Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs,AFLPs and SSRs

In order to get an overview on the genetic relatedness of sorghum (Sorghum bicolor) landraces and cultivars grown in low-input conditions of small-scale farming systems, 46 sorghum accessions derived from Southern Africa were evaluated on the basis of amplified fragment length polymorphism (AFLPs), random amplified polymorphic DNAs (RAPDs) and simple sequence repeats (SSRs). By this approach all sorghum accessions were uniquely fingerprinted by all marker systems. Mean genetic similarity was estimated at 0.88 based on RAPDs, 0.85 using AFLPs and 0.31 based on SSRs. In addition to this, genetic distance based on SSR data was estimated at 57 according to a stepwise mutation model (Deltamu-SSR). All UPGMA-clusters showed a good fit to the similarity estimates (AFLPs: r = 0.92; RAPDs: r = 0.88; SSRs: r = 0.87; Deltamu-SSRs: r = 0.85). By UPGMA-clustering two main clusters were built on all marker systems comprising landraces on the one hand and newly developed varieties on the other hand. Further sub-groupings were not unequivocal. Genetic diversity (H, DI) was estimated on a similar level within landraces and breeding varieties. Comparing the three approaches to each other, RAPD and AFLP similarity indices were highly correlated (r = 0.81), while the Spearman's rank correlation coefficient between SSRs and AFLPs was r = 0.57 and r = 0.51 between RAPDs and SSRs. Applying a stepwise mutation model on the SSR data resulted in an intermediate correlation coefficient between Deltamu-SSRs and AFLPs (r = 0.66) and RAPDs ( r = 0.67), respectively, while SSRs and Deltamu-SSRs showed a lower correlation coefficient (r = 0.52). The highest bootstrap probabilities were found using AFLPs (56% on average) while SSR, Deltamu-SSR and RAPD-based similarity estimates had low mean bootstrap probabilities (24%, 27%, 30%, respectively). The coefficient of variation (CV) of the estimated genetic similarity decreased with an increasing number of bands and was lowest using AFLPs.     

Understanding ploidy complex and geographic origin of the Buchloe dactyloides genome using cytoplasmic and nuclear marker systems

Characterizing and inferring the buffalograss [Buchloe dactyloides (Nutt.) Engelm.] genome organization and its relationship to geographic distribution are among the purposes of the buffalograss breeding and genetics program. This buffalograss study was initiated to: (1) better understand the buffalograss ploidy complex using various marker systems representing nuclear and organelle genomes; (2) determine whether the geographic distribution was related to nuclear and organelle genome variation; and (3) compare the genetic structure of accessions with different ploidy levels. The 20 buffalograss genotypes (15 individuals from each genotype) that were studied included diploid, tetraploid, pentaploid, and hexaploid using nuclear (intersimple sequence repeat (ISSRs), simple sequence repeat (SSRs), sequence related amplified polymorphism (SRAPs), and random amplified polymorphic DNA (RAPDs)) and cytoplasmic markers (mtDNA and cpDNA). There was a significant correlation between the ploidy levels and number of alleles detected using nuclear DNA (ISSR, SSR, and SRAP, r=0.39, 0.39, and 0.41, P<0.05, respectively), but no significant correlation was detected when mitochondrial (r=0.17, P<0.05) and chloroplast (r=0.11, P<0.05) DNA data sets were used. The geographic distribution of buffalograss was not correlated with nuclear and organelle genome variation for the genotypes studied. Among the total populations sampled, regression analysis indicated that geographic distance could not explain genetic differences between accessions. However, genetic distances of those populations from the southern portion of buffalograss adaptation were significantly correlated with geographic distance (r= 0.48, P<0.05). This result supports the hypothesis that genetic relationship among buffalograss populations cannot be estimated based only on geographic proximity.     

Phylogenetic relationships among Portuguese rye based on isozyme, RAPD and ISSR markers

