BMC Genomics 2006, 7:283 http://www.biomedcentral.com/1471-2164/7/283 The marker order on 13 chromosomes (BTA 4, 10, 11, 13, 14, 16, 18, 21, 23, 24, 25, 27 and 28) is in very close agree- ment between the BovGen RH and MARC 2004 maps. For example, the order of the 27 markers on BTA 4 that are in common show only minor inversions of two pairs of linked loci: BMS1840 and MAF70 appear in different order and BMS2571 is located telomeric to BMS779 and BMS3002 on the BovGen RH map, but centromeric on the MARC 2004 genetic map (Figure 2). Despite the similarity the marker order as suggested by the MARC 2004 map is inconsistent with the multipoint map BovGen RH data. If the RH data is forced into the order of the MARC 2004 map a much lower probability for the map is obtained. Thus, in order to determine the true order of these markers additional information is required. On a further 13 chromosomes, minor discrepancies between these maps were observed. On BTA 3, 5, 8, 9, 12, 17, 19, 22 and X the order of markers is essentially the same, but with a number of individual markers at differ- ent positions. For BTA 1, 2, 6 and 26 differences were observed involving the orientation of groups of markers, but with a conserved order of markers within the group. For example, on BTA 26 the marker order is in general consistent between the BovGen RH and the MARC 2004 linkage map, however two small groups of linked markers 26_A (BMS882, TGLA429, BMS2567 and BM6041) and 26_B (MAF36, ILSTS091, MAF92 and BM804) have the same marker order in both maps, but are inverted with only one marker (BM7237) at a divergent position (Figure 3). On four chromosomes major inconsistencies are observed where groups of linked markers map to different chromo- somal positions (BTA 7, 29) or where the order of markers differs within several marker groups (e.g. BTA 7, 15 and 20). On BTA 7, for example, the position of two groups of linked markers 7_A (limited by the markers CSKB071 and TGLA303) and 7_B (limited by the markers BM6105 and BM2607) are exchanged. In addition the group 7_A is in a different orientation in both maps, while the marker order in 7_B is inconsistent (see Figure 4). Nevertheless, these discrepancies only involve about a quarter of the chromosome, and 12 out of the 38 common markers. The map positions of the other 26 markers are in close agree- ment between the two maps. These differences could be further investigated by comparison with additional map- ping information (see below). Comparison with the 6× bovine assembly Of the 3966 markers successfully included in the RH map, 2898 could be unequivocally assigned to a position in the Btau_2.0 bovine sequence, 2767 were assigned to the same chromosome, but 131 mapped on different chro- mosomes between the BovGen RH map and the sequence (Additional File 3). On seven chromosomes inconsistent assignments involving groups of three or more markers were observed (Table 2). On all but two chromosomes (BTA 9 and 14) there were many differences between the map order and the sequence: on many chromosomes large discrepancies involving groups of linked markers and/or large numbers of individual loci were seen, particularly on chromosomes 5, 7, 16, 22, 25 and 29. For example, on chromosome 7 two large groups of linked loci on the BovGen RH map locate to divergent positions in both the Btau_2.0 and MARC 2004 map, however, these latter two maps agree. This inconsistency is similar to an inconsistency observed between the BovGen RH and the MARC 2004 map, result- ing in a good agreement with the Btau_2.0 sequence (Fig- ure 4). Further information from the ILTX 2005 map does not help to resolve this inconsistency as there is only one marker in common with the BovGen RH map in this region. When markers that were at inconsistent positions between the BovGen RH and either the ILTX 2005 or MARC 2004 linkage map were removed, 150 common markers with the ILTX 2005 map and 771 common mark- ers with the MARC 2004 linkage map remained. The map- ping order of these markers was then compared with the order in the bovine sequence. The comparison with the Btau_2.0 sequence still revealed discrepancies across the whole genome. For example, on BTA 5 four markers which could be assigned to positions in the sequence assembly appeared to have inconsistent positions (AGLA293, ILSTS022, CSSM022, ILSTS066) when com- pared between the BovGen RH, the MARC 2004 and/or the ILTX 2005 map. After their removal the remaining cor- responding markers are in close agreement between the three maps but still reveal inconsistencies with the sequence assembly (Figure 5). Many of the markers which are in common between the BovGen RH map and Btau_2.0 are not present in the MARC 2004 map. These markers tend to have a higher inconsistency when com- pared to the sequence assembly. Discussion The ability to determine the order of close markers on genome maps differs between approaches, and all approaches, including the assembly of a whole genome sequence, are prone to errors. In some cases insufficient information is available to assign the correct order or posi- tioning of loci, while data errors can introduce distortions in the maps. The ultimate genome map of a species is the correctly ordered DNA sequence. Achieving the correct sequence assembly uses several sources of information. Sequence information from other species, including the human genome could be used as a template, but this Page 5 of 15 (page number not for citation purposes)