Abstract
BackgroundSeveral approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6× coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process.ResultsAn 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.ConclusionAlignment 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.
Highlights
Several approaches can be used to determine the order of loci on chromosomes and develop maps of the genome
The radiation hybrid (RH) chromosome maps constructed from this data can be viewed and information downloaded from the ArkDB database [27]
Distances on the BovGen RH map are scaled in cR, on the MARC 2004 map in cM
Summary
Several approaches can be used to determine the order of loci on chromosomes and develop maps of the genome. The global importance of cattle production has resulted in considerable efforts to detect the genes controlling variations in economically important traits This task is greatly facilitated by the availability of molecular markers ordered along chromosomes. Several whole genome radiation hybrid (WGRH) panels are available for cattle that have been used to construct RH maps [4,5,6,7,8] These RH maps have been used to create comparative maps between bovine and human chromosomes through the alignment of the loci derived from coding sequences [9,10,11,12,13,14,15]. This additional mapping information facilitates the ordering of fingerprint contigs and the construction of physical
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
