Evaluation of inter-simple sequence repeat analysis for mapping in Citrus and extension of the genetic linkage map

Inter-simple sequence repeat (ISSR) analysis was evaluated for its usefulness in generating markers to extend the genetic linkage map of Citrus using a backcross population previously mapped with restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD) and isozyme markers. ISSR markers were obtained through the simple technique of PCR followed by analysis on agarose gels, using simple sequence repeat (SSR) primers. Optimization of reaction conditions was achieved for 50% of the SSR primers screened, and the primers amplified reproducible polymorphic bands in the parents and progeny of the backcross population. Mendelian segregation of the polymorphic bands was demonstrated, with an insignificant number of skewed loci. Most of the SSR primers produced dominant loci; however co-dominance was observed with loci derived from three primers. A new genetic map was produced by combining the segregation data for the ISSR markers and data for the RFLP, RAPD and isozyme markers from the previous map and creating genetic linkages among all the markers using JoinMap 2.0 mapping software. The new map has an improved distribution of markers along the linkage groups with fewer gaps, and marker order showed partial or complete conservation in the linkage groups. The incorporation of ISSR markers into the genetic linkage map demonstrates that ISSR markers are suitable for genetic mapping in Citrus. Received: 3 February 2000 / Accepted: 12 May 2000     

Development of a large number of SSR and InDel markers and construction of a high-density genetic map based on a RIL population of pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.)

Capsicum annuum, the most widely cultivated species of pepper, is used worldwide for its important nutritional and medicinal values. The construction of an intraspecific high-density genetic linkage map would be of practical value for pepper breeding. However, the numbers of PCR-based simple sequence repeat (SSR) and insertion/deletion (InDel) markers that are available are limited, and there is a need to develop a saturated, intraspecific linkage map. The non-redundant Capsicum species’ expressed sequence tag (EST) database from the National Center for Biotechnology Information was used in this study to develop a total of 902 usable EST-SSR markers. Additionally, 177,587 SSR loci were identified based on the pepper genomic information, including 9182 SSR loci 500 bp both upstream and downstream of coding regions. Another 4497 stable and reliable InDel loci were also developed. From 9182 SSR and 4497 InDel loci, 3356 pairs of genomic SSR primers and 1400 pairs of InDel primers that were evenly distributed in 12 chromosomes were selected. A high-density intraspecific genetic map of C. annuum was constructed using the F₁₀-generation recombinant inbred line of parents PM702 and FS871 as the mapping population, screening the selected 3356 pairs of genomic SSR primers and 1400 pairs of InDel primers and the 902 EST-SSR markers developed earlier, and 524 published SSR markers and 299 orthologous markers (including 263 COSII markers and 36 tomato-derived markers) used previously to develop an interspecific genetic map (C. annuum × C. frutescens). Eventually, a high-density complete genetic intraspecific linkage map of C. annuum containing 12 linkage groups and 708 molecular markers with a length of 1260.00 cM and an average map distance of 1.78 cM was produced. This intraspecific, high-density, complete genetic linkage map of C. annuum contains the largest number of SSR and InDel markers and the highest amount of saturation so far, and it will be of considerable significance for the breeding of improved cultivars of this important field crop in the future.     

Simple sequence repeat map of the sunflower genome

Several independent molecular genetic linkage maps of varying density and completeness have been constructed for cultivated sunflower ( Helianthus annuus L.). Because of the dearth of sequence and probe-specific DNA markers in the public domain, the various genetic maps of sunflower have not been integrated and a single reference map has not emerged. Moreover, comparisons between maps have been confounded by multiple linkage group nomenclatures and the lack of common DNA markers. The goal of the present research was to construct a dense molecular genetic linkage map for sunflower using simple sequence repeat (SSR) markers. First, 879 SSR markers were developed by identifying 1,093 unique SSR sequences in the DNA sequences of 2,033 clones isolated from genomic DNA libraries enriched for (AC)(n) or (AG)(n) and screening 1,000 SSR primer pairs; 579 of the newly developed SSR markers (65.9% of the total) were polymorphic among four elite inbred lines (RHA280, RHA801, PHA and PHB). The genetic map was constructed using 94 RHA280 x RHA801 F(7) recombinant inbred lines (RILs) and 408 polymorphic SSR markers (462 SSR marker loci segregated in the mapping population). Of the latter, 459 coalesced into 17 linkage groups presumably corresponding to the 17 chromosomes in the haploid sunflower genome ( x = 17). The map was 1,368.3-cM long and had a mean density of 3.1 cM per locus. The SSR markers described herein supply a critical mass of DNA markers for constructing genetic maps of sunflower and create the basis for unifying and cross-referencing the multitude of genetic maps developed for wild and cultivated sunflowers.     

Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function.     

Distribution and characterization of simple sequence repeats in Gossypium raimondii genome

Simple sequence repeats (SSRs) can be derived from the complete genome sequence. These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop SSRs for cotton gene mapping, we selected the complete genome sequence of Gossypium raimondii, which consisted of 4447 non-redundant scaffolds. Out of 775.2 Mb sequence examined, a total of 136,345 microsatellites were identified with a density of 5.69 kb per SSR in the G. raimondii genome leading to development of 112,177 primer pairs. The distributions of SSRs in the genome were non-random. Among the different motifs ranging from 1 to 6 bp, penta-nucleotide repeats were most abundant (30.5%), followed by tetra-nucleotide repeats (18.2%) and di-nucleotide repeats (16.9%). Among all identified 457 motif types, the most frequently occurring repeat motifs were poly-AT/TA, which accounted for 79.8% of the total di-nt SSRs, followed by AAAT/TTTA with 51.5% of the total tetra-nucleotede. Further, 18,834 microsatellites were detected from the protein-coding genes, and the frequency of gene containing SSRs was 46.0% in 40,976 genes of G. raimondii. These genome-based SSRs developed in the present study will lay the groundwork for developing large numbers of SSR markers for genetic mapping, gene discovery, genetic diversity analysis, and MAS breeding in cotton.     

Construction of an SSR and RAD Marker-Based Genetic Linkage Map for Carnation (<Emphasis Type="Italic">Dianthus caryophyllus</Emphasis> L.)

A high-density genetic map, an essential tool for comparative genomic studies and quantitative trait locus fine mapping, can also facilitate genome sequence assembly. The sequence-based marker technology known as restriction site-associated DNA (RAD) enables synchronous, single nucleotide polymorphism marker discovery, and genotyping using massively parallel sequencing. We constructed a high-density linkage map for carnation (Dianthus caryophyllus L.) based on simple sequence repeat (SSR) markers in combination with RAD markers developed by double-digest RAD sequencing (ddRAD-seq). A total of 2404 (285 SSR and 2119 RAD) markers could be assigned to 15 linkage groups spanning 971.5 cM, with an average marker interval of 0.4 cM. The total length of scaffolds with identified map positions was 95.6 Mb, which is equivalent to 15.4 % of the estimated genome size. The generated map is the first SSR and RAD marker-based high-density linkage map reported for carnation. The ddRAD-seq pipeline developed in this study should also help accelerate genetic and genomics analyses and molecular breeding of carnation and other non-model crops.     

High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers

Kiwifruit (Actinidia chinensis Planchon) is an important specialty fruit crop that suffers from narrow genetic diversity stemming from recent global commercialization and limited cultivar improvement. Here, we present high-density RAD-seq-based genetic maps using an interspecific F₁ cross between Actinidia rufa ‘MT570001’ and A. chinensis ‘Guihai No4’. The A. rufa (maternal) map consists of 2,426 single-nucleotide polymorphism (SNP) markers with a total length of 2,651 cM in 29 linkage groups (LGs) corresponding to the 29 chromosomes. The A. chinensis (paternal) map consists of 4,214 SNP markers over 3,142 cM in 29 LGs. Using these maps, we were able to anchor an additional 440 scaffolds from the kiwifruit draft genome assembly. Kiwifruit is functionally dioecious, which presents unique challenges for breeding and production. Three sex-specific simple sequence repeats (SSR) markers can be used to accurately sex type male and female kiwifruit in breeding programmes. The sex-determination region (SDR) in kiwifruit was narrowed to a 1-Mb subtelomeric region on chromosome 25. Localizing the SDR will expedite the discovery of genes controlling carpel abortion in males and pollen sterility in females.     

