Genomes and Genes
radiation hybrid mapping
Summary: A method for ordering genetic loci along CHROMOSOMES. The method involves fusing irradiated donor cells with host cells from another species. Following cell fusion, fragments of DNA from the irradiated cells become integrated into the chromosomes of the host cells. Molecular probing of DNA obtained from the fused cells is used to determine if two or more genetic loci are located within the same fragment of donor cell DNA.
- Demeure O, Pomp D, Milan D, Rothschild M, Tuggle C. Mapping of 443 porcine EST improves the comparative maps for SSC1 and SSC7 with the human genome. Anim Genet. 2005;36:381-9 pubmed..Our porcine/human comparative mapping results reveal possible new homologies for SSC1, SSC3, SSC5, SSC6, SSC12 and SSC14 and add markers in synteny breakpoints for chromosome 7. ..
- Roberts M, Hitte C, Hendrickson J, Hoffmann D, Flickinger G, Rutherford M, et al. Characterization and radiation hybrid mapping of expressed sequence tags from the canine brain. Mamm Genome. 2003;14:203-13 pubmed..This work has increased the number of gene-based markers on the canine RH map by approximately 30% and indicates the benefit to be gained by increasing the gene content of the current canine comparative map. ..
- Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, et al. A physical map of the 1-gigabase bread wheat chromosome 3B. Science. 2008;322:101-4 pubmed publisher..This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach. ..
- Cargill E, Paetzold L, Womack J. Radiation hybrid mapping and comparative sequence analysis of bovine RIG-I and MAVS genes. DNA Seq. 2006;17:314-8 pubmed..RIG-I exon 14 and partial MAYS exon five were conserved in all samples examined. One T-A transversion SNP was found in intronic sequence downstream of RIG-I exon 14. ..
- Du H, Chen J, Cui J, Zhang Y, Yerle M, Milan D, et al. Radiation hybrid mapping and sequence analysis of 21 genes on porcine chromosome 15. Anim Genet. 2006;37:181-3 pubmed
- Kurar E, Womack J, Kirkpatrick B. A radiation hybrid map of bovine chromosome 24 and comparative mapping with human chromosome 18. Anim Genet. 2003;34:198-204 pubmed..All genes located on BTA24 were located on human chromosome 18, and previously reported regions of conserved synteny were extended. The comparative data revealed the presence of at least six conserved regions between these chromosomes. ..
- Gao W, Chen Z, Yu J, Raska D, Kohel R, Womack J, et al. Wide-cross whole-genome radiation hybrid mapping of cotton (Gossypium hirsutum L.). Genetics. 2004;167:1317-29 pubmed..The results demonstrate not only the feasibility of WWRH panel construction and mapping, but also complementarity to traditional linkage mapping and cytogenetic methods. ..
- Sidjanin D, Miller B, Kijas J, McElwee J, Pillardy J, Malek J, et al. Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17. Genomics. 2003;81:138-48 pubmed..This order and orientation are preliminary, as high-throughput genomic sequencing of HSA17q-ter has not been fully completed. ..
- Chowdhary B, Raudsepp T, Kata S, Goh G, Millon L, Allan V, et al. The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res. 2003;13:742-51 pubmed
- Everts van der Wind A, Larkin D, Green C, Elliott J, Olmstead C, Chiu R, et al. A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci U S A. 2005;102:18526-31 pubmed
- Rink A, Eyer K, Roelofs B, Priest K, Sharkey Brockmeier K, Lekhong S, et al. Radiation hybrid map of the porcine genome comprising 2035 EST loci. Mamm Genome. 2006;17:878-85 pubmed
- Alexander L, Juneja B, Fahrenkrug S. Isolation and radiation hybrid mapping of 213 porcine microsatellites. Anim Genet. 2006;37:596-7 pubmed
- Schäffer A, Rice E, Cook W, Agarwala R. rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. Bioinformatics. 2007;23:1156-8 pubmed..tar.gz. CONCORDE modified for RH mapping is available in the directory http://www.isye.gatech.edu/~wcook/rh/. The QSopt library needed for CONCORDE is available at http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm ..
- Nonneman D, Smith T, Freking B, Rohrer G. Assignment of 12 genes to porcine chromosome 1 by linkage and radiation hybrid mapping. Anim Genet. 2005;36:532-3 pubmed
- Liu W, Eyer K, Yasue H, Roelofs B, Hiraiwa H, Shimogiri T, et al. A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17. Genomics. 2005;86:731-8 pubmed..A high-resolution SSC12 RH12,000-rad map will be useful in fine-mapping QTL and as a scaffold for sequencing this chromosome. ..
