A High-Resolution Radiation Hybrid Map of Sheep Chromosome X and Comparison with Human and Cattle

Goldammer, Tom; Brunner, Ronald M.; Rebl, Alexander; Wu, Chunhua; Nomura, Kenta; Hadfield, Tracy; Gill, C. A.; Dalrymple, Brian P.; Womack, J. E.; Cockett, Noelle E.

doi:10.1159/000207520

Cited by 9 publications

(11 citation statements)

References 30 publications

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“…Almost the whole q-arm of the cattle X chromosome (BTAXq21-q43.2) covering the BTAX region from about 40 to 89 Mb in Btau build 4.0 shows a locus order inverted with respect to but otherwise similar to region Xp12-q31 in sheep (Dalrymple et al 2007;Goldammer et al 2009; http:// www.ncbi.nlm.nih.gov/; www.livestockgenomics. csiro.au/sheep/oar1.0.php).…”

Section: Resultsmentioning

confidence: 99%

“…BACs have been chosen both from the recently generated radiation hybrid map for OARX (Goldammer et al 2009) and from the virtual sheep OARX map (www.livestockgenomics. csiro.au/perl/gbrowse.cgi/vsheep1.2; Dalrymple et al 2007).…”

Section: Methodsmentioning

confidence: 99%

“…This increases the number of physical anchors for other existing sheep maps such as the virtual (virtual sheep genome browser version 1.2; Dalrymple et al 2007), linkage (Maddox et al 2001), and radiation hybrid (RH) maps (USUoRH5000 ovine whole genome radiation hybrid map; Goldammer et al 2009;Wu et al 2009). It also increases the usefulness of the OARX map for comparative mapping in domestic Bovidae so as to clarify the genome modifications between species and lead to a better understanding of X chromosome evolution in Bovidae.…”

Section: Introductionmentioning

confidence: 99%

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Cytogenetic anchoring of radiation hybrid and virtual maps of sheep chromosome X and comparison of X chromosomes in sheep, cattle, and human

Goldammer¹,

Brunner²,

Rebl³

et al. 2009

Chromosome Res

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A comprehensive physical map was generated for Ovis aries chromosome X (OARX) based on a cytogenomics approach. DNA probes were prepared from bacterial artificial chromosome (BAC) clones from the CHORI-243 sheep library and were assigned to G-banded metaphase spreads via fluorescence in-situ hybridization (FISH). A total of 22 BACs gave a single hybridization signal to the X chromosome and were assigned out of 32 tested. The positioned BACs contained 16 genes and a microsatellite marker which represent new cytogenetically mapped loci in the sheep genome. The gene and microsatellite loci serve to anchor between the existing radiation hybrid (RH) and virtual sheep genome (VSG) maps to the cytogenetic OARX map, whilst the BACs themselves also serve as anchors between the VSG and the cytogenetic maps. An additional 17 links between the RH and cytogenetic maps are provided by BAC end sequence (BES) derived markers that have also been positioned on the RH map. Comparison of the map orders for the cytogenetic, RH, and virtual maps reveals that the orders for the cytogenetic and RH maps are most similar, with only one locus, represented by BAC CH243-330E18, mapping to relatively different positions. Several discrepancies, including an inverted segment are found when comparing both the cytogenetic and RH maps with the virtual map. These discrepancies highlight the value of using physical mapping methods to inform the process of future in silico map construction. A detailed comparative analysis of sheep, human, and cattle mapping data allowed the construction of a comparative map that confirms and expands the knowledge about evolutionary conservation and break points between the X chromosomes of the three mammalian species.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Cytogenetic anchoring of radiation hybrid and virtual maps of sheep chromosome X and comparison of X chromosomes in sheep, cattle, and human

Goldammer¹,

Brunner²,

Rebl³

et al. 2009

Chromosome Res

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“…From an evolutionary point of view, the deleted part of BTAX corresponds to human Xq24-28 [Goldammer et al, 2009]. More precisely, the first gene present on the cattle Xp telomere is SLC6A14 (BTAX 733 kb), whereas the last gene in the Xpdel is GAB3 (BTAX 39,064 kb).…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterization of Xp Chromosome Deletion in a Fertile Cow

Lorenzi

Rossi²,

Genualdo³

et al. 2012

Sex Dev

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A young cow of the Marchigiana breed (central Italy) with normal body conformation and external genitalia underwent routine cytogenetic analyses prior to its use for reproduction. After normal chromosome staining, only one X chromosome was observed with a normal diploid number (2n = 60) in all 200 studied cells. Subsequent cytogenetic analyses by using both CBA- and RBA-banding techniques evidenced that almost all the p arms of the other X chromosome was lacking. Detailed FISH-mapping analyses with BAC covering this Xp arm region demonstrated that this large chromosome region was deleted. RBA-banding showed that the deleted X was late replicating. CGH array analysis evidenced that deletion involves the Xp arm from the telomere to around 39.5 Mb, referring to the BosTau6 cattle genome assembly. This abnormality deletes about 40 Mb of the X chromosome sequence, but, despite the large number of genes deleted, none of them are programmed to escape from inactivation. This can explain the normal phenotype of the female which is actually pregnant. Finally, we evidenced, by analysis of an SNP mapped to the deleted region (SNP rs29024121), that the only normal (e.g. nondeleted) X chromosome present derives from the father. Hence, the deletion has a maternal origin.

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“…Thus no attempt was made to resolve the small potential sheep specific rearrangements within chromosomes where the break points were ambiguous and there was not sufficient marker evidence to support a change in the organisation (Fig 3). The vsg 2.0 has been used in a number of analyses of the genome organisation of sheep and in general a high level of congruence with maps determined using other approaches has been observed (Drogemuller, et al, 2008;Wu, et al, 2008;Goldammer, et al, 2009c;Wu, et al, 2009), although the vsg 2 X chromosome build appears to contain a number of significant discrepancies (Goldammer, et al, 2009a;Goldammer, et al, 2009b …”

Section: Construction Of the Virtual Sheep Genome (Vsg20)mentioning

confidence: 95%

Using Bacterial Artificial Chromosomes to Refine Genome Assemblies and to Build Virtual Genomes

Ratnakumar¹,

Barris²,

McWilliam³

et al. 2011

Bioinformatics - Trends and Methodologies

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A High-Resolution Radiation Hybrid Map of Sheep Chromosome X and Comparison with Human and Cattle

Cited by 9 publications

References 30 publications

Cytogenetic anchoring of radiation hybrid and virtual maps of sheep chromosome X and comparison of X chromosomes in sheep, cattle, and human

Cytogenetic anchoring of radiation hybrid and virtual maps of sheep chromosome X and comparison of X chromosomes in sheep, cattle, and human

Molecular Characterization of Xp Chromosome Deletion in a Fertile Cow

Using Bacterial Artificial Chromosomes to Refine Genome Assemblies and to Build Virtual Genomes

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