BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. Conclusion: The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material. Background Complete genome sequences of many plants, including economically important small grain cereals such as barley, are unlikely to be available in the near future if they have large genomes and contain much repetitive DNA. The bar- ley genome is 5200 Mbp, which is more than twelve times rice, and composed of at least 80% highly repetitive DNA, which is likely to preclude a whole-genome assembly from shotgun sequences obtained with currently available technologies. However, access to most of the genes of bar- ley and numerous other organisms can be gained through cDNAs (generally expressed sequence tags; ESTs) and sequenced PCR amplicons, which provide a facile route to single nucleotide polymorphisms (SNPs) in protein- encoding transcribed genes. As of the January 2, 2009 release of dbEST, there were 525,527 Sanger-sequenced ESTs from barley. These were derived principally from eight malting barley cultivars and one wild barley acces- sion, with a minor fraction from several other barley gen- otypes. Here we describe the use of the majority of this transcriptome sequence resource to develop high- throughput SNP genotyping in barley, application of the new SNP methods to the production of a high-density and high quality SNP map that can be related readily to prior maps through shared markers and other grass genomes through synteny, and deployment of these new resources in support of marker-assisted breeding and association genetic analyses. In recent years there has been a surge in marker density and convergence toward consensus maps for barley. Ros- toks et al. [1] developed a consensus map containing 1230 markers (RFLP, AFLP, SSR, SNP) from three doubled haploid populations. Wenzl et al. [2] combined DArT with RFLP, SSR and STS from nine mapping populations to create a consensus map containing 2935 markers. Mar- cel et al. [3] compiled RFLP, AFLP and SSR data from six mapping populations to produce a consensus map con- taining 3458 markers. Stein et al. [4] used three doubled haploid mapping populations and combined new data from 1,055 markers (RFLP, SSR, SNP) with prior data from 200 anchor markers to produce a 1255 marker con- sensus map. Varshney et al. [5] produced a 775 SSR con- sensus map by joining six independent maps. Potokina et al. [6] combined SNP and other transcript derived mark- ers to position 1596 loci on the Steptoe × Morex [7] link- age map. Hearnden et al. [8] combined 1000 SSR and DArT markers on a map from a wide cross. Several addi- tional maps which have used portions of the SNP data described in the present work have been published or are nearing publication including a 2890 SNP and STS map from the Haruno Nijo × OUH602 population [9] and a 2383 marker map (DArT, SNP, SSR, AFLP, RFLP, STS, QTL) from the Oregon Wolfe Barley population [10], among others. Marker intersection between these maps is significant, but missing data, non-uniform data quality and anonymity of many markers constrain the accuracy of Page 2 of 13 (page number not for citation purposes)