- Bosak N, Faraut T, Mikawa S, Uenishi H, Kiuchi S, Hiraiwa H, et al. Construction of a high-resolution comparative gene map between swine chromosome region 6q11-->q21 and human chromosome 19 q-arm by RH mapping of 51 genes. Cytogenet Genome Res. 2003;102:109-15 pubmed..For the ERF and PSMD8 genes assigned to SSCs other than SSC6, additional mapping using somatic cell hybrid (SCH) panels was performed to confirm the results of RH-mapping. ..
- McKay S, Schnabel R, Murdoch B, Aerts J, Gill C, Gao C, et al. Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping. Anim Genet. 2007;38:120-5 pubmed..0) in a fraction of the time it would have taken with conventional typing and genotyping methods. ..
- Leroux S, Dottax M, Bardes S, Vignoles F, Feve K, Pitel F, et al. Construction of a radiation hybrid map of chicken chromosome 2 and alignment to the chicken draft sequence. BMC Genomics. 2005;6:12 pubmed..The alignment of our RH map to the first draft of the chicken genome sequence assembly revealed a good agreement between both sets of data, indicative of a low error rate. ..
- Park C, Ahn S, Bloom J, Lin A, Wang R, Wu T, et al. Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids. Nat Genet. 2008;40:421-9 pubmed publisher..Further, this work identifies 2,761 trans ceQTLs harboring no known genes, and provides evidence for a mode of gene expression autoregulation specific to the X chromosome. ..
- Hossain K, Riera Lizarazu O, Kalavacharla V, Vales M, Maan S, Kianian S. Radiation hybrid mapping of the species cytoplasm-specific (scsae) gene in wheat. Genetics. 2004;168:415-23 pubmed..A radiation hybrid mapping population was developed from a hemizygous (lo) scsae--line using 35 krad gamma rays...
- Larkin D, Everts van der Wind A, Rebeiz M, Schweitzer P, Bachman S, Green C, et al. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res. 2003;13:1966-72 pubmed..The BAC clone-based comparative map provides a foundation for the evolutionary analysis of mammalian karyotypes and for sequencing of the cattle genome. ..
- Breen M, Hitte C, Lorentzen T, Thomas R, Cadieu E, Sabacan L, et al. An integrated 4249 marker FISH/RH map of the canine genome. BMC Genomics. 2004;5:65 pubmed..These results provide a necessary resource for the canine genome mapping community to undertake positional cloning experiments and provide new insights into the comparative canine-human genome maps. ..
- Leyva Baca I, Schenkel F, Sharma B, Jansen G, Karrow N. Identification of single nucleotide polymorphisms in the bovine CCL2, IL8, CCR2 and IL8RA genes and their association with health and production in Canadian Holsteins. Anim Genet. 2007;38:198-202 pubmed..04 +/- 0.02, P = 0.05), which might indicate a possible association in support of other published studies. Lastly, we assigned CCR2 to BTA22q24, where a previously QTL for SCS was identified. ..
- Liu Z, Hansen M, Womack J, Antoniou E. A comparative map of interstitial bovine chromosome 5 with human chromosomes 12 and 22. Cytogenet Genome Res. 2003;101:147-54 pubmed..Breakpoints of synteny are located with high accuracy. Overall, this work reveals widespread chromosomal rearrangements between bovine, human and mouse genomes. ..
- Pitel F, Abasht B, Morisson M, Crooijmans R, Vignoles F, Leroux S, et al. A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes. BMC Genomics. 2004;5:66 pubmed..Only two discrepancies were observed in relation to the sequence assembly recently reported for this chromosome. ..
- Yamada T, Taniguchi Y, Nishimura S, Yoshioka S, Takasuga A, Sugimoto Y, et al. Radiation hybrid mapping of genes showing intramuscular fat deposition-associated expression changes in bovine musculus longissimus muscle. Anim Genet. 2006;37:184-5 pubmed
- Genini S, Nguyen T, Malek M, Talbot R, Gebert S, Rohrer G, et al. Radiation hybrid mapping of 18 positional and physiological candidate genes for arthrogryposis multiplex congenita on porcine chromosome 5. Anim Genet. 2006;37:239-44 pubmed..2 on SSC5 correspond to HSA12p13 and HSA12q12. We identified seven distinct chromosomal blocks, further supporting extensive rearrangements between genes on HSA12 and HSA22 in the AMC region on SSC5...
