BMC Genomics 2006, 7:283 http://www.biomedcentral.com/1471-2164/7/283 sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process. Results: An RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6× bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map. Conclusion: Alignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6× sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information. Background The global importance of cattle production has resulted in considerable efforts to detect the genes controlling varia- tions in economically important traits. This task is greatly facilitated by the availability of molecular markers ordered along chromosomes. In the last decade a number the bovine genome maps have been published, many of them based on genetic linkage between markers [1-3]. A major disadvantage of linkage maps is that only polymor- phic loci can be included, whereas, RH maps can be con- structed using sequence information from non- polymorphic loci. Therefore, RH maps potentially contain more coding loci than linkage maps facilitating compara- tive mapping across species. In contrast to linkage maps, which exploit the frequency of natural recombination between markers to calculate distances and orders of markers, RH maps are constructed using the probability of breaks between markers induced by radiation. Several whole genome radiation hybrid (WGRH) panels are avail- able for cattle that have been used to construct RH maps [4-8]. These RH maps have been used to create compara- tive maps between bovine and human chromosomes through the alignment of the loci derived from coding sequences [9-15]. The RH maps can also be integrated with other bovine physical maps such as BAC maps con- structed by fingerprinting methods by identifying the marker loci within e.g. BAC end sequences [16,17]. This additional mapping information facilitates the ordering of fingerprint contigs and the construction of physical BAC maps covering whole chromosomes. Such physical BAC maps provide a valuable starting point for genome sequencing [18-21]. Fingerprint contig BAC maps have been constructed for cattle using clones from the INRA BAC library [22] and the CHORI-240 BAC library [23]. The ultimate map for a species is the correctly assembled genome sequence. The bovine genome sequencing project started in 2003 and uses a combination of whole genome shotgun sequences (WGS) and sample sequencing of a minimum tiling path of BAC clones spanning the genome. The current, publicly available, bovine genomic sequence (Btau_2.0) has 6-fold genome coverage from WGS assembled into scaffolds and aligned on the chro- mosomes using limited mapping data. The use of RH and linkage map information [24] would greatly improve the genome sequence assembly [25]. Here we report a second generation RH map of the bovine genome which can be used to improve the construction of an integrated bovine genomic map. Sequences of the markers used to construct the map were aligned with the MARC 2004 linkage map and the Illinois-Texas (ILTX 2005) RH map [15] to investigate discrepancies. Loci that were unambiguously placed in all the maps were then aligned with the Btau_2.0 sequence to identify potential problems in the current sequence assembly. Results Radiation hybrid map 2735 markers were added to those on the first-generation RH map of Williams et al. [7], of which 2473 are newly mapped loci and 262 are previously reported AFLP mark- ers [26], giving a final total of 3966 markers (Table 1). The majority of the new markers, 1999, are within genes, 1072 are microsatellite loci, 262 AFLP markers, 376 BAC end sequences and 257 are from ESTs sequences that do not show convincing similarity to the annotated bovine sequence. The RH chromosome maps constructed from this data can be viewed and information downloaded from the ArkDB database [27]. The total length of the whole genome RH map, including all bovine autosomes and the X chromosome is 760 Rays (R). The map of BTA 28 is the shortest at 1141 cR and the longest is BTA 7 (4408 cR). The average marker interval, Page 2 of 15 (page number not for citation purposes)