Molecular Marker Map Research Articles

A major QTL on chromosome C05 significantly reduces acid detergent lignin (ADL) content and increases seed oil and protein content in oilseed rape (Brassica napus L.).

A reduction in acid detergent lignin content in oilseed rape resulted in an increase in seed oil and protein content. Worldwide increasing demand for vegetable oil and protein requires continuous breeding efforts to enhance the yield of oil and protein crop species. The oil-extracted meal of oilseed rape is currently mainly used for feeding livestock, but efforts are undertaken to use the oilseed rape protein in food production. One limiting factor is the high lignin content of black-seeded oilseed rape that negatively affects digestibility and sensory quality of food products compared to soybean. Breeding attempts to develop yellow seeded oilseed rape with reduced lignin content have not yet resulted in competitive cultivars. The objective of this work was to investigate the inheritance of seed quality in a DH population derived from the cross of the high oil lines SGDH14 and cv. Express. The DH population of 139 lines was tested in field experiments in 14 environments in north-west Europe. Seeds harvested from open pollinated plants were used for extensive seed quality analysis. A molecular marker map based on the Illumina Infinium 60K Brassica SNP chip was used to map QTL. Amongst others, one major QTL for acid detergent lignin content, explaining 81% of the phenotypic variance, was identified on chromosome C05. Lines with reduced lignin content nevertheless did not show a yellowish appearance, but showed a reduced seed hull content. The position of the QTL co-located with QTL for oil and protein content of the defatted meal with opposite additive effects, suggesting that the reduction in lignin content resulted in an increase in oil and protein content.

Identification of quantitative trait loci (QTL) associated with sheath blight tolerance in rice

Sheath blight, caused by the pathogen Rhizoctonia solani Kuhn, is one of the most serious diseases of rice and leads to severe yield losses worldwide. A recombinant inbred line (RIL) population consisting of 122 lines was constructed from a cross between Danteshwari a high yielding popular rice cultivar but moderately susceptible to water stress, susceptible to sheath blight and Dagad Deshi a tall deep rooted poor yielder and tolerant to water stress and sheath blight. Five traits, namely infected tillers per hill, lesion size (total coalescing lesions) and individual lesion (one spot) and lesion's length and width) were used to evaluate sheath blight resistance. Using the RIL population and 162 molecular markers, 11 quantitative trait loci (QTLs) were identified for the five traits. Identification of map position was accomplished by identifying BAC or PAC clones that simultaneously contained a hit from the microsatellite/HvSSR marker further helped us to generate a high resolution molecular marker map of the identified QTL region. Identified QTLs were located on seven chromosomes. A major QTL for infected tillers per hill on chromosome 1 was identified with phenotypic variance of 18.02%. Six QTL's with positive additive effect and one with negative additive effects was identified indicating alleles at these loci are being contributed by either of the parents respectively.

Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays.

Polymorphic probes identified via a sequence-based approach are suitable to infer the genotypes of recombinant inbred lines from hybridisation intensities of GeneChip ® transcript profiling experiments. The sequences of the probes of the ATH1 GeneChip® exactly match transcript sequences of the Arabidopsis thaliana reference genome Col-0, whereas nucleotide differences and/or insertions/deletions may be observed for transcripts of other A.thaliana accessions. Individual probes of the GeneChip® that show sequence polymorphisms between different A.thaliana accessions may serve as single-feature polymorphism (SFP) markers, provided that the sequence changes cause differences in hybridisation intensity for the accessions of interest. A sequence-based approach identified features on the high-density oligonucleotide array that showed sequence polymorphisms between A.thaliana accessions Col-0 and C24. Hybridisation intensities of polymorphic probes were extracted from genome-wide transcript profiles of Col-0/C24 and C24/Col-0 recombinant inbred lines and assessed after standardisation via sliding window analyses to identify SFP markers. The genotypes of the recombinant inbred lines were determined with the SFP markers and the resulting data were integrated with information, which had been established previously with single nucleotide polymorphism and insertion/deletion markers, to enrich the linkage map of the Col-0/C24 and C24/Col-0 recombinant inbred populations. Congruence between the molecular marker map and the sequence maps of the A.thaliana Col-0 chromosomes proved the reliability of the genotype information which was deduced from the transcript profiles of the Col-0/C24 and C24/Col-0 recombinant inbred lines.