- Hunter L, Sidjanin D, Johnson J, Zangerl B, Galibert F, Andre C, et al. Radiation hybrid mapping of cataract genes in the dog. Mol Vis. 2006;12:588-96 pubmed..Canine models can serve as large animal models intermediate between mouse and man for both gene discovery and the development of novel cataract therapies. ..
- Krushna Padhi B, Akimenko M, Ekker M. Independent expansion of the keratin gene family in teleostean fish and mammals: an insight from phylogenetic analysis and radiation hybrid mapping of keratin genes in zebrafish. Gene. 2006;368:37-45 pubmed..By comparative sequence analysis and radiation hybrid mapping, we identified 16 type I and 7 type II keratin genes in the zebrafish genome...
- Goldammer T, Kata S, Brunner R, Kuhn C, Weikard R, Womack J, et al. High-resolution comparative mapping between human chromosomes 4 and 8 and bovine chromosome 27 provides genes and segments serving as positional candidates for udder health in cattle. Genomics. 2004;84:696-706 pubmed..Defined evolutionary break points increase the accuracy of comparative in silico mapping of further human genes in conserved chromosome segments of BTA27. ..
- Wilder S, Bihoreau M, Argoud K, Watanabe T, Lathrop M, Gauguier D. Integration of the rat recombination and EST maps in the rat genomic sequence and comparative mapping analysis with the mouse genome. Genome Res. 2004;14:758-65 pubmed..The integration of rat linkage maps in the draft genomic sequence of the rat and that of other species represents an essential step for translating rat QTL intervals into human chromosomal targets. ..
- Hamasima N, Suzuki H, Mikawa A, Morozumi T, Plastow G, Mitsuhashi T. Construction of a new porcine whole-genome framework map using a radiation hybrid panel. Anim Genet. 2003;34:216-20 pubmed..6%. The total map length was 5596.2 centiRay (cR). Using an estimated physical length of 2718 Mbp, the average ratio between cR and physical distance over the porcine genome was estimated to be 0.49 Mb/cR. ..
- Weikard R, Goldammer T, Laurent P, Womack J, Kuehn C. A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits. BMC Genomics. 2006;7:53 pubmed..Furthermore, the high-resolution sequence-referenced BTA6 map will enable precise identification of multi-species conserved chromosome segments and evolutionary breakpoints in mammalian phylogenetic studies. ..
- Stafuzza N, Ianella P, Miziara M, Agarwala R, Schaffer A, Riggs P, et al. Preliminary radiation hybrid map for river buffalo chromosome 6 and comparison to bovine chromosome 3. Anim Genet. 2007;38:406-9 pubmed..Also, resources for positional candidate cloning in river buffalo are enhanced. ..
- Rabie T, Crooijmans R, Morisson M, Andryszkiewicz J, van der Poel J, Vignal A, et al. A radiation hybrid map of chicken Chromosome 4. Mamm Genome. 2004;15:560-9 pubmed..This enhanced comparative mapping resolution enabled the identification of multiple rearrangements between GGA4 and human Chromosomes 4q and Xp. ..
- Servin B, de Givry S, Faraut T. Statistical confidence measures for genome maps: application to the validation of genome assemblies. Bioinformatics. 2010;26:3035-42 pubmed publisher..Methods are implemented in two freely available softwares: Carthagene (http://www.inra.fr/mia/T/CarthaGene/) and a companion software (metamap, available at: http://snp.toulouse.inra.fr/~servin/index.cgi/Metamap). ..
- Riera Lizarazu O, Leonard J, Tiwari V, Kianian S. A method to produce radiation hybrids for the D-genome chromosomes of wheat (Triticum aestivum L.). Cytogenet Genome Res. 2010;129:234-40 pubmed publisher..On the other hand, the chromosomes from the D-genome are present in one copy (hemizygous) and allow radiation hybrid mapping of all D-genome chromosomes simultaneously...
- Miziara M, Goldammer T, Stafuzza N, Ianella P, Agarwala R, Schaffer A, et al. A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 1 (BBU1). Cytogenet Genome Res. 2007;119:100-4 pubmed..The BBU1 map provides a starting point for comparison of gene order rearrangements between river buffalo chromosome 1 and its bovine homologs. ..