The phylogenetic relationships of 10 rye landraces and cultivars from the north of Portugal and from Brazil were analysed using 20 isozyme loci, and a total of 511 PCR markers (342 ISSRs and 169 RAPDs). The isozymes were analysed in at least 100 plants of each population/cultivar and, therefore, we have data about intra and inter population/cultivar genetic variability. However, the analyses with ISSRs and RAPDs were obtained using a mix of 25 plants of each population. Therefore, each population/cultivar was reduced to one tube and we have no data about intra genetic variability. As expected in a cross pollinated crop we found genetic diversity and a larger variation within than among the populations using isozymes. Somewhat unexpectedly, however, we found that the breeding cultivars have the same level of heterozygosity as the landraces. The phylogenetic relationships obtained using isozymes among the landraces, synthetic cultivar and the cultivars from breeding programs do not reflect their origin. Moreover, the cultivar from Brazil is not separated from the remaining populations/cultivars studied. However, the data observed using RAPDs and ISSRs are in agreement with their known origin. The populations maintained by the farmers in the north of Portugal are grouped in a cluster in the phenogram and the C902591 (from Brazil), the Alv?o (synthetic variety) and Larouco (a hybrid between Montalegre and Brazil) are in a different cluster. The ISSRs and RAPDs provide a rapid method for the production of polymorphic markers, which appear to correspond to known pedigree information.     

Molecular diversity and genetic relationships in <Emphasis Type="Italic">Secale</Emphasis>

The objective of this study was to quantify the molecular diversity and to determine the genetic relationships among Secale spp. and among cultivars of Secale cereale using RAPDs, ISSRs and sequence analysis of six exons of ScMATE1 gene. Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR primers. A total of 435 markers (242 RAPDs and 193 ISSRs) were obtained, with 293 being polymorphic (146 RAPDs and 147 ISSRs). Two RAPD and nine ISSR primers generated more than 80% of polymorphism. The ISSR markers were more polymorphic and informative than RAPDs. Further, 69% of the ISSR primers selected achieved at least 70% of DNA polymorphism. The study of six exons of the ScMATE1 gene also demonstrated a high genetic variability that subsists in Secale genus. One difference observed in exon 1 sequences from S. vavilovii seems to be correlated with Al sensitivity in this species. The genetic relationships obtained using RAPDs, ISSRs and exons of ScMATE1 gene were similar. S. ancestrale, S. kuprijanovii and S. cereale were grouped in the same cluster and S. segetale was in another cluster. S. vavilovii showed evidences of not being clearly an isolate species and having great intraspecific differences.     

Genetic Diversity and Population Differentiation of Liaoning Weedy Rice Detected by RAPD and SSR Markers

Weedy rice refers to populations of usually annual Oryza species that diminish farmer income through reduction of grain yield and lowered commodity value at harvest. The genetic diversity and population genetic structure of weedy rice in Liaoning Province were studied by RAPD and SSR markers. The results indicate that the level of genetic diversity of Liaoning weedy rice is very low, with polymorphic loci being only 3.70% (RAPDs) and 47.62% (SSRs). On the other hand, high genetic differentiation was found among populations, in particular between two regions (Shenyang and Dandong), with Fst values of 0.746 (RAPDs) and 0.656 (SSRs), suggesting that more than two thirds of the genetic variation resides among regions. Combined with our investigations of cultural traditions, the low level of genetic diversity in Liaoning Province is attributed to its narrow genetic background enhanced by exchanges of cultivar seeds, whereas the high genetic differentiation between the two regions is most likely the result of different founding parents and gene flow from local rice varieties to weedy rice. The rice cultivars in the two regions are all local varieties and are different genetically. A comparison of the two marker systems demonstrates that SSR is more informative and powerful in terms of the assessment of genetic variability, although both RAPD and SSR provide useful genetic information on weedy rice.     

A comparative assessment of molecular marker assays (AFLP, RAPD and SSR) for white yam (Dioscorea rotundata) germplasm characterization

Several DNA‐based marker systems are available for genetic fingerprinting of plants but information on their relative usefulness for yam germplasm characterisation is lacking. The efficiency of RAPD, AFLP and SSR markers for the assessment of genetic relationships, and for cultivar identification and discrimination among 45 West and Central African white yam cultivars belonging to 22 morphotypes/cultivar groups was investigated. Dendrograms were produced based on band pattern scores using the UPGMA method. Results showed that each of the three techniques could unequivocably identify each cultivar, but that techniques differed in the mean number of profiles generated per primer (or primer pair) per cultivar, referred to as genotype index (GI). The order of merit based on this criterion in this study was AFLPs (GI = 2.56), SSRs (GI = 0.39) and RAPDs (GI = 0.35). Yam genotypes classified in the same cultivar group based on morphology were often genetically different, emphasising the need for molecular fingerprinting in yam germplasm characterisation. AFLPs showed the highest efficiency in detecting polymorphism and revealed genetic relationships that most closely reflected morphological classification.     

Development of a second generation linkage map for almond using RAPD and SSR markers.

