BACKGROUND
sorghum  is one of the five dominant crops in the world including corn , wheat , rice  and barley  .
with the advantages of high yielding, good adaptability, drought, salt and alkali tolerance, it is one of the most valuable energy crops for the future  <cit> .
sorghum is a typical c <dig> crop and mainly used as a human food and beverage source.
sorghum grain is the main ingredient of top-grade alcohols and its stem can be used as fodder.
both grain and stem including all plant are stock for bioethanol and other bio-industrial products.
the genome size of sorghum  is 3– <dig> times smaller than corn, thus it was regarded as a diploid model crop for energy plants like polyploidy sugarcane and miscanthus  <cit> .
a genetic map is a foundation for quantitative and qualitative gene mapping and cloning, and plays a key role in marker-assisted breeding program.
high-density genetic maps of sorghum can be used for genome comparison, useful gene mining and gene mapping.
the genes for disease and insect-resistance, stress tolerance, sugar concentrations and biological yield can be identified by comparing homology in different plant species, and they can also be located on chromosomes by mapping, which lays a foundation for gene cloning and application.
high-density genetic mapping has great importance in increasing statistical power and precision of detecting genes and qtls.
genetic map construction of sorghum began in 1990s.
the early linkage maps of sorghum were constructed mainly by using labor-intensive or dominant markers such as rflp , aflp  and rapd  .
these maps have played important role in sorghum gene  mapping, comparative genomics and genetics studies.
however, these genetic marker systems have limited marker numbers, dominant expression, and not repeatable in different maps.
more informative marker types can effectively overcome the disadvantages mentioned above are required.
due to the quick development of sequencing and genotyping technologies, simple sequence repeat  with features of high reproducibility, co-dominant inheritance, multi-allelic variation and abundance in the genome, have replaced dominant markers for constructing linkage maps.
ssr markers were first used for polymorphism detecting and linkage group identification  <cit> , then were used to construct sorghum genetic maps with the development of a large amount of ssr markers  <cit> .
several linkage maps with ssr markers or mainly based on ssr markers have been developed and have been using in sorghum gene  mapping, genome evolution, molecular genetics and marker-assisted breeding .
however, the above technologies such as rapd, rflp, aflp and ssr to determine genetic fingerprints have limitations to cover full genome which requires the identification of a large number of polymorphic markers.
with these technologies this is a step by step approach that is labor intensive and plagued by process variation.
diversity arrays technology  was initially used to detect a large number of genetic differences between plant and animal varieties.
recently this technology was introduced for sorghum map construction.
dart markers were integrated into a sorghum consensus map which consisted of a total of  <dig> markers mapped to  <dig> unique loci  spanning  <dig>  cm and with an average marker density of  <dig> marker/ <dig>  cm  <cit> .
great progress has been made in the sequencing technologies and bioinformatics at an exponentially reduced cost, which led to a revolution in the field of genotyping technologies.
restriction associated dna sequencing  and genotyping by sequencing  have emerged as powerful genotyping platforms, which are capable of identifying, sequencing, and genotyping thousands of markers across almost any genome of interest and number of individuals in a population  <cit> .
the next generation sequencing can directly determine differences in dna sequence with high accuracy, thus it has been widely used for plant and animal genetic analysis.
slaf  markers, which has been used for genetic investigation, have the properties of being present in large amount, being evenly distributed and avoiding repeated sequences  <cit> .
these markers have been used for crop genetic analysis such as sesame, millet, rice and soybean , especially in the applications of high-density genetic map construction and functional genes verification.
exploiting this approach to scan the whole sorghum genome has great importance for high density marker development and gene mining for sorghum breeding.
the purpose of this study is to construct a high-density linkage map with snps through next generation sequencing technology.
the map can provide information and serve as a reference for effective gene exploration and lay a foundation for marker assisted breeding.
further, it can benefit the development of biological energy resources.