A comparative assessment of morphological and molecular diversity among Sechium edule (Jacq.) Sw. accessions in India

Genetic variation of 36 Sechium edule accessions collected across 12 states in India was assessed using morphological traits and DAMD markers. Eighteen fruit morphological traits (both qualitative and quantitative) were evaluated to confirm the variations in the present collection. Quantitative traits showed major variations with respect to fruit weight (7.85–498.33 g/fruit), fruit length (5.8–15 cm/fruit), fruit diameter (6–28 cm/fruit) and length of the spine (0–5 cm). Qualitative traits were also diverse in fruit colour, shape, spine density, reticulation, flexibility of spine and furrow depth. The first six principle components showed 82.88% variation in the principal component analysis. The principal component analysis revealed that fruit weight, fruit width, fruit diameter, fruit shape, length of spine, spine density and furrow depth had a significant contribution to the total variation. The DNA analysis performed using DAMD primers were used for deducing the diversity at DNA level. The collection produced 102 bands out of which 97 were polymorphic and the percentage polymorphism ranged between 66.66 and 100 per primer. Discrete pattern of clustering was obtained using UPGMA method of complete linkage percent disagreement revealing high diversity among the collected accessions. Thus, the present study indicates that molecular and morphological marker map would improve our knowledge of S. edule and would facilitate efforts to breed improved S. edule cultivars.

Analysis of cold resistance and identification of SSR markers linked to cold resistance genes in Brassica rapa L.

Currently, cold temperatures are one of the main factors threatening rapeseed production worldwide; thus, it is imperative to identify cold-resistant germplasm and to cultivate cold-resistant rapeseed varieties. In this study, the cold resistance of four Brassica rapa varieties was analyzed. The cold resistance of Longyou6 and Longyou7 was better than that of Tianyou2 and Tianyou4. Thus, an F2 population derived from Longyou6 and Tianyou4 was used to study the correlation of cold resistance and physiological indexes. Our results showed that the degree of frost damage was related to the relative conductivity and MDA content (r1 = 0.558 and r2 = 0.447, respectively). In order to identify the markers related to cold resistance, 504 pairs of SSR (simple sequence repeats) primers were used to screen the two parents and F2 population. Four and five SSR markers had highly significant positive correlation to relative conductivity and MDA, respectively. In addition, three of these SSR markers had a highly significant positive correlation to both of these two indexes. These three SSR markers were subsequently confirmed to be used to distinguish between cold-resistant and non-cold-resistant varieties. The results of this study will lay a solid foundation for the mapping of cold-resistant genes and molecular markers assisted selection for the cold-resistance.

Mapping of molecular markers linked with MYMIV and yield attributing traits in mungbean

The present study employed recombinant inbred lines (RILs) derived from the cross between a susceptible cultivar Sonali and resistant wild relative of mungbean (Vigna radiata var. sublobota to map molecular markers linked with mungbean yellow mosaic Indian virus (MYMIV) resistance and yield attributing traits in mungbean. Resistance to the virus was evaluated in RIL population under field conditions during two consecutive years 2013 and 2014. A set of 224 molecular markers were employed for the identification of polymorphism between parents. Only 46 markers showed polymorphism between Sonali and V. radiata var. sublobota. Twenty two polymorphic markers were used to construct a linkage map comprising 11 linkage groups. QTL analysis identified molecular markers linked with MYMIV resistance and agronomic traits viz., no. of pods per plant, no. of seeds per pod and 100seed weight. Molecular markers identified to be linked with MYMIV were confirmed in 93 diverse mungbean accessions screened for yellow mosaic disease. The molecular markers linked to the MYMIV and yield attributing traits identified in this study will be useful in marker assisted breeding for development of high yielding mungbean varieties resistant to MYMIV.