Exploiting EST databases for the mining and characterization of short sequence repeat (SSR) markers in Catharanthus roseus L

Periwinkle (Catharanthus roseus L.) (Family: Apocyanaceae) is a ornamental plants with great medicinal properties. Although it is represented by seven species, little work has been carried out on its genetic characterization due to non-availability of reliable molecular markers. Simple sequence repeats (SSRs) have been widely applied as molecular markers in genetic studies. With the rapid increase in the deposition of nucleotide sequences in the public databases and advent of bioinformatics tools, it has become a cost effective and fast approach to scan for microsatellite repeats and exploit the possibility of converting it into potential genetic markers. Expressed sequence tags (EST's) from Catharanthus roseus were used for the screening of Class I (hyper variable) simple sequence repeats (SSR's). A total of 502 microsatellite repeats were detected from 21730 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs account to 1 SSR per 10.21 kb of EST. Mononucleotides was the most abundant class of microsatellite motifs. It accounted for 44.02% of the total, followed by the trinucleotide (26.09%) and dinucleotide repeats (14.34%). Among all the repeat motifs, (A/T)n accounted for the highest Proportion (36.25%) followed by (AAG)n. These detected SSRs can be used to design primers that have functional importance and should also facilitate the analysis of genetic diversity, variability, linkage mapping and evolutionary relationships in plants especially medicinal plants.     

Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation

Microsatellite or single sequence repeat (SSR) markers have been commonly used in genetic research in many crop species, including common bean (Phaseolus vulgaris L.). A limited number of existing SSR markers have been designed from high-throughput sequencing of the genome, warranting the exploitation of new SSR markers from genomic regions. In this paper, we sequenced total DNA from the genotype Hong Yundou with a 454-FLX pyrosequencer and found numerous SSR loci. Based on these, a large number of SSR markers were developed and 90 genomic-SSR markers with clear bands were tested for mapping and diversity detection. The new SSR markers proved to be highly polymorphic for molecular polymorphism, with an average polymorphism information content value of 0.44 in 131 Chinese genotypes and breeding lines, effective for distinguishing Andean and Mesoamerican genotypes. In addition, we integrated 85 primers of the 90 polymorphism markers into the bean map using an F2 segregating population derived from Hong Yundou crossed with Jingdou. The distribution of SSR markers among 11 chromosomes was not random and tended to cluster on the linkage map, with 14 new markers mapped on chromosome Pv01, whereas only four loci were located on chromosome Pv04. Overall, these new markers have potential for genetic mapping, genetic diversity studies and map-based cloning in common bean.     

Analysis of simple sequence repeats (SSRs)dynamics in fungus Fusarium graminearum

The abundance and inherent potential for variations in simple sequence repeats (SSRs) or microsatellites resulted in valuable source for genetic markers in eukaryotes. We describe the organization and abundance of SSRs in fungus Fusarium graminearum (causative agent for Fusarium head blight or head scab of wheat). We identified 1705 SSRs of various nucleotide repeat motifs in the sequence database of F. graminearum. It is observed that mononucleotide repeats (62%) were most abundant followed by di- (20%) and trinucleotide repeats (14%). It is noted that tetra-, penta- and hexanucleotide repeats accounted for only 4% of SSRs. The estimated frequency of Class I SSRs (perfect repeats ≥20 nucleotides) was one SSR per 124.5 kb, whereas the frequency of Class II (perfect repeats >10 nucleotides and ≫20 nucleotides) was one SSR per 25.6 kb. The dynamics of SSRs will be a powerful tool for taxonomic, phylogenetic, genome mapping and population genetic studies as SSR based markers show high levels of allelic variation, codominant inheritance and ease of analysis.     

