dańkowskie nowe and włoszanowskie, dańkowskie nowe and petkus. the ils included in the experiment were analyzed previously with respect to genetic similarity based on data from pcr-based markers. the result of the 2-way mantel test used for the comparison of similarity matrices from both studies was not statistically significant. this result is not surprising since dart markers exploit a different source of polymorphism then the pcr- based markers used earlier. a poor correlation between estimates of similarity based on data derived using different markers systems was observed also in other studies. at this point, it is not possible to judge, which markers - dart or pcr-based - reflect the genetic relationships between rye genotypes more accurately, since only a small number of genotypes was common for both studies and for some of them a detailed prodigy information is not available. moreover, pedigree information can be an insufficient criterion to conclude about genetic relationships between rye lines obtained using selfing. since rye varieties are highly heterozygous, it can be expected that inbred lines selected from the same variety or cross will differ in a number of loci. to resolve this issue an additional study of a larger set of rye genotypes involving an analysis of phenotypic features is needed. the average gs coefficient values were and for dart and pcr-based markers, respectively. hence, in case of this study, the discriminating power of dart markers didn't differ significantly from that of pcr-based markers. dart markers, however, offer substantial advantages over pcr-based markers such as independence form gel electrophoresis and sequence information, transferability, reproducibility, automated scoring and high throughput, which allow obtaining more reliable results in a more cost effective way. these advantages make dart a method of choice over serially produced low-plex markers for diversity studies. the principal correspondence plot generated from dart data is shown in figure the first principal axis, explaining 9% of the variation, differentiates rye varieties from ils and resolves the differences within ils, the second principal axis, explaining % of the variation, differentiates il from the remaining ils and varieties. chromosomal location of dart markers genotyping of wheat-rye addition lines on the rye genotyping array revealed dart markers that were present in genomic representation of only one of the addition lines, and therefore their chromosomal location could be determined. proportions of dart markers localized on individual chromosomes were not uniform and varied from % for the chromosome 1r to % for the chromosome 6r. the result of the spearman rank correlation analysis of these proportions with physical lengths of rye chromosomes was not statistically significant. from the dart marker with determined chromosomal location, displayed polymorphism in parental lines of mapping population and could be used as anchor loci during map construction. genetic mapping of dart markers the mendelian nature of dart markers was demonstrated previously by jacccoud at al., wenzl et al. and akbari et al.. darts turned out to be highly efficient also in genetic mapping of rye. in total dart markers differentiated ils l and l and segregated in the rils. record separated them into linkage groups with marker number ranging from to. based on the presence of anchor loci the linkage groups were assembled using joinmap into larger linkage groups representing rye chromosomes. the resulting map contains markers. among them loci were unique, non co-segregating with other markers. number of markers per chromosome ranged from for 3r to for 4r with an average of markers per chromosome. the map spans cm, providing an average density of one unique marker every cm. markers were not evenly distributed along the chromosomes - clustering of markers was apparent in certain chromosome regions, on the other hand, intervals that are longer than cm long can be found on the map on the chromosomes 2r, 4r, 6r and 7r. a consensus map of rye based on data from five mapping populations was published recently by gustafson et al.. the existence of five gaps of cm or longer in the map was reported: four at the telomeric ends of the chromosomes - 1r, 4r and 5r - and one in the middle of the short arm of the chromosome 6r. the complete lack of common markers between the l × l and the consensus map makes the comparison of gap locations impossible. we expect, however, that the ongoing creation of a dart-based integrated map of several rye mapping population, including the ds × rxl cross, will deliver the information necessary to answer, whether the particular gaps are population specific, result from limitation of the marker system used, or are conserved in rye. the length of the newly constructed l × l linkage map exceeded more than twice the length of the most saturated rye linkage map published to date, created by bednarek et al., based on analysis of a f population, which spanned cm and comprised loci. this can be explained by map expansion due to the use of rils, resulting from the multiple rounds of meiosis undergone. a similar length relation between f and ril-based genetic maps was observed earlier in maize. as shown by knox and ellis, another factor that contributes to genetic map expansion is excess heterozygosity. an overrepresentation of heterozygots in l × l rils was revealed in the earlier study of the population employing a larger number of ssr markers. of polymorphic markers, deviated from the expected segregation ratio at the 1% level. consistently with the results of previous mapping experiments conducted in rye on the same and a different mapping population, the highest proportion of distorted unique markers was found on the chromosome 7r. the percentage of distorted markers on remaining chromosomes varied from to. hackauf and wehling attributed the high percentage of distorted markers on the rye chromosome 7r maps to the existence of a locus governing zygotic selection on that chromosome. a high proportion of markers with segregation distortion observed on the chromosome 1r can be explained in a similar way as the self-incompability locus s is located there. the segregation distortion is very likely to occur in a population of an out crossing crop suffering from inbreeding depression due to several cycles of selfing. segregation distortion is a common phenomenon in rye and in other plant species. importantly, it was shown not to influence the quality of mapping results both with simulated