<b>Mapping and validation of molecular markers of genes <i>Dt1</i> and <i>Dt2</i> to determine the type of stem growth in soybean

The type of stem growth in soybean is a distinguishing feature of cultivars. The genes Dt1 and Dt2 affect the termination of the stem, and the types of growth are classified as determinate, semi- determinate and indeterminate. Phenotypic characterization of the type of growth is complex and is occasionally erroneously described. The objective of this study was to map and validate molecular markers to classify the type of soybean growth to facilitate the description of cultivars and genotypic selection. Two populations were used for mapping and validation of molecular markers F2:3: T 117 (semi-determinate growth type) x Igra RA 518 RR (indeterminate growth type) and CD 235RR (determinate growth type) x Igra RA 518 RR. The study demonstrates that the association of the molecular marker with the gene GmTFL1b was efficient in the classification of soybean growth types. The marker sat_064 is connected to the Dt2 gene, which is located in the Liaison Group G of the consensus map of soybeans with a recombination frequency of 19.4%. Molecular markers for Dt1 and Dt2 genes efficiently described the genotypes of soybean stem growth and selection.

High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion

Tyramide FISH was used to locate relatively small genomic amplicons from molecular markers linked to Ms locus onto onion chromosome 2 near the centromere, a region of relatively low recombination. Fluorescence in situ hybridization (FISH) has not been readily exploited for physical mapping of molecular markers in plants due to the technical challenge of visualizing small single-copy probes. Signal amplification using tyramide (tyr) FISH can increase sensitivity up to 100-fold. We used tyr-FISH to physically locate molecular markers tightly linked to the nuclear male-fertility (Ms) restoration locus of onion onto mitotic metaphase, pachytene, and super-stretched pachytene chromosomes. Relatively short genomic amplicons (846-2251 bp) and a cDNA clone (666 bp) were visualized in 9-42 % of observed cells. The markers were assigned to proximal locations close to the centromere on the long arm of chromosome 2, a region of lower recombination, revealing that tightly linked markers may be physically distant from Ms. This result explains why several labs have identified molecular markers tightly linked to the Ms locus after screening relatively few DNA clones or primers and segregating progenies. Although these markers are still useful for marker-aided selection, our results indicate that map-based cloning of Ms will likely be difficult due to reduced recombination near this gene.

DEVELOPMENT OF THE WAGRHSNP AXIOM SNP ARRAY BASED ON SEQUENCES FROM TETRAPLOID CUT ROSES AND GARDEN ROSES

Rose, as many other important ornamental, vegetable and field crops, is polyploid. This poses constraints in genetic analyses due to the occurrence of multiple alleles at marker and trait loci and the existence of multiple allele dosages. Developments in marker discovery (next generation sequencing), detection (SNP arrays) and analysis (software for dosage scoring) now make it feasible to develop high-density molecular marker maps for the homologous chromosomes in tetraploids separately, and thus perform QTL analysis in tetraploids. We developed a SNP array for rose to develop genetic maps in tetraploid garden roses and cut roses, which are to be used for inheritance studies and genetic mapping. Here we have indicated the general strategy followed for developing a SNP array and for scoring and using the SNP data generated, and elaborated on the activities undertaken to use the WagRhSNP Axiom array in rose. The array design is not proprietary but can be used by all researchers working in rose

가축육종을 위한 유전체 선발의 새로운 접근(총설)

Selection based on phenotype in the traditional manner does not help in tracking the selected gene. Molecular genetics has revolutionized the old established breeding techniques. A new epoch of molecular markers has been acquainted for genetic improvement of livestock. This study is engaged on the neoteric molecular markers used in various fields of livestock. DNA markers are more encouraging in selecting genomes that have recombination events close to the target gene. Molecular markers rely on DNA assay and are better than the morphological and biochemical markers. In this study DNA-based molecular markers developed during the past decagons for animal genome analysis are reviewed. Mapping of molecular markers provide a framework, required for its subsequent use in the selection procedure. Molecular techniques help in the utilization of genetic variability in breeding population. At the same time livestock genomes play important role in human genomics and their role for understanding human genomics cannot be overlooked. Recently, in the epigenetic and transcriptomic studies, RNA sequencing as a part of next generation sequencing has revolutionized the approach and ongoing trends of analysis. Keeping in mind the goals, these molecular techniques can be implemented successfully by following well defined, crisp and integrated strategy.

