A Radiation Hybrid Map of BTA23: Identification of a Chromosomal Rearrangement Leading to Separation of the Cattle MHC Class II Subregions

Band, Mark; Larson, Joshua H.; Womack, James E.; Lewin, Harris A.

doi:10.1006/geno.1998.5507

Cited by 55 publications

(43 citation statements)

References 42 publications

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“…Table 1; Barendse et al 1994Barendse et al , 1997Bishop et al 1994;Ma et al 1996;Kappes et al 1997). Optimization of the primers and PCR amplification using the RH 5000 panel was performed as described (Womack et al 1997;Band et al 1998;Band et al 2000).…”

Section: Methods Marker Selection and Mapping Strategymentioning

confidence: 99%

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

Wind¹,

Kata²,

Band³

et al. 2004

Genome Res.

138

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A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle–human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH5000 panel to 1913. Of these, 1463 have significant BLASTN hits (E < e–5) against the human genome sequence. A cattle–human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle–human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes.

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Section: Methods Marker Selection and Mapping Strategymentioning

confidence: 99%

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

Wind¹,

Kata²,

Band³

et al. 2004

Genome Res.

138

View full text Add to dashboard Cite

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“…Thus, the boundaries of conserved chromosomal segments are rather poorly defined, and very few genes are ordered reliably. The recent development of a whole genome cattle-hamster radiation hybrid (RH) panel (11) has fueled a new thrust in cattle genomics and comparative gene mapping (12)(13)(14)(15). However, mapping on the cattle RH panel has not progressed rapidly because of limited homologous DNA sequence information.…”

mentioning

confidence: 99%

“…All 56 markers were screened against a 5,000-rad whole genome RH panel in 20-l PCR reactions as described by Band et al (13). Annealing temperatures and extension times for PCRs are shown in Table 2.…”

mentioning

confidence: 99%

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Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping

Ozawa¹,

Band²,

Larson³

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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A whole genome cattle-hamster radiation hybrid cell panel was used to construct a map of 54 markers located on bovine chromosome 5 (BTA5). Of the 54 markers, 34 are microsatellites selected from the cattle linkage map and 20 are genes. Among the 20 mapped genes, 10 are new assignments that were made by using the comparative mapping by annotation and sequence similarity strategy. A LOD-3 radiation hybrid framework map consisting of 21 markers was constructed. The relatively low retention frequency of markers on this chromosome (19%) prevented unambiguous ordering of the other 33 markers. The length of the map is 398.7 cR, corresponding to a ratio of Ϸ2.8 cR 5,000͞cM. Type I genes were binned for comparison of gene order among cattle, humans, and mice. Multiple internal rearrangements within conserved syntenic groups were apparent upon comparison of gene order on BTA5 and HSA12 and HSA22. A similarly high number of rearrangements were observed between BTA5 and MMU6, MMU10, and MMU15. The detailed comparative map of BTA5 should facilitate identification of genes affecting economically important traits that have been mapped to this chromosome and should contribute to our understanding of mammalian chromosome evolution.radiation hybrid ͉ expressed sequence tag ͉ BTA5 ͉ HSA12

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“…A new strategy of comparative mapping by annotation and sequence similarity (COMPASS; ref. 18) has accelerated the comparative gene-mapping process (19,20). By using this approach, more than 1,000 markers were assigned and presented in a combined first generation cattle WGRH 5,000 and cattle͞human whole-genome comparative map (21).…”

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confidence: 99%

A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice

Goldammer

Kata²,

Brunner³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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A comprehensive radiation hybrid (RH) map and a high resolution comparative map of Bos taurus (BTA) chromosome 18 were constructed, composed of 103 markers and 76 markers, respectively, by using a cattle-hamster somatic hybrid cell panel and a 5,000 rad whole-genome radiation hybrid (WGRH) panel. These maps include 65 new assignments (56 genes, 3 expressed-sequence tags, 6 microsatellites) and integrate 38 markers from the first generation WGRH5,000 map of BTA18. Fifty-nine assignments of coding sequences were supported by somatic hybrid cell mapping to markers on BTA18. The total length of the comprehensive map was 1666 cR5,000. Break-point positions within the chromosome were refined and a new telomeric RH linkage group was established. Conserved synteny between cattle, human, and mouse was found for 76 genes of BTA18 and human chromosomes (HSA) 16 and 19 and for 34 cattle genes and mouse chromosomes (MMU) 7 and 8. The new RH map is potentially useful for the identification of candidate genes for economically important traits, contributes to the expansion of the existing BTA18 gene map, and provides new information about the chromosome evolution in cattle, humans, and mice.

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A Radiation Hybrid Map of BTA23: Identification of a Chromosomal Rearrangement Leading to Separation of the Cattle MHC Class II Subregions

Cited by 55 publications

References 42 publications

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping

A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice

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