BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 the map merging process and the resolution of synteny between barley and other genomes. Here we describe a new element of the map convergence equation, a high fidelity and dense consensus map produced entirely from transcribed gene SNPs using only a very robust portion of genotyping data derived from four mapping populations utilizing the Illumina GoldenGate assay (Illumina Inc., San Diego, CA). Maps that include SNPs in protein-cod- ing genes facilitate genome content comparisons by virtue of the high conservation of protein sequences across gen- era, thus enabling sequence similarity searches to find orthologs. The SNPs and data described herein have been made available incrementally in parallel with their pro- duction since mid-2005 to the barley community to facil- itate research. Here we provide full details of the development of the SNP genotyping platform and some of the insight it has brought. Results and Discussion Identification of SNPs and development of GoldenGate Assays Details of the identification of approximately 22,000 SNPs from EST and PCR amplicon sequence alignments, and development of three test phase and two production scale Illumina GoldenGate oligonucleotide pool assays (OPAs), are briefly summarized in Methods and provided more fully in Supplemental Text (Additional File 1). In total, 4596 SNPs were tested using 576 DNA samples on pilot OPAs POPA1 and POPA2, and 480 DNA samples on POPA3, followed by selection of 3072 technically satisfac- tory and genetically most informative SNPs for represen- tation on two production OPAs (BOPA1, BOPA2) (Figure 1). Of these 4596 SNPs, 3456 originated from ESTs and 1140 from PCR amplicons derived from genomic sequences. Of the 3072 SNPs selected for two production OPAs, 2279 were from ESTs and 793 from PCR ampli- cons. There was considerable intersection in the sets of SNPs provided by each identification path. For all OPAs preference was given to SNPs identified by amplicon sequencing. The final tally of surviving SNPs from each selection path included 65.9% (2279/3456) of the EST- derived and 69.6% (793/1140) of the PCR amplicon- derived SNPs. By this metric, the overall success rates were essentially equal for the two strategies for SNP discovery, ESTs versus genomic amplicon sequences. The yield of SNPs from each of 253 pairwise genotype alignments of ESTs (see Supplemental Text for SNP selec- tion details, Additional File 1) revealed a strong linear relationship (r2 = 0.84) between the number of SNPs and the product of the number of ESTs. For example, the ini- tial set of 36 pairwise genotype comparisons between eight malting barley cultivars and one wild barley acces- sion (used for POPA1 and POPA2) is provided in Figure S1, Additional File 2), where this linear relationship and PilotOPA1 1_xxxx PilotOPA2 2_xxxx PilotOPA3 3_xxxx 705 832 406 178 952 BarleyOPA1 11_xxxxx BarleyOPA2 12_xxxxx FFiivgeu1r5e316-plex GoldenGate assays Five 1536-plex GoldenGate assays. The numbers of SNPs selected from each Pilot OPA (POPA1, POPA2, POPA3) for the design of each production scale OPA (BOPA1, BOPA2) are indicted next to the arrows connect- ing the pilot and production OPAs. See Supplemental Text (Additional File 1) for complete details. the higher frequency of SNPs when including the wild barley accession are readily apparent. In retrospect, it was fortuitous for SNP discovery that researchers in each coun- try chose their own local favourite malting barley for EST sequencing. Genetic linkage maps For each of the four mapping populations the linkage groups separated cleanly using MSTMap (see Methods) at LOD 4 or 5 and generally remained intact at higher LOD values. The four maps from individual crosses were fused using MergeMap (see Methods) to form a consensus map containing 2943 SNP loci with a total map length of 1099 cM (Table 1). The identity and polarity of linkage groups were determined by integrating 110 previously mapped bin markers [11] into the SxM and consensus maps (Table S1, Additional File 3). Because the SNP data are more complete and seem generally to be of higher quality than the SxM bin marker data, the 2943 "SNP-only" map and its distance coordinates are taken as the central point of reference in this paper (Figure S2, Additional File 4). Table S1 (Additional File 3) provides map coordinates for each of the four individual maps, the SxM map with 110 bin markers, the 2943 SNP-only consensus map and the 3053 marker consensus map containing 2943 SNPs and 110 SxM bin markers. The number and distribution of loci for each individual SNP-only map and the consensus SNP- only map are given in Table 1. In all maps, chromosome 5H has the greatest length, a mean of 198 cM, consistent with previously published linkage maps. Chromosome 5H is also the most populated with 535 SNP loci and is Page 3 of 13 (page number not for citation purposes)