BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 EFxigaumrpele2s of SNP data Examples of SNP data. A) Typical clustering of satisfac- tory data for POPA SNP 3_0004; red cluster area = homozygous AA, blue = homozygous BB, green dots within purple cluster area are 1:1 mixtures of parental DNA for three DH mapping populations. One germplasm sample (black dot) was outside of any call cluster and was thus scored "no call". B) Typical theta compressed data for POPA SNP 3_1104; although the polymorphism can be mapped in an individual population there are often wrong calls in such data and the cluster separation is problematic for general use in germplasm analyses or with multiple mapping populations; set to Gentrain 0.000, 100% "no call". C) Typical vertically separated clusters for POPA SNP 3_0070; generally poly- morphic for a different locus than the source of the targeted SNP, which results in wrong annotation and degraded syn- teny; set to Gentrain 0.000, 100% "no call". D) Data for POPA SNP 1_1166 (ABC07305-1-4-322) from the OWB population; two DH samples behave as heterozygotes (pur- ple cluster), far from the homozygotes (red = AA; blue = BB), instead with the 1:1 mixture of parental DNAs (green dot in purple cluster). markers range from 120 when including all maps except MxB to 321 when including all maps except HxO. The lower number of shared markers involving the HxO map is due to the fact that this population was genotyped using only BOPA1, whereas the other three populations were genotyped using all three Pilot OPAs (see Methods). Table S1 (Additional File 3) provides complete information on the map locations of all markers, where it can also be seen that there was no disagreement in the order of shared markers in any of the six pairwise comparisons of linkage maps, or between the consensus map and any individual map. It should be noted, however, that this does not guar- antee that the marker order in the 2943-SNP consensus map perfectly matches the order of the corresponding nucleotides within the genome sequence. The consensus map is simply one of many possible non-conflicting lin- ear representations of the consensus DAGs (Figure 4, Fig- ures S3-S9, Additional Files 6, 7, 8, 9, 10, 11 and 12). The limit of knowledge of non-shared marker order is more accurately shown in the consensus DAGs of each linkage group. As more data accumulate from additional mapping populations, linkage disequilibrium analyses and genome sequencing, the number of non-conflicting linear map orders will be reduced, ideally to just one possible order. Naturally, the consensus map will evolve toward finer res- olution and convergence on the correct order of all mark- ers. Segregation distortion was observed in all four mapping populations, being most pronounced in the MxB popula- tion in the pericentric regions of 1H, 2H, 5H and 7H and the long arm of 7H. Interestingly, on 7H the distortion was toward the maternal allele (Morex) in the pericentric region but toward the paternal allele (Barke) on the long arm. Alternative marker names Table S3 (Additional File 13) provides a cross-reference between synonymous marker names, relating SNPs mapped in the present work to the same genes mapped previously using other marker systems [3]. To generate this cross reference, all of the HarvEST:Barley assembly #35 unigenes (U35; Table S4, Additional File 14) were searched using BLASTN against the GrainGenes "Sequenced Probes" database http://wheat.pw.usda.gov/ GG2/index.shtml at a cut-off of 1e-10. Probes that matched more than three U35 unigenes were ignored. The result was 636 previously mapped probes matching 1114 unigenes. The list of probes was then reduced to those mapped in Marcel et al. [3] and the list of unigenes was limited to those which were sources of the 2943 mapped SNPs. Finally, the map position of the SNP and the previ- ously mapped probe were compared, discarding a few with gross mismatches in genome location (presumably paralogous loci mapped by the probe). The resulting intersection contains 55 SNPs representing 51 U35 uni- genes matching 51 sequenced probes. By comparing the map positions in Table S3 (Additional File 13) one can see that there is perfect co linearity of shared marker order between the two maps, though there are differences in map distances throughout each linkage group. There are no shared markers on 4HL, which illustrates the need for a more comprehensive cross-reference resource than just these two consensus maps. A similar operation can be per- formed to relate other maps to the present 2943 SNP map. It should be noted also that the original SNP names from SCRI ("ABC" format, Table S4, Additional File 14) corre- spond in many cases to SNPs used in Rostoks et al. [1] and the original SNP names from IPK ("ConsensusGBS" for- mat, Table S4, Additional File 14) correspond to SNPs in Kota et al. [12]. Thus, those two maps can be readily cross- referenced to the present map using in-common marker names. Also, as stated above, 110 bin markers from the Page 5 of 13 (page number not for citation purposes)