BMC Genomics 2006, 7:283 http://www.biomedcentral.com/1471-2164/7/283 related loci and not the target locus. Of greater importance for the interpretation of the map information are incon- sistencies affecting whole groups of linked markers. To minimise the propagation of errors in individual maps we eliminated individual markers that were inconsistently placed between BovGen RH, ILTX 2005 and MARC 2004 maps from a further combined analysis against the sequence assembly. While the BovGen RH map is in general agreement with the ILTX map and the MARC 2004 map, there is poor agreement with the Btau_2.0 sequence at specific chromo- somal regions. In such regions, e.g. those described above on chromosomes 7, 25 and 29, the assembled Btau_2.0 sequence is most consistent with the linkage map. This is not surprising, because, among other sources of informa- tion, the MARC 2004 map was used to order the sequence scaffolds in Btau_2.0. Recalculating the BovGen data for these chromosomes and forcing the markers into the order they appear in the sequence assembly significantly increases the map length and reduces the probability showing that our data are not consistent with the sequence order. Further information must be generated to resolve such inconsistencies. Assignment of markers to different chromosomes A problem in the genome assembly is that of erroneous assignments of sequence scaffolds. By comparing assign- ments among the different RH and linkage maps [1,39,40] and also using comparative human [30,31,41- 45] or mouse [29] information, it seems likely that the assignment in the bovine assembly is most often at fault (Table 2). For example the markers PTK2B, BZ948637 and B4GALT1 (Table 2, case 4) are closely linked on the Bov- Gen RH map of BTA 8 and the linkage map of Barendse et al. [1] which also places these genes on BTA 8. This is also consistent with data from Fiedorek & Kay [29] who mapped PYK2B (alias PTK2B or Fadk) on murine chromo- some 15 and Inazawa et al. [30] who mapped the gene on human chromosome 8 at positions which share conserva- tion of synteny with BTA 8 [15]. However, these marker loci are placed on chromosome 5 in the Btau_2.0 sequence assembly. All three markers are located on a sin- gle sequence scaffold (chr5.80), suggesting that the chro- mosomal assignment of this scaffold is likely to be incorrect. A group of neighbouring markers formed by KIAA0284, Q9Y4F5, KNS2 and BTBD6 were assigned to BTA 11 on the BovGen RH map; however, this assignment is not con- sistent with other mapping data (Table 2, case 5). The human homologues of these loci are located on human chromosome 14 [31], suggesting that this group is cor- rectly assigned in the Btau_2.0 sequence to chromosome 21 and that in this case the BovGen RH assignment is incorrect. Nevertheless, the linkage of this group to other markers on BTA 11 is convincing with LOD linkage values up to 13.8 between the extreme marker KIAA0284 and the neighbouring markers on the BovGen RH map. If this marker group is tested with the markers located on BTA 21 using the BovGen RH datasets it shows no linkage. In the Btau_2.0 assembly this marker group is at an extreme tel- omeric position which suggests that the statistical support for this assignment is weak. This chromosomal assign- ment may have been made on the expected position derived from the supposed conservation of synteny between human and cattle chromosomes and should be tested using independent evidence. The markers BZ850749, CC517527 and CC471629 are assigned to BTA 14 on the BovGen RH map and to BTA 25 in the Btau_2.0 sequence assembly (Table 2, case 6). These markers are derived from BAC end sequences of clones from the CHORI-240 library and are not present on other maps. All these markers are assigned to the scaffold Chr25.84 and are in a chromosomal region of the assem- bly with a low density of corresponding markers. In con- trast on the BovGen RH map, the markers in the same region are at a higher density. This suggests that these markers are more tightly linked on the BovGen RH map. No further information is available to resolve this incon- sistency. Independent information is essential to produce the best maps of the bovine genome and to assemble the most accurate sequence. In addition to the RH mapping approach and linkage mapping that have been discussed here the refinement of the sequence should use additional sources of information such as BAC FPC maps, compara- tive mapping, fluorescent in situ hybridization, and somatic cell hybrid mapping. Conclusion There is reasonable consistency between the RH map pre- sented here, the MARC 2004 linkage map and the ILTX 2005 map. However, where the maps differed it is usually not possible to determine which order of markers is cor- rect. Manipulating the data to make the different maps match is not productive. When the major discrepancies are removed a number of inconsistencies with the Btau_2.0 bovine sequence assembly still remain. Using the various mapping information it is possible to identify potential errors in the assembly of the current bovine genome sequence which should be investigated further to aid the improvement of the next sequence build. Using the information presented here it will not be possi- ble to reach a final version of the sequence. The Btau_2.0 sequence assembly contains more than 100,000 scaffolds of which only 4409 are anchored to chromosomes using Page 11 of 15 (page number not for citation purposes)