Fifty-four RAPD (random amplified polymorphic DNA) markers and 6 SSRs (simple sequence repeats) were included in a molecular marker map with 120 RFLPs (restriction fragment length polymorphisms) and 7 isozyme genes previously constructed using the offspring of a cross between the almond (Prunus amygdalus) cultivars 'Ferragnès' and 'Tuono'. Only highly reproducible RAPDs segregating 1:1 were used. To identify these markers, a total of 325 primers were screened, from which 41 produced RAPDs useful for mapping. Polymorphism was detected in six of the eight Prunus SSRs (simple sequence repeats) studied, thus enabling these to be mapped. All markers were placed on the 8 linkage groups previously identified. The number of new markers included in the map of 'Ferragnès' was 33 for a total of 126, and 30 in the map of 'Tuono' for a total of 99. The sizes of the maps of 'Ferragnès' (415 cM) and 'Tuono' (416 cM) were similar, representing a 5% increase over the maps constructed solely with isozymes and RFLPs. The estimated total size of the almond map was of 457 cM. Some markers were placed in zones with low density of markers and others in the extreme of linkage groups. The use of RAPD markers to complete genetic maps constructed with transferable markers is discussed.     

New genetic map of rye composed of PCR-based molecular markers and its alignment with the reference map of the DS2 × RXL10 intercross

A new genetic map of rye, developed by using the 541 x Ot1-3 F2 intercross, consists of 148 marker loci, including 99 RAPDs, 18 SSRs, 14 STSs, 9 SCARs and 7 ISSRs, and spans the distance of 1401.4 cM. To the 7 rye chromosomes, 8 linkage groups were assigned and compared with the reference map of the DS2 x RXL10 F2 intercross by using 24 common markers. The 2 combined maps contain altogether 611 marker loci (70-109 per chromosome) and constitute a substantial source of information useful for further genomic studies in rye. From 21 to 37 RAPD marker loci are distributed randomly along each chromosome length and their total number for all 7 rye chromosomes is 177. This abundance of RAPD marker loci in the rye genetic map can be exploited for development of SCARs in regions containing important genes or QTL.     

采用RAPD和ISSR标记研究古尔班通古特沙漠东南缘梭梭种群的遗传结构

梭梭(Haloxylon ammodendron(CA Mey.)Bunge)是一种沙漠旱生优势树种,具有重要的生态和经济价值,然而,我们对梭梭种群的遗传多样性和遗传结构所知甚少.本文采用RAPD和ISSR标记对来自古尔班通古特沙漠东南缘的4个天然梭梭种群的遗传多样性和遗传结构进行了检测.5个RAPD引物和8个ISSR引物分别扩增出61和195条带,多态性位点比率分别为83.6%和89.7%,Shannon信息指数分别为0.333和0.367,RAPD和ISSR分析均表明梭梭种群的遗传多样性水平较高.利用分子方差分析(AMOVA)研究梭梭种群的遗传结构,结果表明,大部分遗传变异存在于种群内,通过RAPD分析发现138.2%的遗传变异发生在种群内;通过ISSR分析发现89.4%的遗传变异发生在种群内;而种群间的遗传分化很小.通过RAPD标记没有检测到种群间的遗传分化,ISSR分析表明10.6%的遗传变异发生在种群内.我们推测梭梭种群较高的遗传多样性水平可能源于对异质、高胁迫环境的长期适应,但还需要进一步的研究加以证实.种群间遗传分异低的主要原因是种群间存在强大的基因流.     

Genetic diversity assessment of a germplasm collection of Salvia miltiorrhiza Bunge. based on morphology,ISSR and SRAP markers

Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants for its therapeutic effects. In the present study, morphological traits, ISSR (inter-simple sequence related) and SRAP (sequence-related amplified polymorphism) markers were used to analyze the genetic diversity of 59 S. miltiorrhiza phenotypes. Out of the 100 ISSR primers and 100 SRAP primer combinations screened, 13 ISSRs and 7 SRAPs were exploited to evaluate the level of polymorphism and discriminating capacity. The results showed that the 13 ISSRs generated 190 repeatable amplified bands, of which 177 (93.2%) were polymorphic, with an average of 13.6 polymorphic fragments per primer. The 7 SRAPs produced 286 repeatable amplified bands, of which 266 (93.4%) were polymorphic, with an average of 38.1 polymorphic fragments per primer. Cluster analysis readily separated different morphological accessions, wild and cultivated controls based on morphological traits, ISSR and SRAP markers. The study indicated that morphological traits, ISSR and SRAP markers were reliable and effective for assessing the genetic diversity of phenotypic S. miltiorrhiza accessions. The overall results suggested that the introduction of genetic variation from morphology-based germplasms enlarged the genetic base for the collection, conservation and further breeding program of S. miltiorrhiza germplasm.     

