1H 215 60 168 65 148 49 93 46 341 125 2H 279 72 235 73 217 57 131 65 485 161 3H 246 77 255 91 242 63 123 58 475 152 BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 Table 1: Distribution of SNPs in four individual maps and consensus map All 1652 443 1562 509 1270 396 732 362 2943 975 Chromosome 4H 141 39 211 60 130 49 97 48 338 113 5H 299 74 278 89 225 80 108 58 535 180 6H 219 54 202 64 122 40 92 40 352 111 7H 248 65 213 67 183 57 88 47 417 133 134.0 151.9 178.1 112.4 195.7 133.8 158.9 1064.9 145.4 181.0 199.3 121.8 231.1 152.3 186.7 1217.6 139.7 148.8 154.7 141.5 187.3 123.8 140.8 1036.6 145.2 162.6 162.7 124.5 176.4 123.0 182.5 1076.7 141.1 161.1 173.7 125.1 197.6 133.2 167.2 1099.0 Map Morex × Barke Oregon Wolfe Barley Count type markers bins cM markers Steptoe × Morex markers Haruna Nijo × OHU602 markers Consensus markers bins cM bins cM bins cM bins cM subdivided into the largest number of marker bins (180). On the lower end of the spectrum chromosome 4H has only 338 SNP loci distributed among 113 marker bins covering 125 cM. The relationship of nearly one marker bin per cM holds for all seven linkage groups. Once the SNP loci were arranged by position on the con- sensus map, graphical visualization enabled inspection of the distribution of recombination events. The genotype data and graphical genotype displays for three of the four mapping populations (MxB, OWB, SxM) are provided in Table S2 (Additional File 5), where it can be seen that there are no singleton double recombinant loci in densely marked regions of any of the maps. Since such loci are often indicative of genotyping errors, the complete absence of suspicious double recombinants can be con- sidered an indicator of high fidelity of the data from the 2943 SNP loci selected for linkage map production. Other quality metrics include the frequency of missing data or apparent heterozygosity; aside from two instances of apparent heterozygosity at locus 1_1166 in two seemingly identical OWB doubled haploid lines #22 and #70 (Figure 2D, Table S2, Additional File 5), all individuals in all three mapping populations had homozygous genotype calls for all loci and no missing data. This is 100% of 153,636 pos- sible genotype calls in the MxB population, 99.999% of 145,266 possible genotype calls in the OWB population and 100% of 116,840 possible genotype calls in the SxM population. The high fidelity and lack of missing data among these selected 2943 SNPs facilitated the produc- tion of individual and consensus maps. More than 300 SNPs with imperfect but still high quality data (for exam- ple 3_1104, Figure 2C) were not utilized for this map. Figure 3 illustrates the number of shared markers between any two, any three and all four maps. The substantial number of shared markers facilitated the production of a consensus map. The number of pairwise shared markers ranged from 303 between the HxO and OWB maps to 786 shared between the MxB and SxM maps. Three-way shared Page 4 of 13 (page number not for citation purposes)