A consensus map for Ug99 stem rust resistance loci in wheat.

Key message This consensus map of stem rust genes, QTLs, and molecular markers will facilitate the identification of new resistance genes and provide a resource of in formation for development of new markers for breeding wheat varieties resistant to Ug99. The global effort to identify new sources of resistance to wheat stem rust, caused by Puccinia graminis f. sp. tritici race group Ug99 has resulted in numerous studies reporting both qualitative genes and quantitative trait loci. The purpose of our study was to assemble all available information on loci associated with stem rust resistance from 21 recent studies on Triticum aestivum L. (bread wheat) and Triticum turgidum subsp. durum desf. (durum wheat). The software LPmerge was used to construct a stem rust resistance loci consensus wheat map with 1,433 markers incorporating Single Nucleotide Polymorphism, Diversity Arrays Technology, Genotyping-by-Sequencing as well as Simple Sequence Repeat marker information. Most of the markers associated with stem rust resistance have been identified in more than one population. Several loci identified in these populations map to the same regions with known Sr genes including Sr2, SrND643, Sr25 and Sr57 (Lr34/Yr18/Pm38), while other significant markers were located in chromosome regions where no Sr genes have been previously reported. This consensus map provides a comprehensive source of information on 141 stem rust resistance loci conferring resistance to stem rust Ug99 as well as linked markers for use in marker-assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-014-2326-7) contains supplementary material, which is available to authorized users.

Mapping of QTL for the seed storage proteins cruciferin and napin in a winter oilseed rape doubled haploid population and their inheritance in relation to other seed traits

Cruciferin (cru) and napin (nap) were negatively correlated and the cru/nap ratio was closely negative correlated with glucosinolate content indicating a link between the two biosynthetic pathways. Canola-type oilseed rape (Brassica napus L.) is an economically important oilseed crop in temperate zones. Apart from the oil, the canola protein shows potential as a value-added food and nutraceutical ingredient. The two major storage protein groups occurring in oilseed rape are the 2 S napins and 12 S cruciferins. The aim of the present study was to analyse the genetic variation and the inheritance of napin and cruciferin content of the seed protein in the winter oilseed rape doubled haploid population Express 617 × R53 and to determine correlations to other seed traits. Seed samples were obtained from field experiments performed in 2 years at two locations with two replicates in Germany. A previously developed molecular marker map of the DH population was used to map quantitative trait loci (QTL) of the relevant traits. The results indicated highly significant effects of the year and the genotype on napin and cruciferin content as well as on the ratio of cruciferin to napin. Heritabilities were comparatively high with 0.79 for napin and 0.77 for cruciferin. Napin and cruciferin showed a significant negative correlation (-0.36**) and a close negative correlation of the cru/nap ratio to glucosinolate content was observed (-0.81**). Three QTL for napin and two QTL for cruciferin were detected, together explaining 47 and 35 % of the phenotypic variance. A major QTL for glucosinolate content was detected on linkage group N19 whose confidence interval overlapped with QTL for napin and cruciferin content. Results indicate a relationship between seed protein composition and glucosinolate content.

Biotechnology of mulberry (Morus L.) - A review

Mulberry (Morus sp.) is one of the economically important trees grown in Asian countries. It is cultivated to provide leaves for feeding the caterpillars of the silk producing insect (Bombyx mori L.). In addition, it adds value through production of edible fruits, timber and several pharmaceutically important chemicals. Improvement of mulberry through conventional breeding is limited due to high heterozygosity and long generation period. Attempts have recently been made to complement conventional breeding with modern biotechnological tools such as plant tissue culture, recombinant DNA technology and molecular markers to facilitate mulberry genetic improvement. The techniques of tissue culture have grown considerably in mulberry and encompassed areas including micropropagation, plant regeneration from leaf discs, and screening for stress tolerance. Recently, genetic engineering was adopted to enhance drought and salt tolerance in mulberry using HVA1 and Osmotin genes. Molecular markers such as Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and simple sequence repeats (SSR) have been used for molecular characterization of mulberry germplasm, biodiversity analysis, genetic mapping and identification of molecular markers for growth and yield . However, still a number of issues such as resistance to fungal and bacterial diseases, combating infestation of pests and insects, and tolerance to drought and salinity are to be sorted out to achieve sustainable mulberry cultivation to meet the increasing demand of the silk industry. This review describes the developments of tissue culture, transgenesis and molecular markers in mulberry and highlights the current constraints and future prospects.