RESULTS
parents and f <dig> population for map construction
an f <dig> population consisting of  <dig> individuals from a cross of keter × j <dig> was used for genetic map construction.
the maternal parent is a sweet sorghum variety and the paternal parent is a grain sorghum variety.
there have been great differences in phenotypic characters between the two parents, such as plant height, heading time, seed coat color, etc.
therefore, their offspring will have considerable variations which are good for polymorphic marker screening and linkage group construction.
marker identification
the slaf number and sequencing depth identified in the parents and their offspring were plotted in fig.
1a.
the slaf marker number in paternal and maternal parents was  <dig>  and  <dig> , respectively.
the sequencing depth on average was  <dig> -fold in paternal parent and  <dig> -fold in maternal parent.
the slaf numbers for each f <dig> individual ranged from  <dig>  to  <dig>  with an average of  <dig> .
<dig>  the sequencing depth shifted from  <dig>  to  <dig> -fold with an average of  <dig> -fold .
among the  <dig>   qualified slaf markers,  <dig> were polymorphic with a polymorphism rate of only  <dig> % .
of the  <dig> polymorphic slaf markers,  <dig>  were classified into eight segregation patterns .
among them  <dig>  markers fell into segregation pattern aa × bb.
because individuals in the f <dig> population which was obtained by selfing the f <dig> of a cross between two fully homozygous parents showed this genotype, only the aa × bb segregation pattern in the f <dig> population was used to construct the genetic map.
finally  <dig>   markers were assigned onto linkage groups.fig.
<dig> the slaf number and the sequencing-depth in the parents and f <dig> individuals.
a number of slaf markers.
b sequencing-depth of slaf markers.
the x-axis in  and  indicates individuals including maternal parent , paternal parent  and  <dig> individuals from the f <dig> population.
the y-axis indicates the number of reads in  and the sequencing-depth in
fig.
<dig> the marker numbers in different segregation patterns.
the x-axis indicates different segregation patterns.
the y-axis indicates the slaf number in each pattern
the average sequencing depths were  <dig> -fold in the parents and  <dig> -fold in the offsprings on linked markers .
this integrity and depth of markers were enough to guarantee the accuracy for genetic map construction  <cit> .table  <dig> the sequencing depth of assigned makers in the parents and f <dig> population
linkage map construction
all the  <dig> assigned markers were grouped to  <dig> chromosomes, the linear alignments of markers on chromosomes were built by the genetic distances between adjacent markers.
finally the  <dig> markers were assigned onto the genetic map with a total length of  <dig>  cm and average distance between markers of  <dig>  cm.
the degree of linkage between markers was reflected by gap less than and/or equal to  <dig>  cm  ranging between  <dig> % and  <dig> % with an average value of  <dig> %.
the largest gap on chromosome  <dig> is  <dig>  cm.
on average  <dig>  markers were assigned on each chromosome with a length of  <dig>  cm .table  <dig> map information based on high quality slafs obtained from population sequencing
among the  <dig> markers,  <dig> were assigned on chromosome  <dig> which was the largest in the ten chromosomes.
the total length was  <dig>  cm with an average distance of only  <dig>  cm between adjacent markers.
a large gap of  <dig>  cm was located between  <dig>  to  <dig>  cm, the gap < =  <dig> ratio was  <dig> %.
the fewest markers  were on chromosome  <dig>  which was  <dig>  cm in length with an average distance of  <dig>  cm between adjacent markers.
a large gap of  <dig>  cm was located at the end of the chromosome.
the gap < =  <dig> ratio was  <dig> % which indicates the good quality of marker assignment .
map evaluation
three types of markers were assigned to the genetic map including  <dig> ‘snp_only’,  <dig> ‘indel_only’, and  <dig> ‘snp&indel’ markers.
‘snp_only’ was the predominant marker type accounting for  <dig> % of the markers.