Construction of a genetic linkage map using simple sequence repeat markers from expressed sequence tags for cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz)

Cassava (Manihot esculenta) is an economically important crop that is grown in tropical and sub-tropical regions. Use of molecular technology for genetic improvement of cassava has been limited by the lack of a large set of DNA markers and a genetic map. Therefore, the aims here were to develop additional simple sequence repeat (SSR) markers from the public expressed sequence tags (ESTs), and to construct a genetic linkage map. In this study, we designed 425 EST-SSR markers from sequences obtained from the cassava EST database in GenBank, and integrated them with 667 SSR markers from a microsatellite-enriched genomic sequence received from the International Center for Tropical Agriculture (CIAT). Of these, 107 EST-SSR and 500 genomic SSR primer pairs showed polymorphic patterns when screened in two cassava varieties, Hauy Bong 60 and Hanatee, which were used as female and male parental lines, respectively. Within the 107 and 500 primer pairs, 81 and 226 EST-SSR and SSR primer pairs were successfully genotyped with 100 samples of F₁ progeny, respectively. The results showed 20 linkage groups consisting of 211 markers—56 EST-SSR and 155 SSR markers—spanning 1,178 cM, with an average distance between markers of 5.6 cM and about 11 markers per linkage group. These novel EST-SSR markers provided genic PCR-based co-dominant markers that were useful, reliable and economical. The EST-SSRs were used together with SSR markers to construct the cassava genetic linkage map which will be useful for the identification of quantitative trait loci controlling the traits of interest in cassava breeding programs.     

A genetic map constructed using a doubled haploid population derived from two elite Chinese common wheat varieties

Genetic mapping provides a powerful tool for the analysis of quantitative trait loci (QTLs) at the genomic level.Herein,we report a new genetic linkage map developed from an F1-derived doubled haploid (DH) population of 168 lines,which was generated from the cross between two elite Chinese common wheat (Triticum aestivum L.) varieties,Huapei 3 and Yumai 57.The map contained 305 loci,represented by 283 simple sequence repeat (SSR) and 22 expressed sequence tag (EST)-SSR markers,which covered a total length of 2141.7 cM with an average distance of 7.02 cM between adjacent markers on the map.The chromosomal locations and map positions of 22 new SSR markers were determined,and were found to distribute on 14 linkage groups.Twenty SSR loci showed different chromosomal locations from those reported in other maps.Therefore,this map offers new information on the SSR markers of wheat.This genetic map provides new opportunities to detect and map QTLs controlling agronomically important traits.The unique features of this map are discussed.     

Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao

Theobroma cacao L. is a major cash crop for tropical countries, providing incomes for 14 million small farmers. Establishing sustainable disease resistance and maintaining cocoa qualities are among the major objectives of breeding programs. To enrich the high-density genetic map, useful for all cocoa genetic studies, with gene-based markers, a recently produced large EST resource was mined to develop expressed sequence tag-based simple sequence repeat markers (EST-SSRs) defined in genes with a putative known function. A set of 174 polymorphic EST-SSRs was identified from a selection of 314 non-redundant EST-SSRs with a putative known function. Of them, 115 loci were mapped on the cocoa reference map. This new map contains 582 codominant markers arranged in ten linkage groups corresponding to the haploid number of chromosomes. An average interval between markers of 1.3?cM was found, with approximately one SSR every 2?cM. This new set of EST-SSRs includes 14 candidate genes for plant resistance or cocoa qualities. The percentage of polymorphic SSRs varied depending on the different gene regions from which they originated, with respectively 54%, 69%, and 82% of polymorphic EST-SSRs originating from coding sequences, and from the non-coding untranslated 5??UTR and 3??UTR regions. This new map contains a set of 384 SSR markers that are easily transferable across different mapping populations and useful for all genetic analyses in T. cacao. The new set of EST-SSRs will be a useful tool for studying the functional diversity of populations and for carrying out association mapping studies.     

Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.)

