A. 1.5 1.0 0.5 0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 B. C. 1.5 1.0 0.5 0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 1.5 1.0 0.5 0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 Chutimanitsakun et al. BMC Genomics 2011, 12:4 http://www.biomedcentral.com/1471-2164/12/4 Page 4 of 13 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 Figure 1 Segregation distortion on chromosome 2H linkage maps in the Oregon Wolfe Barley mapping population. The results of mapping with two different data sets are shown in A) the OWB-2383 map + 463 RAD loci, B) the 436 RAD and morphological marker loci and C) the OWB-2383 map. The X axis represents map distance in cM and the Y axis represent -log of the c2 p-value for segregation distortion. A positive value means distortion in favor of OWB-D whereas a negative value means distortion in favor of OWB-R. Dashed lines represent significance thresholds at 0.05. Marker positions are represented as perpendicular lines to the X axis. observed in all maps at the equivalent positions con- firming that this was due to non-random distribution of alleles to haploid progeny and not to scoring errors. The pronounced segregation distortion on 2H is attributable to the ZEO locus, with selection against the “dwarfing” alleles of the dominant parent. Table 1 Summary of chromosome length in three linkage maps Linkage map Chromosome Total 1H OWB-2383* 158 OWB-2383 + 463RAD 158 RAD only 175 2H 188 188 158 3H 4H 5H 6H 7H 208 127 238 163 206 1288 208 127 238 163 204 1286 228 123 226 134 216 1260 *The OWB-2383 map was reported by Szűcs et al. [3]. Lengths (in Haldane cM) for linkage groups corresponding to barley chromosomes 1H - 7H of the Oregon Wolfe Barley mapping population. The presence of duplicate sets of lines in the OWB population provides an additional test for data quality. The members of each set were not identified as identical in previous iterations of the map (e.g. Costa et al. [19]) due to differences at loci that have been progressively removed from the data set based on quality control cri- teria. The lines within each subset are identical for the Illumina SNPs and all other loci included in the Szűcs et al. OWB map [3]. That the lines within each set are also identical for all RADs confirms the repeatability of the RAD genotyping assay and that the lines are identi- cal. The most likely explanation for the presence of these identical sets of lines in the population is that multiple haploids were inadvertently advanced from callus regenerated from a single embryo. Removal of the sets of identical lines reduces the mapping population size from 93 to 82. There are no differences in locus