QTL mapping for important horticultural traits in pepper (Capsicum annuum L.)

Quantitative trait loci (QTLs) for plant height (PHT) and other yield-related traits including number of fruits per plant (NFP), ten fruits weight (TFW), fruit length (FL), fruit width (FW), total fruit weight (ToFW) and pericarp thickness (PT) were mapped in intraspecific advanced recombinant inbred line (RIL) populations of pepper. The RILs were evaluated for 2 years (F8 and F9) for plant height and seven other yield-related traits. Three types of molecular markers; simple sequence repeat (SSR), sequenced characterized amplified region (SCAR) and random amplified polymorphic DNA (RAPD)—were used to generate linkage maps. A total of 10 QTLs for yield-related traits were mapped on four linkage groups (LG). QTLs for plant height were mapped on LG5. The phenotypic contribution of these QTLs ranged from 8 % to 51 % in mean over environments. Out of 10 QTLs detected, nine were stable in both environments except the QTL for fruit length (Qfl.iivr.3.4) on LG3. The five QTLs; Qfw.iivr-2.1, Qtfw.iivr-2.1, Qtofw.iivr-2.1, Qnfp.iivr-2.1 and Qpt.iivr-2.1 were on the same marker interval on LG2 and one QTL, Qtofw.iivr-3.1 were tightly linked on LG3, which suggests that these genomic regions play an important role in enhancing pepper production. The genomic regions of all stable QTLs identified may serve as potential target regions for fine mapping and development of molecular markers for manipulation of yield and morphological traits in pepper.

Mapping of QTL for seed dormancy in a winter oilseed rape doubled haploid population

Following winter oilseed rape cultivation, considerable numbers of volunteer oilseed rape plants may occur in subsequent years in following crops. The appearance of volunteer oilseed rape plants is based on the capability of the seeds to become secondary dormant and to survive in this stage for many years in the soil. Genetic reduction of secondary seed dormancy in oilseed rape could provide a means to reduce the frequency of volunteer plants and especially the dispersal of transgenic oilseed rape. The objective of the present study was to analyse the inheritance of primary and secondary seed dormancy in a winter oilseed rape doubled haploid population derived from the cross Express 617×R53 and to study correlations to other seed traits. Field experiments were performed in Germany for 2years at two locations with two replicates. Seeds harvested from open pollinated plants were used for all analyses, including a laboratory test for seed dormancy. A previously developed molecular marker map of the doubled haploid population was used to map QTL of the relevant traits. For primary, secondary and total seed dormancy, the results showed significant effects of the genotypes and their interactions, with years and locations. Two, four and five QTL were detected for primary, secondary and total seed dormancy which explained 19, 35 and 42% of the phenotypic variance, respectively. Results show that secondary seed dormancy is a heritable trait and that selection for low secondary seed dormancy is possible.

A New Genetic Linkage Map of the Zygomycete Fungus Phycomyces blakesleeanus

Phycomyces blakesleeanus is a member of the subphylum Mucoromycotina. A genetic map was constructed from 121 progeny of a cross between two wild type isolates of P. blakesleeanus with 134 markers. The markers were mostly PCR-RFLPs. Markers were located on 46 scaffolds of the genome sequence, covering more than 97% of the genome. Analysis of the alleles in the progeny revealed nine or 12 linkage groups, depending on the log of the odds (LOD) score, across 1583.4 cM at LOD 5. The linkage groups were overlaid on previous mapping data from crosses between mutants, aided by new identification of the mutations in primary metabolism mutant strains. The molecular marker map, the phenotype map and the genome sequence are overall congruent, with some exceptions. The new genetic map provides a genome-wide estimate for recombination, with the average of 33.2 kb per cM. This frequency is one piece of evidence for meiosis during zygospore development in Mucoromycotina species. At the same time as meiosis, transmission of non-recombinant chromosomes is also evident in the mating process in Phycomyces. The new map provides scaffold ordering for the genome sequence and a platform upon which to identify the genes in mutants that are affected in traits of interest, such as carotene biosynthesis, phototropism or gravitropism, using positional cloning.