- Lahbib Mansais Y, Karlskov Mortensen P, Mompart F, Milan D, Jørgensen C, Cirera S, et al. A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: identification of synteny breakpoints. Genomics. 2005;86:405-13 pubmed..The homology of the SSC17 pericentromeric region was extended to other human chromosomes (HSA4, HSA8) and the chromosomal breakpoint boundaries were accurately defined. In total 15 breakpoints were identified. ..
- Amaral M, Owens K, Elliott J, Fickey C, Schaffer A, Agarwala R, et al. Construction of a river buffalo (Bubalus bubalis) whole-genome radiation hybrid panel and preliminary RH mapping of chromosomes 3 and 10. Anim Genet. 2007;38:311-4 pubmed
- Morisson M, Leroux S, Jiguet Jiglaire C, Assaf S, Pitel F, Lagarrigue S, et al. A gene-based radiation hybrid map of chicken microchromosome 14: comparison to human and alignment to the assembled chicken sequence. Genet Sel Evol. 2005;37:229-51 pubmed..Finally, the alignment of the RH map to the assembled chicken sequence showed a small number of discordances, most of which involved the same region of the chromosome spanning between 40.5 and 75.9 cR(6000) on the RH map. ..
- Marques E, de Givry S, Stothard P, Murdoch B, Wang Z, Womack J, et al. A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly. BMC Genomics. 2007;8:254 pubmed..This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering. ..
- Goldammer T, Weikard R, Miziara M, Brunner R, Agarwala R, Schaffer A, et al. A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 7 and comparative mapping to the cattle and human genomes. Cytogenet Genome Res. 2007;119:235-41 pubmed publisher..The data obtained in our study define the evolutionarily conserved segment on BBU7 and HSA4 to be between 3.5 megabases (Mb) and 115.8 Mb in the HSA4 (genome build 36) DNA sequence...
- Lowe J, Kukekova A, Kirkness E, Langlois M, Aguirre G, Acland G, et al. Linkage mapping of the primary disease locus for collie eye anomaly. Genomics. 2003;82:86-95 pubmed..076), in a region corresponding to human chromosome 2q35. These results suggest the presence of a developmental regulatory gene important in ocular embryogenesis, with potential implications for other disorders of ocular vascularization. ..
- Douaud M, Feve K, Gerus M, Fillon V, Bardes S, Gourichon D, et al. Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping. BMC Genomics. 2008;9:129 pubmed publisher..The strategy used here for the characterization of GGA25 could be used to improve knowledge on the other uncharacterized small, yet gene-rich microchromosomes. ..
- Hitte C, Lorentzen T, Guyon R, Kim L, Cadieu E, Parker H, et al. Comparison of MultiMap and TSP/CONCORDE for constructing radiation hybrid maps. J Hered. 2003;94:9-13 pubmed
- Robic A, Faraut T, Iannuccelli N, Lahbib Mansais Y, Cantegrel V, Alexander L, et al. A new contribution to the integration of human and porcine genome maps: 623 new points of homology. Cytogenet Genome Res. 2003;102:100-8 pubmed..toulouse.inra.fr/lgc/pig/msat/). Moreover all conserved syntenic segments were defined on human chromosomes. ..
- Aldenhoven J, Spötter A, Distl O. Radiation hybrid mapping of 10 genes to porcine chromosomes. Anim Genet. 2005;36:540-2 pubmed
- Gautier M, Hayes H, Eggen A. A comprehensive radiation hybrid map of bovine Chromosome 26 (BTA26): comparative chromosomal organization between HSA10q and BTA26 and BTA28. Mamm Genome. 2003;14:711-21 pubmed..Finally, the INRA bovine BAC library was screened for most of the BTA26 markers considered in this study to provide anchors for the bovine physical map. ..
- Menotti Raymond M, David V, Agarwala R, Schaffer A, Stephens R, O Brien S, et al. Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome. Cytogenet Genome Res. 2003;102:272-6 pubmed..These resources can also be extended to the remaining 36 species of the cat family for population genetic and evolutionary genomic analyses. ..
- Connor E, Cates E, Williams J, Bannerman D. Cloning and radiation hybrid mapping of bovine toll-like receptor-4 (TLR-4) signaling molecules. Vet Immunol Immunopathol. 2006;112:302-8 pubmed..TOLLIP and TRAF 6 and to position these genes, as well as MyD88 and TICAM1, on the bovine genome using radiation hybrid mapping. Results of this work indicate differences with a previously published bovine sequence for LY96 and a ..