‘indel_only’ markers were assigned on chromosomes  <dig>   <dig> and  <dig>  respectively.
while  <dig> ‘snp&indel’ markers were assigned on chromosomes  <dig>   <dig>   <dig> and  <dig>  respectively .
of the all  <dig> snp markers, most were transition type snps with r  and y  types accounting for  <dig> % and  <dig> %, respectively.
the other four snp types were transversions including s , m , k , and w  with percentages of  <dig> ,  <dig> ,  <dig>  and  <dig>  of all snps, respectively .table  <dig> different snp types in the linkage group
markers that showed significant  segregation distortion  were finally assigned onto the map  and most of them were clustered at the two ends of chromosomes and some located at chromosome centers such as chromosome  <dig> .
more than half  of the assigned markers showed significant  segregation distortion which distributed on each chromosome.
the largest chromosome  had the highest percentage of segregation distortion markers  and the smallest chromosome  had the lowest percentage of segregation distortion markers .
all the distorted markers clustered into  <dig> segregation distortion regions  which distributed on each chromosome.
similarly  <dig> sdrs were found on chr  <dig> and  <dig> on chr  <dig> .
among the three different marker types assigned to the final map, no one marker type was observed to show a particular tendency for skewness.
besides ‘snp-only’ markers, one out of  <dig> ‘indel-only’ and  <dig> out of  <dig> ‘snp&indel’ markers showed segregation distortion, respectively.fig.
<dig> ten linkage groups of sorghum from a cross of keter × j <dig>  slaf marker names and their locations are listed on the right and left sides of the axis.
segregation distortion markers on the map are highlighted in green
χ
2
p
discussion
in the present study an f <dig> mapping population from a cross between a sweet and a grain sorghum variety was employed to construct a sorghum linkage map.
the great character variations between the two parents benefited the marker polymorphism discovery.
the high-throughput sequencing technology used in the present study has greatly enhanced the identification and guaranteed the quantity and quality of markers.
therefore a high density genetic map was successfully constructed.
some existing sorghum maps are unsatisfactory for gene identification because of lacking adequate markers from the whole genome, and broken chromosome segments.
in the present study a dense genetic map was generated in which the whole sorghum genome sequence was surveyed, high quality markers were identified and uniformly distributed on  <dig> chromosomes.
each chromosome contains 123– <dig> markers and its length ranged from  <dig>  to  <dig>  cm.
this high density snp-based linkage map for sorghum can serve as a reference map for cultivated sorghum species and will be useful in genetic mapping.
dna marker distribution is not random with some clear marker-dense regions and some marker deserts.
in the present map, marker deserts  were observed with varied sizes.
most  of the gaps on every linkage group are less than and/or equal to  <dig>  cm.
in total only  <dig> gaps larger than  <dig>  cm were detected in all chromosomes except chr  <dig> suggesting that such gaps are not restricted to a particular chromosome.
gaps larger than  <dig>  cm were found on chromosomes  <dig>   <dig>   <dig> and  <dig>  the longest one was  <dig>  cm on the distal end of chr  <dig>  the presence of these gaps may have negative effects on the application of mapped dna markers, for example, genomic regions that lack dna markers will make detection of quantitative trait loci  difficult  <cit> .
therefore, more comparable markers between different sorghum maps are needed to fill in the gaps to obtain a more complete coverage of the sorghum genome.
segregation distortion is a common phenomenon in which the genotypic frequency of a marker deviates from a typical mendelian ratio.
previous studies have showed that a large number of segregation distortions and sdrs occur in many species, such as maize  <cit> , barley  <cit>  potato  <cit> , sesame  <cit> , peanut  <cit>  and sorghum  <cit> .
the genetic basis of segregation distortion is still under debate, and gametophyte and/or zygotic selection and chromosomal rearrangements may be the main cause of this phenomenon  <cit> .
however, some studies found segregation distortion in a non-random and consistent distribution pattern suggested that distorted segregation is due to the elimination of gametes or zygotes by a lethal factor located in a neighboring region of the marker  <cit> .