An Integrated Linkage, Chromosome, and Genome Map for the Yellow Fever Mosquito Aedes aegypti

Background Aedes aegypti, the yellow fever mosquito, is an efficient vector of arboviruses and a convenient model system for laboratory research. Extensive linkage mapping of morphological and molecular markers localized a number of quantitative trait loci (QTLs) related to the mosquito's ability to transmit various pathogens. However, linking the QTLs to Ae. aegypti chromosomes and genomic sequences has been challenging because of the poor quality of polytene chromosomes and the highly fragmented genome assembly for this species.Methodology/Principal FindingsBased on the approach developed in our previous study, we constructed idiograms for mitotic chromosomes of Ae. aegypti based on their banding patterns at early metaphase. These idiograms represent the first cytogenetic map developed for mitotic chromosomes of Ae. aegypti. One hundred bacterial artificial chromosome clones carrying major genetic markers were hybridized to the chromosomes using fluorescent in situ hybridization. As a result, QTLs related to the transmission of the filarioid nematode Brugia malayi, the avian malaria parasite Plasmodium gallinaceum, and the dengue virus, as well as sex determination locus and 183 Mbp of genomic sequences were anchored to the exact positions on Ae. aegypti chromosomes. A linear regression analysis demonstrated a good correlation between positions of the markers on the physical and linkage maps. As a result of the recombination rate variation along the chromosomes, 12 QTLs on the linkage map were combined into five major clusters of QTLs on the chromosome map.ConclusionThis study developed an integrated linkage, chromosome, and genome map—iMap—for the yellow fever mosquito. Our discovery of the localization of multiple QTLs in a few major chromosome clusters suggests a possibility that the transmission of various pathogens is controlled by the same genomic loci. Thus, the iMap will facilitate the identification of genomic determinants of traits responsible for susceptibility or refractoriness of the mosquito to diverse pathogens.

Integrating cereal genomics to support innovation in the Triticeae.

The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.

In Vitro Osmotic Stress Tolerance in Potato and Identification of Major QTLs

Identification of quantitative trait loci (QTL) responsible for stress tolerance could help to develop new tolerant potato cultivars through markers-assisted selection. The objective of the research was to identify and map loci that may play major role in the control of osmotic stress tolerance in potato under in vitro vegetative growth conditions. Mannitol-induced osmotic stress response of cv. White Lady and breeding line S440 as well as their 85F1 progeny for root number and root length under in vitro conditions was investigated. Interval mapping based on 200 informative markers produced a molecular marker map comprising 13 linkage groups for White Lady and 14 for S440. In total, 14 QTLs with LOD > 2 were identified from which 6 were confirmed as major QTLs. Of those six, three were associated with root length and three with root number. For root length, one major QTL was identified on chromosome XII (LOD = 4.8), which explained 52.3 % of the phenotypic variance. Two other major QTLs from an unidentified chromosome explained 64.9 and 51 % of the phenotypic variance with LODs of 5.34 and 4.8, respectively. For root number, one QTL with 19.2 % of the phenotypic variance (LOD of 2.9) was tentatively identified on chromosome IX, while another was putatively identified on chromosome XII (LOD of 2.4), together explaining 26.8 % of the phenotypic variance.

Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

BackgroundMolecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs) for any genomic regions. Here a sequence based polymorphic (SBP) marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described.ResultsA ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0) was obtained by applying Illumina's sequencing by synthesis (Solexa) technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0) genome sequence identified putative single nucleotide polymorphisms (SNPs) throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated.ConclusionsThe SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for cloning genes based on their genetic map positions and identifying tightly linked molecular markers for selecting desirable genotypes in animal and plant breeding experiments.