In order to develop simple sequence repeat (SSR) markers in Italian ryegrass, we constructed a genomic library enriched for (CA)n-containing SSR repeats. A total of 1,544 clones were sequenced, of which 1,044 (67.6%) contained SSR motifs, and 395 unique clones were chosen for primer design. Three hundred and fifty-seven of these clones amplified products of the expected size in both parents of a two-way pseudo-testcross F₁ mapping population, and 260 primer pairs detected genetic polymorphism in the F₁ population. Genetic loci detected by a total of 218 primer pairs were assigned to locations on seven linkage groups, representing the seven chromosomes of the haploid Italian ryegrass karyotype. The SSR markers covered 887.8 cM of the female map and 795.8 cM of the male map. The average distance between two flanking SSR markers was 3.2 cM. The SSR markers developed in this study will be useful in cultivar discrimination, linkage analysis, and marker-assisted selection of Italian ryegrass and closely related species.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Construction of a high-density SNP genetic map in flue-cured tobacco based on SLAF-seq

Tobacco (Nicotiana tabacum L., 2n = 48) is an important agronomic crop and model plant. Flue-cured tobacco is the most important type and accounts for approximately 80 % of tobacco production worldwide. The low genetic diversity of flue-cured tobacco impedes the construction of a high-density genetic linkage map using simple sequence repeat (SSR) markers and warrants the exploitation of single nucleotide polymorphic (SNP) markers from genomic regions. In this article, initially using specific locus-amplified fragment sequencing, we discovered 10,891 SNPs that were subsequently used as molecular markers for genetic map construction. Combined with SSR markers, a final high-density genetic map was generated containing 4215 SNPs and 194 SSRs distributed on 24 linkage groups (LGs). The genetic map was 2662.43 cM in length, with an average distance of 0.60 cM between adjacent markers. Furthermore, by mapping the SNP markers to the ancestral genomes of Nicotiana tomentosiformis and Nicotiana sylvestris, a large number of genome rearrangements were identified as occurring after the polyploidization event. Finally, using this novel integrated map and mapping population, two major quantitative trait loci (QTLs) were identified for flue-curing and mapped to the LG6 of tobacco. This is the first report of SNP markers and a SNP-based linkage map being developed in tobacco. The high-density genetic map and QTLs related to tobacco curing will support gene/QTL fine mapping, genome sequence assembly and molecular breeding in tobacco.     

Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.)

We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines 'Lynx-037DH' and 'Monty-028DH'. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed.     

Simple sequence repeat genetic linkage maps of A-genome diploid cotton (Gossypium arboreum)

This study introduces the construction of the first intraspacific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat (SSR) markers using 189 F2 plants derived from the cross of two Asiatic parents were detected using 6 092 pairs of SSR primers. Two-hundred and sixty-eight pairs of SSR pdmers with better polymorphisms were picked out to analyze the F2 population. In total, 320 polymorphic bands were generated and used to construct a linkage map with JoinMap3.0. Two-hundred and sixty-seven loci, Including three phenotypic traits were mapped at a logarithms of odds ratio (LOD) ≥ 3.0 on 13 linkage groups. The total length of the map was 2 508.71 cM, and the average distance between adjacent markers was 9.40 cM. Chromosome assignments were according to the association of linkages with our backbone tetraploid specific map using the 89 similar SSR loci. Comparisons among the 13 suites of orthologous linkage groups revealed that the A-genome chromosomes are largely collinear with the At and Dt sub-genome chromosomes. Chromosomes associated with inversions suggested that allopolyploidization was accompanied by homologous chromosomal rearrangement. The inter-chromosomal duplicated loci supply molecular evidence that the A-genome diploid Asiatic cotton is paleopolyploid.     

SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz)

Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety 'Huay Bong 60' and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F(1) line mapping population was developed from the cross Huay Bong 60 by 'Hanatee'. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3?cM, distributed on 23 linkage groups with a mean distance between markers of 4.54?cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F(1) genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.     

A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping

Background

Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.

Results

High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology^® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman’s rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r² threshold = 0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.

Conclusions

The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-873) contains supplementary material, which is available to authorized users.