on a sorghum consensus map, chr  <dig> has the highest proportion of chromosomal regions associated with skewed segregation .
two other chromosomes  also have over 50% of the chromosomal regions associated with skewed segregation   <cit> .
in the present study, an f <dig> mapping population was employed to construct a linkage map, among the  <dig> assigned markers,  <dig> markers  showed significant segregation distortion.
all the skewed markers clustered into segregation distortion regions.
although it is not exactly the same, chr  <dig> has the highest proportion  of skewed markers and chr  <dig> has the biggest number  of sdrs in this final map, which indicates that there may be similar mechanism of skewed segregation phenomenon between the two studies.
further, studies have proved that the presence of segregation distortion markers will not affect the use of linkage maps for applications such as qtl mapping  <cit> .
genomic approaches such as high-throughput sequencing and large-scale genotyping technologies have been used in genetic linkage mapping.
the slaf-seq method provided significant advantages to generate enough polymorphic markers for high-density genetic map construction.
the high density map is sufficient to ensure adequate polymorphic marker coverage in regions of interest and can be used as a reference map for sorghum genetic studies.
CONCLUSIONS
a high density sorghum map was constructed in this study by employing slaf markers developed from high-throughput sequencing technology.
the total map length is  <dig>  cm covering sorghum  <dig> chromosomes with a total of  <dig> slaf markers.
the construction of this map can provide detailed information for gene localization, cloning and application of marker-assisted breeding.

 sorghum is one of the five dominant crops in the world including corn, wheat, rice and barley. with the advantages of high yielding, good adaptability, drought, salt and alkali tolerance, it is one of the most valuable energy crops for the future. sorghum is a typical c crop and mainly used as a human food and beverage source. sorghum grain is the main ingredient of top-grade alcohols and its stem can be used as fodder. both grain and stem including all plant are stock for bioethanol and other bio-industrial products. the genome size of sorghum is 3– times smaller than corn, thus it was regarded as a diploid model crop for energy plants like polyploidy sugarcane and miscanthus. a genetic map is a foundation for quantitative and qualitative gene mapping and cloning, and plays a key role in marker-assisted breeding program. high-density genetic maps of sorghum can be used for genome comparison, useful gene mining and gene mapping. the genes for disease and insect-resistance, stress tolerance, sugar concentrations and biological yield can be identified by comparing homology in different plant species, and they can also be located on chromosomes by mapping, which lays a foundation for gene cloning and application. high-density genetic mapping has great importance in increasing statistical power and precision of detecting genes and qtls. genetic map construction of sorghum began in 1990s. the early linkage maps of sorghum were constructed mainly by using labor-intensive or dominant markers such as rflp, aflp and rapd. these maps have played important role in sorghum gene mapping, comparative genomics and genetics studies. however, these genetic marker systems have limited marker numbers, dominant expression, and not repeatable in different maps. more informative marker types can effectively overcome the disadvantages mentioned above are required. due to the quick development of sequencing and genotyping technologies, simple sequence repeat with features of high reproducibility, co-dominant inheritance, multi-allelic variation and abundance in the genome, have replaced dominant markers for constructing linkage maps. ssr markers were first used for polymorphism detecting and linkage group identification, then were used to construct sorghum genetic maps with the development of a large amount of ssr markers. several linkage maps with ssr markers or mainly based on ssr markers have been developed and have been using in sorghum gene mapping, genome evolution, molecular genetics and marker-assisted breeding. however, the above technologies such as rapd, rflp, aflp and ssr to determine genetic fingerprints have limitations to cover full genome which requires the identification of a large number of polymorphic markers. with these technologies this is a step by step approach that is labor intensive and plagued by process variation. diversity arrays technology was initially used to detect a large number of genetic differences between plant and animal varieties. recently this technology was introduced for sorghum map construction. dart markers were integrated into a sorghum consensus map which consisted of a total of markers mapped to unique loci spanning  cm and with an average marker density of marker/  cm. great progress has been made in the sequencing technologies and bioinformatics at an exponentially reduced cost, which led to a revolution in the field of genotyping technologies. restriction associated dna sequencing and genotyping by sequencing have emerged as powerful genotyping platforms, which are capable of identifying, sequencing, and