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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 26 compared with the corresponding MARC 2004 linkage 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. Locations of discussed marker groups and their orientation are indicated by arrows. Distances on the BovGen RH map are scaled in cR, on the MARC 2004 map in cM.
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Figure 3: BovGen RH map of BTA 26 compared with the corresponding MARC 2004 linkage 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. Locations of discussed marker groups and their orientation are indicated by arrows. Distances on the BovGen RH map are scaled in cR, on the MARC 2004 map in cM.

Mentions: On a further 13 chromosomes, minor discrepancies between these maps were observed. On BTA 3, 5, 8, 9, 12, 17, 19, 22 and X the order of markers is essentially the same, but with a number of individual markers at different positions. For BTA 1, 2, 6 and 26 differences were observed involving the orientation of groups of markers, but with a conserved order of markers within the group. For example, on BTA 26 the marker order is in general consistent between the BovGen RH and the MARC 2004 linkage map, however two small groups of linked markers 26_A (BMS882, TGLA429, BMS2567 and BM6041) and 26_B (MAF36, ILSTS091, MAF92 and BM804) have the same marker order in both maps, but are inverted with only one marker (BM7237) at a divergent position (Figure 3).


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 26 compared with the corresponding MARC 2004 linkage 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. Locations of discussed marker groups and their orientation are indicated by arrows. Distances on the BovGen RH map are scaled in cR, on the MARC 2004 map in cM.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: BovGen RH map of BTA 26 compared with the corresponding MARC 2004 linkage 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. Locations of discussed marker groups and their orientation are indicated by arrows. Distances on the BovGen RH map are scaled in cR, on the MARC 2004 map in cM.
Mentions: On a further 13 chromosomes, minor discrepancies between these maps were observed. On BTA 3, 5, 8, 9, 12, 17, 19, 22 and X the order of markers is essentially the same, but with a number of individual markers at different positions. For BTA 1, 2, 6 and 26 differences were observed involving the orientation of groups of markers, but with a conserved order of markers within the group. For example, on BTA 26 the marker order is in general consistent between the BovGen RH and the MARC 2004 linkage map, however two small groups of linked markers 26_A (BMS882, TGLA429, BMS2567 and BM6041) and 26_B (MAF36, ILSTS091, MAF92 and BM804) have the same marker order in both maps, but are inverted with only one marker (BM7237) at a divergent position (Figure 3).

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