BMC Genomics 2006, 7:283 http://www.biomedcentral.com/1471-2164/7/283 Table 2: Inconsistent chromosome assignments between the BovGen RH map and Btau_2.0 sequence. Only the seven most significant cases are listed, involving at least three linked markers. Case Markers involved Assignment Bodge RH BTA Assignment Btau_2.0 BTA Other assignments species, chromosome [reference] 1 2 3 4 5 6 7 BMS4030 BOVGEN_158 BOVGEN_91 MAF23 BZ855103 BZ864360 ADH7 ADH1A ADN1C PTK2B BZ948637 B4GALT1 KIAA0284 Q9Y4F5 KNS2 BTBD6 BZ850749 CC517527 CC471629 ACLY KLHL11 SC65 JUP E0362G17 1 5 6 8 11 14 19 4 4 21 5 21 25 23 BTA 1 [39] BTA 5 [40] HSA 4a [42, 42, 43] HSA 14a [31] - HSA 17a [44, 45] BTA 8 [1], MMU 15a [29], HSA 8a [30] a HSA 4 is a homologue to BTA 6, MMU 15 and HSA 8 to BTA 8, HSA 14 to BTA 21 and HSA 17 to BTA 19 [15]. Most likely assignments are indicated by bold font. approach should be treated with extreme caution as spe- cies specific variations are known [28]. Therefore, direct sequence information is used for the local assembly of shotgun sequence reads into contigs, and these contigs are then assembled into scaffolds using additional informa- tion, such as overlapping clones, and sequences from paired clone ends. The ordering of these scaffolds on chro- mosomes and assembly of the final sequence relies on additional mapping information, including BAC finger- print contig maps, linkage maps and RH maps. In this paper we describe an RH map with almost 4000 mapped loci which will contribute to the assembly of the bovine genome sequence. Comparison with other linkage and RH maps The consistency in ordering of common loci can be assessed across different maps, however, it is important that the information used when assembling the maps is independent, as circular arguments can give a false meas- ure of agreement. The approach of e.g. Itoh et al. [8] was to use the linkage map as template for their RH map; in contrast we did not use any prior information to construct the RH map presented here. This was because the aim was to assemble the most likely map using completely inde- pendent data and so not to propagate potential errors across different maps. Resolving these inconsistencies often requires the use of additional independent evidence such as BAC FPC mapping data or cytogenetic (fluorescent in-situ hybridisation, FISH) information. We carried out an alignment of the BovGen RH map with the other avail- able bovine genome maps and the Btau_2.0 sequence assembly, but only after the RH maps had been con- structed. While this approach relies on only one source of information it may not result in the "best" possible map, however, it avoids bias and the resulting independent map can then be used to develop a combined map which carries a measure of map confidence based on similarity and differences between maps. The BovGen and ILTX 2005 RH map appear to be more consistent with each other than with the MARC 2004 link- age map. Some inconsistencies between linkage and RH maps may be due to the different mapping approaches. However, the observation of the apparently higher con- sistency between the RH maps must be treated with care as the BovGen RH map has fewer loci in common with the ILTX 2005 map than with the MARC 2004 linkage map, and so fewer discrepancies could be detected. The ILTX 2005 map was constructed on the basis of the first-gener- ation map (ILTX 2004) by increasing the marker density and a subsequent rigorous removal of markers which did not pass a quality control procedure [15]. In this process a significant number of markers common to both the Bov- Gen RH and the ILTX 2004 map were removed and as a Page 9 of 15 (page number not for citation purposes)