genotyping thousands of markers across almost any genome of interest and number of individuals in a population. the next generation sequencing can directly determine differences in dna sequence with high accuracy, thus it has been widely used for plant and animal genetic analysis. slaf markers, which has been used for genetic investigation, have the properties of being present in large amount, being evenly distributed and avoiding repeated sequences. these markers have been used for crop genetic analysis such as sesame, millet, rice and soybean, especially in the applications of high-density genetic map construction and functional genes verification. exploiting this approach to scan the whole sorghum genome has great importance for high density marker development and gene mining for sorghum breeding. the purpose of this study is to construct a high-density linkage map with snps through next generation sequencing technology. the map can provide information and serve as a reference for effective gene exploration and lay a foundation for marker assisted breeding. further, it can benefit the development of biological energy resources.  parents and f population for map construction an f population consisting of individuals from a cross of keter × j was used for genetic map construction. the maternal parent is a sweet sorghum variety and the paternal parent is a grain sorghum variety. there have been great differences in phenotypic characters between the two parents, such as plant height, heading time, seed coat color, etc. therefore, their offspring will have considerable variations which are good for polymorphic marker screening and linkage group construction. marker identification the slaf number and sequencing depth identified in the parents and their offspring were plotted in fig. 1a. the slaf marker number in paternal and maternal parents was and, respectively. the sequencing depth on average was -fold in paternal parent and -fold in maternal parent. the slaf numbers for each f individual ranged from to with an average of. the sequencing depth shifted from to -fold with an average of -fold. among the qualified slaf markers, were polymorphic with a polymorphism rate of only %. of the polymorphic slaf markers, were classified into eight segregation patterns. among them markers fell into segregation pattern aa × bb. because individuals in the f population which was obtained by selfing the f of a cross between two fully homozygous parents showed this genotype, only the aa × bb segregation pattern in the f population was used to construct the genetic map. finally  markers were assigned onto linkage groups.fig. the slaf number and the sequencing-depth in the parents and f individuals. a number of slaf markers. b sequencing-depth of slaf markers. the x-axis in and indicates individuals including maternal parent, paternal parent and individuals from the f population. the y-axis indicates the number of reads in and the sequencing-depth in fig. the marker numbers in different segregation patterns. the x-axis indicates different segregation patterns. the y-axis indicates the slaf number in each pattern the average sequencing depths were -fold in the parents and -fold in the offsprings on linked markers. this integrity and depth of markers were enough to guarantee the accuracy for genetic map construction.table the sequencing depth of assigned makers in the parents and f population linkage map construction all the assigned markers were grouped to chromosomes, the linear alignments of markers on chromosomes were built by the genetic distances between adjacent markers. finally the markers were assigned onto the genetic map with a total length of  cm and average distance between markers of  cm. the degree of linkage between markers was reflected by gap less than and/or equal to  cm ranging between % and % with an average value of %. the largest gap on chromosome is  cm. on average markers were assigned on each chromosome with a length of  cm.table map information based on high quality slafs obtained from population sequencing among the markers, were assigned on chromosome which was the largest in the ten chromosomes. the total length was  cm with an average distance of only  cm between adjacent markers. a large gap of  cm was located between to  cm, the gap < = ratio was %. the fewest markers were on chromosome which was  cm in length with an average distance of  cm between adjacent markers. a large gap of  cm was located at the end of the chromosome. the gap < = ratio was % which indicates the good quality of marker assignment. map evaluation three types of markers were assigned to the genetic map including ‘snp_only’, ‘indel_only’, and ‘snp&indel’ markers. ‘snp_only’ was the predominant marker type accounting for % of the markers. ‘indel_only’ markers were assigned on chromosomes and respectively. while ‘snp&indel’ markers were assigned on chromosomes and respectively. of the all snp markers, most were transition type snps with r and y types accounting for % and %, respectively. the other four snp types were transversions including s, m, k, and w with percentages of,, and of all snps, respectively.table different snp types in the linkage group markers that showed significant segregation distortion were finally assigned onto the map and most of them were clustered