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Comparative Study
. 2006 Nov 6:7:283.
doi: 10.1186/1471-2164-7-283.

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

Oliver C Jann  1 , Jan Aerts, Michelle Jones, Nicola Hastings, Andy Law, Stephanie McKay, Elisa Marques, Aparna Prasad, Jody Yu, Stephen S Moore, Sandrine Floriot, Marie-Françoise Mahé, André Eggen, Licia Silveri, Riccardo Negrini, Elisabetta Milanesi, Paolo Ajmone-Marsan, Alessio Valentini, Cinzia Marchitelli, Maria C Savarese, Michal Janitz, Ralf Herwig, Steffen Hennig, Chiara Gorni, Erin E Connor, Tad S Sonstegard, Timothy Smith, Cord Drögemüller, John L Williams
Affiliations
Comparative Study

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

Oliver C Jann et al. BMC Genomics. .

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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Figures

Figure 1
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).
Figure 2
Figure 2
BovGen RH map of BTA 4 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. Distances on the BovGen RH map are scaled in cR, on the MARC 2004 map in centimorgan (cM).
Figure 3
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.
Figure 4
Figure 4
BovGen RH map of BTA 7 (left) compared with the corresponding MARC 2004 linkage map and Btau_2.0 (right). 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 are marked and the orientation of the group 7_A indicated by arrows. Distances on the BovGen RH map are scaled in cR, on the MARC 2004 map in cM.
Figure 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.
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References

    1. Barendse W, Vaiman D, Kemp SJ, Sugimoto Y, Armitage SM, Williams JL, Sun HS, Eggen A, Agaba M, Aleyasin SA, Band M, Bishop MD, Buitkamp J, Byrne K, Collins F, Cooper L, Coppettiers W, Denys B, Drinkwater RD, Easterday K, Elduque C, Ennis S, Erhardt G, Ferretti L, Flavin N, Gao Q, Georges M, Gurung R, Harlizius B, Hawkins G, Hetzel J, Hirano T, Hulme D, Jorgensen C, Kessler M, Kirkpatrick BW, Konfortov B, Kostia S, Kuhn C, Lenstra JA, Leveziel H, Lewin H, Leyhe B, Lil L, Martin Burriel I, McGraw RA, Miller JR, Moody DE, Moore SS, Nakane S, Nijman IJ, Olsaker I, Pomp D, Rando A, Ron M, Shalom A, Teale AJ, Thieven U, Urquhart BGD, Vage DI, Van de Weghe A, Varvio S, Velmala R, Vilkki J, Weikard R, Woodside C, Womack JE. A medium-density genetic linkage map of the bovine genome. Mamm Genome. 1997;8:21–28. doi: 10.1007/s003359900340. Erratum in: Mamm Genome 1997, 8:798. - DOI - PubMed
    1. Kappes SM, Keele JW, Stone RT, McGraw RA, Sonstegard TS, Smith TP, Lopez-Corrales NL, Beattie CW. A second-generation linkage map of the bovine genome. Genome Res. 1997;7:235–249. - PubMed
    1. Ihara N, Takasuga A, Mizoshita K, Takeda H, Sugimoto M, Mizoguchi Y, Hirano T, Itoh T, Watanabe T, Reed KM, Snelling WM, Kappes SM, Beattie CW, Bennett GL, Sugimoto Y. A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Res. 2004;14:1987–1998. doi: 10.1101/gr.2741704. - DOI - PMC - PubMed
    1. Womack JE, Johnson JS, Owens EK, Rexroad CE, 3rd, Schlapfer J, Yang YP. A whole-genome radiation hybrid panel for bovine gene mapping. Mamm Genome. 1997;8:854–856. doi: 10.1007/s003359900593. - DOI - PubMed
    1. Rexroad CE, Schlapfer JS, Yang Y, Harlizius B, Womack JE. A radiation hybrid map of bovine chromosome one. Anim Genet. 1999;30:325–332. doi: 10.1046/j.1365-2052.1999.00504.x. - DOI - PubMed

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