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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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Related in: MedlinePlus

BovGen RH map of BTA 14 compared with the ILTX 2005 map. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Lines between the maps connect markers common in both maps. For an improved legibility only marker names common in both maps are displayed. Distances on the BovGen RH map are scaled in cR, on the ILTX 2005 map in travelling salesman units (TSP).
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Figure 1: BovGen RH map of BTA 14 compared with the ILTX 2005 map. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Lines between the maps connect markers common in both maps. For an improved legibility only marker names common in both maps are displayed. Distances on the BovGen RH map are scaled in cR, on the ILTX 2005 map in travelling salesman units (TSP).

Mentions: Three chromosomes (BTA 19, 28 and 29) cannot be assessed for consistency of their order between the ILTX 2005 and BovGen RH map because they have no markers in common. For the remaining 27 chromosomes, 19 are consistent with the BovGen RH map. For example, the BovGen RH map of chromosome 14 has 9 markers in common with the ILTX 2005 map and the order agrees between maps (Figure 1). Out of the 27 chromosomes another 7 have one marker out of 3 to 9 corresponding loci inconsistently positioned. On BTA 8 there are marker order discrepancies between the maps involving 2 out of the 11 corresponding markers.


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 14 compared with the ILTX 2005 map. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Lines between the maps connect markers common in both maps. For an improved legibility only marker names common in both maps are displayed. Distances on the BovGen RH map are scaled in cR, on the ILTX 2005 map in travelling salesman units (TSP).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: BovGen RH map of BTA 14 compared with the ILTX 2005 map. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Lines between the maps connect markers common in both maps. For an improved legibility only marker names common in both maps are displayed. Distances on the BovGen RH map are scaled in cR, on the ILTX 2005 map in travelling salesman units (TSP).
Mentions: Three chromosomes (BTA 19, 28 and 29) cannot be assessed for consistency of their order between the ILTX 2005 and BovGen RH map because they have no markers in common. For the remaining 27 chromosomes, 19 are consistent with the BovGen RH map. For example, the BovGen RH map of chromosome 14 has 9 markers in common with the ILTX 2005 map and the order agrees between maps (Figure 1). Out of the 27 chromosomes another 7 have one marker out of 3 to 9 corresponding loci inconsistently positioned. On BTA 8 there are marker order discrepancies between the maps involving 2 out of the 11 corresponding markers.

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