at the two ends of chromosomes and some located at chromosome centers such as chromosome. more than half of the assigned markers showed significant segregation distortion which distributed on each chromosome. the largest chromosome had the highest percentage of segregation distortion markers and the smallest chromosome had the lowest percentage of segregation distortion markers. all the distorted markers clustered into segregation distortion regions which distributed on each chromosome. similarly sdrs were found on chr and on chr. among the three different marker types assigned to the final map, no one marker type was observed to show a particular tendency for skewness. besides ‘snp-only’ markers, one out of ‘indel-only’ and out of ‘snp&indel’ markers showed segregation distortion, respectively.fig. ten linkage groups of sorghum from a cross of keter × j slaf marker names and their locations are listed on the right and left sides of the axis. segregation distortion markers on the map are highlighted in green χ 2 p discussion in the present study an f mapping population from a cross between a sweet and a grain sorghum variety was employed to construct a sorghum linkage map. the great character variations between the two parents benefited the marker polymorphism discovery. the high-throughput sequencing technology used in the present study has greatly enhanced the identification and guaranteed the quantity and quality of markers. therefore a high density genetic map was successfully constructed. some existing sorghum maps are unsatisfactory for gene identification because of lacking adequate markers from the whole genome, and broken chromosome segments. in the present study a dense genetic map was generated in which the whole sorghum genome sequence was surveyed, high quality markers were identified and uniformly distributed on chromosomes. each chromosome contains 123– markers and its length ranged from to  cm. this high density snp-based linkage map for sorghum can serve as a reference map for cultivated sorghum species and will be useful in genetic mapping. dna marker distribution is not random with some clear marker-dense regions and some marker deserts. in the present map, marker deserts were observed with varied sizes. most of the gaps on every linkage group are less than and/or equal to  cm. in total only gaps larger than  cm were detected in all chromosomes except chr suggesting that such gaps are not restricted to a particular chromosome. gaps larger than  cm were found on chromosomes and the longest one was  cm on the distal end of chr the presence of these gaps may have negative effects on the application of mapped dna markers, for example, genomic regions that lack dna markers will make detection of quantitative trait loci difficult. therefore, more comparable markers between different sorghum maps are needed to fill in the gaps to obtain a more complete coverage of the sorghum genome. segregation distortion is a common phenomenon in which the genotypic frequency of a marker deviates from a typical mendelian ratio. previous studies have showed that a large number of segregation distortions and sdrs occur in many species, such as maize, barley potato, sesame, peanut and sorghum. the genetic basis of segregation distortion is still under debate, and gametophyte and/or zygotic selection and chromosomal rearrangements may be the main cause of this phenomenon. however, some studies found segregation distortion in a non-random and consistent distribution pattern suggested that distorted segregation is due to the elimination of gametes or zygotes by a lethal factor located in a neighboring region of the marker. on a sorghum consensus map, chr has the highest proportion of chromosomal regions associated with skewed segregation. two other chromosomes also have over 50% of the chromosomal regions associated with skewed segregation. in the present study, an f mapping population was employed to construct a linkage map, among the assigned markers, markers showed significant segregation distortion. all the skewed markers clustered into segregation distortion regions. although it is not exactly the same, chr has the highest proportion of skewed markers and chr has the biggest number of sdrs in this final map, which indicates that there may be similar mechanism of skewed segregation phenomenon between the two studies. further, studies have proved that the presence of segregation distortion markers will not affect the use of linkage maps for applications such as qtl mapping. genomic approaches such as high-throughput sequencing and large-scale genotyping technologies have been used in genetic linkage mapping. the slaf-seq method provided significant advantages to generate enough polymorphic markers for high-density genetic map construction. the high density map is sufficient to ensure adequate polymorphic marker coverage in regions of interest and can be used as a reference map for sorghum genetic studies.  a high density sorghum map was constructed in this study by employing slaf markers developed from high-throughput sequencing technology. the total map length is  cm covering sorghum chromosomes with a total of slaf markers. the construction of this map can provide detailed information for gene localization, cloning and application of marker-assisted breeding. 
