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A second generation radiation hybrid map to aid the assembly of the bovine genome sequence.

Jann OC, Aerts J, Jones M, Hastings N, Law A, McKay S, Marques E, Prasad A, Yu J, Moore SS, Floriot S, Mahé MF, Eggen A, Silveri L, Negrini R, Milanesi E, Ajmone-Marsan P, Valentini A, Marchitelli C, Savarese MC, Janitz M, Herwig R, Hennig S, Gorni C, Connor EE, Sonstegard TS, Smith T, Drögemüller C, Williams JL - BMC Genomics (2006)

Bottom Line: 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.This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK. Oliver.Jann@bbsrc.ac.uk

ABSTRACT

Background: Several 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 6x 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.

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 6x 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 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

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BovGen RH map of BTA 5 compared with MARC 2004 (far left), Btau_2.0 (left), and the ILTX 2005 map (right). Only labels of corresponding markers of the MARC 2004 and ILTX 2005 map are displayed. Lines between the maps connect common markers. Correspondences of consistently ordered markers included in Btau_2.0 and BovGen RH are highlighted by dark blue. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Distances on the Btau_2.0 are scaled in Mbp. Distances on Btau_2.0 are scaled in Mbp, on the BovGen RH map in cR, on the MARC 2004 map in cM and on the ILTX 2005 map in TSP.
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Figure 5: BovGen RH map of BTA 5 compared with MARC 2004 (far left), Btau_2.0 (left), and the ILTX 2005 map (right). Only labels of corresponding markers of the MARC 2004 and ILTX 2005 map are displayed. Lines between the maps connect common markers. Correspondences of consistently ordered markers included in Btau_2.0 and BovGen RH are highlighted by dark blue. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Distances on the Btau_2.0 are scaled in Mbp. Distances on Btau_2.0 are scaled in Mbp, on the BovGen RH map in cR, on the MARC 2004 map in cM and on the ILTX 2005 map in TSP.

Mentions: 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 markers with the MARC 2004 linkage map remained. The mapping 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 compared between the BovGen RH, the MARC 2004 and/or the ILTX 2005 map. After their removal the remaining corresponding 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 compared to the sequence assembly.


A second generation radiation hybrid map to aid the assembly of the bovine genome sequence.

Jann OC, Aerts J, Jones M, Hastings N, Law A, McKay S, Marques E, Prasad A, Yu J, Moore SS, Floriot S, Mahé MF, Eggen A, Silveri L, Negrini R, Milanesi E, Ajmone-Marsan P, Valentini A, Marchitelli C, Savarese MC, Janitz M, Herwig R, Hennig S, Gorni C, Connor EE, Sonstegard TS, Smith T, Drögemüller C, Williams JL - BMC Genomics (2006)

BovGen RH map of BTA 5 compared with MARC 2004 (far left), Btau_2.0 (left), and the ILTX 2005 map (right). Only labels of corresponding markers of the MARC 2004 and ILTX 2005 map are displayed. Lines between the maps connect common markers. Correspondences of consistently ordered markers included in Btau_2.0 and BovGen RH are highlighted by dark blue. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Distances on the Btau_2.0 are scaled in Mbp. Distances on Btau_2.0 are scaled in Mbp, on the BovGen RH map in cR, on the MARC 2004 map in cM and on the ILTX 2005 map in TSP.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1636650&req=5

Figure 5: BovGen RH map of BTA 5 compared with MARC 2004 (far left), Btau_2.0 (left), and the ILTX 2005 map (right). Only labels of corresponding markers of the MARC 2004 and ILTX 2005 map are displayed. Lines between the maps connect common markers. Correspondences of consistently ordered markers included in Btau_2.0 and BovGen RH are highlighted by dark blue. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Distances on the Btau_2.0 are scaled in Mbp. Distances on Btau_2.0 are scaled in Mbp, on the BovGen RH map in cR, on the MARC 2004 map in cM and on the ILTX 2005 map in TSP.
Mentions: 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 markers with the MARC 2004 linkage map remained. The mapping 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 compared between the BovGen RH, the MARC 2004 and/or the ILTX 2005 map. After their removal the remaining corresponding 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 compared to the sequence assembly.

Bottom Line: 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.This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK. Oliver.Jann@bbsrc.ac.uk

ABSTRACT

Background: Several 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 6x 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.

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 6x 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 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

Show MeSH
Related in: MedlinePlus