Comparative Analysis of Genetic Diversity Among Indian Populations of Scirpophaga incertulas by ISSR-PCR and RAPD-PCR

Genetic variation between 28 Indian populations of the rice pest, Scirpophaga incertulas was evaluated using inter-simple sequence repeats (ISSR)-PCR assay. Nine SSR primers gave rise to 79 amplification products of which 67 were polymorphic. A dendrogram constructed from this data indicates that there is no geographical bias to the clustering and that gene flow between populations appears to be relatively unrestricted, substantiating our earlier conclusion based on the RAPD (random amplified polymorphic DNA) data. The dendrograms obtained using each of these marker systems were poorly correlated with each other as determined by Mantel's test for matrix correlation. Estimates of expected heterozygosity and marker index for each of these marker systems suggests that both these marker systems are equally efficient in determining polymorphisms. Matrix correlation analyses suggest that reliable estimates of genetic variation among the S. incertulas pest populations can be obtained by using RAPDs alone or in combination with ISSRs, but ISSRs alone cannot be used for this purpose.     

Comparative study of the discriminating capacity of RAPD,AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive

RAPDs, AFLPs and SSRs were compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among 32 olive cultivars cultivated in Italy and Spain. SSRs presented a higher level of polymorphism and a greater information content, as assessed by the expected heterozygosity, than AFLPs and RAPDs. The lowest values of expected heterozygosity were obtained for AFLPs, which, nevertheless were the most efficient marker system due to their capacity to reveal the highest number of bands per reaction and because of the high values achieved for a considerable number of indexes. All three techniques discriminated the genotypes very effectively, but only SSRs were able to discriminate the cultivars Frantoio and Cellina. The correlation coefficients of similarity were statistically significant for all three marker systems used but were lower for the SSR data than for RAPDs and AFLPs. For all markers a high similarity in dendrogram topologies was obtained although some differences were observed. All the dendrograms, including that obtained by the combined use of all the marker data, reflect some relationships for most of the cultivars according to their geographic diffusion. AMOVA analysis detected greater genetic differentiation among cultivars within each country than it did between the two countries.Communicated by H.F. Linskens     

Molecular genetic diversity of the French-American grapevine hybrids cultivated in North America.

French-American hybrid grapevines are most popular in eastern and mid-western North America: they are hardy cultivars derived from crosses between the European Vitis vinifera and American wild vines. The aim of this study was to characterize their genetic background using 6 microsatellite (SSR) markers and a set of 33 diagnostic RAPD markers. The latter were reproducible with different PCR thermal cyclers. Two SSR loci were found to be synonymous, VrZAG47 and VVMD27. The DNA profile frequencies estimated for each cultivar were much lower with multi-locus SSR data than that obtained from multi-fragment RAPD data. There was no significant correlation between the multi-locus DNA profile frequencies derived from SSRs and those from RAPDs. Estimates of genetic diversity derived from SSRs were generally higher and the average similarity between cultivars was generally lower than values reported for subgroups of V. vinifera, in accordance with expectations for hybrid cultivars. The phenetic relationships depicted by UPGMA (unweighted pair-group method with arithmetic averaging) and neighbor-joining analyses of microsatellite data were congruent and, to a large extent, in agreement with the known pedigree or history of each cultivar. A major dichotomy was observed between one group where the known genetic background was dominated by the North American Vitis riparia and Vitis labrusca, and another one where the genetic background was dominated by the European V. vinifera. Two Kulhmann varieties thought to be synonymous were found to be different, though closely related.     

松花型花椰菜主要品种鉴定的分子标记分析

利用RAPD、ISSR和SRAP 3种分子标记对我国南方地区松花型花椰菜主栽品种进行鉴定,分析了品种间的遗传多样性。3种标记共产生370条扩增带,238条为多态性条带,其多态率为64.32%。其中只有SRAP标记的引物m e1/em1可将20个品种全部鉴别。遗传相似系数分析表明,松花型花椰菜品种之间的亲缘关系较近,遗传背景比较狭窄。聚类分析表明品种间的亲缘关系与熟性、地理分布相关。研究表明,分子标记能有效地应用于花椰菜品种鉴定,且综合多种分子标记分析品种间的遗传多样性将更加准确可靠。     

Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice

Computational screening of the chromosome-4 sequence of the rice cultivar Nipponbare (Oryza sativa L. japonica) revealed 1,844 tandem simple sequence repeats (SSRs) or microsatellites with SSR motifs 20 bp and repeated unit length of 1–6 base pairs. Thus SSRs occur once in every 18.8 kb, on the average, on the chromosome with one SSR per 23.8 kb and 16 kb on the short and long arms, respectively. No SSR was detected in the core region of the centromere. Poly(AT) _n repeats represented the most abundant and length polymorphic class of SSRs on the chromosome, but it did not occur in the exons. GC-rich trinucleotide repeats were most abundant in the coding regions, representing 71.69% of the SSRs identified in the exons. Two hundred and twenty four SSRs were associated with the repetitive DNA sequences, most of them were poly(AT) _n tracts. Sequence variations of SSRs between two cultivars, representing the two subspecies of the Asian cultivated rice indica and japonica, were identified, revealing that divergence and convergence of the two subspecies could be traced by the analysis of SSRs. These results provide a great opportunity for SSR-based marker development and comparative genome analysis of the two subspecies of the Asian cultivated rice.Electronic Supplementary Material Supplementary material is available in the online version of this article at .Communicated by Q. Zhang     

Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato

The application of AFLPs, RAPDs and SSRs to examine genetic relationships in the primary northwestern European cultivated potato gene pool was investigated. Sixteen potato cultivars were genotyped using five AFLP primer combinations, 14 RAPD primers, and 17 database-derived SSR primer pairs. All three approaches successfully discriminated between the 16 cultivars using a minimum of one assay. Similarity matrices produced for each marker type on the basis of Nei and Li coefficients showed low correlations when compared with different statistical tests. Dendrograms were produced from these data for each marker system. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, or EMR) and the amount of polymorphism detected (diversity index, or DI). AFLPs had the highest EMR, and SSRs the highest DI. A single parameter, marker index (MI), which is the product of DI and EMR, was used to evaluate the overall utility of each marker system. The use of these PCR-based marker systems in potato improvement and statutory applications is discussed.Abbreviations: PCR, polymerase chain reaction; AFLP, amplified fragment length polymorphism; RAPD, randomly amplified polymorphic DNA; DNA, deoxyribonucleic acid; EMR, effective multiplex ratio; DI, diversity index; MI, marker index; RFLP, restriction fragment length polymorphism.     

Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers

Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid (2n?=?2x?=?14), cool-season legume crop and is consumed worldwide as a rich source of protein (~24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F₂ plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil.     

Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean

Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs.     

Lack of genetic variation of an invasive clonal plant Eichhornia crassipes in China revealed by RAPD and ISSR markers

Random amplified polymorphic DNAs (RAPDs) and inter-simple sequence repeats (ISSRs) markers were used to analyze genetic structure of six populations of invasive plant Eichhornia crassipes that were sampled from its introduced regions in Southern China. Using 25 RAPD primers and 18 ISSR primers, 172 RAPD bands and 145 ISSR bands were produced respectively. But no polymorphic band was detected either within population or among populations by both markers, indicating the genetic diversity of E. crassipes in Southern China is extremely low, and all populations most likely consist of the same genotype. This study suggested that some other adaptability related factors, other than the genetic diversity, are responsible to the E. crassipes rapid expansion in China.     

An ultradense genetic recombination map for <Emphasis Type="Italic">Brassica napus</Emphasis>, consisting of 13551 SRAP markers

Sequence related amplified polymorphism (SRAP) was used to construct an ultradense genetic recombination map for a doubled haploid (DH) population in B. napus. A total of 1,634 primer combinations including 12 fluorescently labeled primers and 442 unlabeled ones produced 13,551 mapped SRAP markers. All these SRAPs were assembled in 1,055 bins that were placed onto 19 linkage groups. Ten of the nineteen linkage groups were assigned to the A genome and the remaining nine to the C genome on the basis of the differential SRAP PCR amplification in two DH lines of B. rapa and B. oleracea. Furthermore, all 19 linkage groups were assigned to their corresponding N1–N19 groups of B. napus by comparison with 55 SSR markers used to construct previous maps in this species. In total, 1,663 crossovers were detected, resulting in a map length span of 1604.8 cM. The marker density is 8.45 SRAPs per cM, and there could be more than one marker in 100 kb physical distance. There are four linkage groups in the A genome with more than 800 SRAP markers each, and three linkage groups in the C genome with more 1,000 SRAP markers each. Our studies suggest that a single SRAP map might be applicable to the three Brassica species, B. napus, B. oleracea and B. rapa. The use of this ultra high-density genetic recombination map in marker development and map-based gene cloning is discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.