sorghum is mainly used as a human food and beverage source, playing an important role in the production of ethanol and other bio-industrial products. this map can provide information and serve as a reference for effective gene exploration, and for marker assisted-breeding program. a high-throughput sequencing method was adopted to screen slaf markers with 130 f individuals from a cross between a grain sorghum variety, j and a sweet sorghum variety, keter. genetic map construction is the foundation for marker-assisted selection and gene cloning. in the present study, suitable slaf markers out of, pair-end reads were chosen to conduct genetic map construction, % of which were polymorphic. the markers on each chromosome ranged from to with a mean value of, the distance between adjacent markers ranged from to  cm with an average distance of only  cm. a high-density linkage map was constructed using specific-locus amplified fragments markers. however marker numbers and chromosome coverage are limited. the total length was  cm covering all chromosomes with a total number of slaf markers. as a result, it is difficult to get consistent results and the maps are hard to unify. so far several sorghum linkage maps have been reported using different kinds of molecular markers. finally slaf markers were obtained to construct a high-density genetic linkage map. the total distance of linkage map covering all chromosomes was  cm. sorghum bicolorhigh-throughput sequencingslaf markerlinkage map constructionhttp://dx.doi.org/ /501100003787natural science foundation of hebei provincec2012301002ji guisu research funds in technology and development of haasa2015030201ji guisu earmarked fund for china agricultural research systemissue-copyright-statement© the author 2017 thus it is regarded as a model crop for energy plants. in the present study, the genomes of individuals consisting an f population together with their parents were surveyed using a high-throughput sequencing technique.
 sorghum is mainly used as a human food and beverage source, playing an important role in the production of ethanol and other bio-industrial products. thus it is regarded as a model crop for energy plants. genetic map construction is the foundation for marker-assisted selection and gene cloning. so far several sorghum linkage maps have been reported using different kinds of molecular markers. however marker numbers and chromosome coverage are limited. as a result, it is difficult to get consistent results and the maps are hard to unify. in the present study, the genomes of individuals consisting an f population together with their parents were surveyed using a high-throughput sequencing technique. a high-density linkage map was constructed using specific-locus amplified fragments markers. this map can provide information and serve as a reference for effective gene exploration, and for marker assisted-breeding program.  a high-throughput sequencing method was adopted to screen slaf markers with 130 f individuals from a cross between a grain sorghum variety, j and a sweet sorghum variety, keter. in the present study, suitable slaf markers out of, pair-end reads were chosen to conduct genetic map construction, % of which were polymorphic. among the polymorphic slaf markers, were successfully genotyped in the f mapping population. finally slaf markers were obtained to construct a high-density genetic linkage map. the total distance of linkage map covering all chromosomes was  cm. the largest gap on each chromosome was  cm on average. the proportion of gaps less than and/or equal to  cm was averagely %. the markers on each chromosome ranged from to with a mean value of, the distance between adjacent markers ranged from to  cm with an average distance of only  cm.  a high density sorghum genetic map was constructed in this study. the total length was  cm covering all chromosomes with a total number of slaf markers. the construction of this map can provide detailed information for accurate gene localization and cloning and application of marker-assisted breeding. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords sorghum bicolorhigh-throughput sequencingslaf markerlinkage map constructionhttp://dx.doi.org/ /501100003787natural science foundation of hebei provincec2012301002ji guisu research funds in technology and development of haasa2015030201ji guisu earmarked fund for china agricultural research systemissue-copyright-statement© the author 2017 