and experimental data, even in the case of a ril-based map with a higher proportion of distorted markers that reported in this study. the dart based l × l linkage map is the most saturated of the rye maps based solely on transferable markers available at the moment. in our opinion, the potential for its practical application is increased by the kind of the population used. rils allow for repeated measurements and therefore for identifying loci influencing various traits of interest for breeders and researchers, but are relatively rarely used in rye genetics. the extent and uniformity of the genome coverage are still not sufficient for map based cloning and alignment of the physical map. however, using the same array as used in this study for genotyping several other mapping populations, we identified over markers segregating in at least one of these populations. integrating the information from several populations typed on the commercially available dart array resulted in the construction of a high density consensus map of barley and a similar strategy will be deployed to construct a + dart marker map of the rye genome. having such a resource combined with a bac anchoring strategy using dart arrays, there is an opportunity to rapidly integrate genetic and physical mapping information for rye. importantly, the relatively low level of marker redundancy observed in the mapping data points clearly to a potential for further array expansion using more candidate clones from additional varieties representing different germplasm pools. as some of the apparent marker redundancy in mapping data is likely to be due to genetic linkage rather than sequence redundancy, we can anticipate doubling the number of markers on the next generation array for the psti/taqi representation. an even larger increase in dart marker density can be achieved by deploying other methods of complexity reduction opening opportunities for rapid identification of tightly linked markers and providing a platform for positional cloning of rye genes.  the presented study has demonstrated that the diversity arrays technology can be efficiently and effectively used for the rye genome analyses - assessment of genetic similarity and linkage mapping. the 11520-clone rye genotyping panel, including dart markers with chromosomal location determined using wheat-rye addition lines, and the dart based genetic linkage map of the population l × l can be a valuable resource for studies on rye genome organization and in molecular breeding of the species. the array developed in the course of this study has been already applied with success to type a number of rye mapping populations. 
chromosomal location of dart markers was determined using wheat-rye addition lines and dart markers were placed on a genetic linkage map of the cross l × l providing an average density of one unique marker every cm. diversity arrays technology is a microarray-based method allowing for detection of dna polymorphism at several thousand loci in a single assay without relying on dna sequence information. the objective of this study was the development and application of diversity arrays technology for rye. the diversity arrays technology can be efficiently and effectively used for rye genome analyses - assessment of genetic similarity and linkage mapping. using the psti/taqi method of complexity reduction we created a rye diversity panel from dna of rye varieties and rye inbred lines, including parents of a mapping population consisting of recombinant inbred lines. hierarchical clustering and ordination analysis were performed based on the dart markers to reveal genetic relationships between the rye varieties and inbred lines included in the study. implementation of molecular breeding in rye improvement programs depends on the availability of high-density molecular linkage maps. the 11520-clone rye genotyping panel with several thousand markers with determined chromosomal location and accessible through an inexpensive genotyping service is a valuable resource for studies on rye genome organization and in molecular breeding of the species. the usefulness of a wheat diversity panel for identification of dart markers for rye was also demonstrated. this is the most saturated rye linkage map based solely on transferable markers available at the moment, providing rye breeders and researches with a better choice of markers and a higher probability of finding polymorphic markers in the region of interest.
 implementation of molecular breeding in rye improvement programs depends on the availability of high-density molecular linkage maps. however, the number of sequence-specific pcr-based markers available for the species is limited. diversity arrays technology is a microarray-based method allowing for detection of dna polymorphism at several thousand loci in a single assay without relying on dna sequence information. the objective of this study was the development and application of diversity arrays technology for rye.  using the psti/taqi method of complexity reduction we created a rye diversity panel from dna of rye varieties and rye inbred lines, including parents of a mapping population consisting of recombinant inbred lines. the usefulness of a wheat diversity panel for identification of dart markers for rye was also demonstrated. we identified clones that were polymorphic in the genotyped ils and varieties and clones that differentiated the parental lines l and l and segregated in the mapping population. hierarchical clustering and ordination analysis were performed based on the dart markers to reveal genetic relationships between the rye varieties and inbred lines included in the study. chromosomal location of dart markers was determined using wheat-rye addition lines and dart markers were placed on a genetic linkage map of the cross l × l providing an average density of one unique marker every cm. this is the most saturated rye linkage map based solely on transferable markers available at the moment, providing rye breeders and researches with a better choice of markers and a higher probability of finding polymorphic markers in the region of interest.  the diversity arrays technology can be efficiently and effectively used for rye genome analyses - assessment of genetic similarity and linkage mapping. the 11520-clone rye genotyping panel with several thousand markers with determined chromosomal location and accessible through an inexpensive genotyping service is a valuable resource for studies on rye genome organization and in molecular breeding of the species. 