Abstract
Radiation hybrid (RH) mapping has become one of the most well-established techniques for economically and efficiently navigating genomes of interest. The success of the technique relies on random chromosome breakage of a target genome, which is then captured by recipient cells missing a preselected marker. Selection for hybrid cells that have DNA fragments bearing the marker of choice, plus a random set of DNA fragments from the initial irradiation, generates a set of cell lines that recapitulates the genome of the target organism several-fold. Markers or genes of interest are analyzed by PCR using DNA isolated from each cell line. Statistical tools are applied to determine both the linear order of markers on each chromosome, and the confidence of each placement. The resolution of the resulting map relies on many factors, most notably the degree of breakage from the initial radiation as well as the number of hybrid clones and mean retention value.
A high-resolution RH map of a genome derived from low pass or survey sequencing (coverage from 1 to 2 times) can provide essentially the same comparative data on gene order that is derived from high-coverage (greater than ×7) genome sequencing. When combined with fluorescence in situ hybridization, RH maps are complete and ordered blueprints for each chromosome. They give information about the relative order and spacing of genes and markers, and allow investigators to move between target and reference genomes, such as those of mouse or human, with ease although the approach is not limited to mammal genomes.
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References
Mellersh, C. S., Langston, A. A., Acland, G. M., et al. (1997) A linkage map of the canine genome. Genomics 46, 326–336.
Priat, C., Hitte, C., Vignaux, F., et al. (1998) A whole-genome radiation hybrid map of the dog genome. Genomics 54, 361–378.
Vignaux, F., Hitte, C., Priat, C., Chuat, J. C., Andre, C., and Galibert, F. (1999) Construction and optimization of a dog whole-genome radiation hybrid panel. Mamm. Genome 10, 888–894.
Mellersh, C. S., Hitte, C., Richman, M., et al. (2000) An integrated linkage-radiation hybrid map of the canine genome. Mamm. Genome 11, 120–130.
Ostrander, E. A. and Wayne, R. K. (2005) The canine genome. Genome Res. 15, 1831–1837.
Parker, H. G. and Ostrander, E. A. (2005) Canine genomics and genetics: running with the pack. PLoS Genet. 1(5).
Breen, M., Bullerdiek, J., and Langford, C. F. (1999) The DAPI banded karyotype of the domestic dog (Canis familiaris) generated using chromosome-specific paint probes. Chromosome Res. 7, 401–406.
Breen, M., Thomas, R., Binns, M. M., Carter, N. P., and Langford, C. F. (1999) Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog (Canis familiaris) and human. Genomics 61, 145–155.
Yang, F., O’Brien, P. C., Milne, B. S., et al. (1999) A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps. Genomics 62, 189–202.
Yang, F., Graphodatsky, A. S., O’Brien, P. C., et al. (2000) Reciprocal chromosome painting illuminates the history of genome evolution of the domestic cat, dog and human. Chromosome Res. 8, 393–404.
Breen, M., Langford, C. F., Carter, N. P., et al. (1999) FISH mapping and identification of canine chromosomes. J. Hered. 90, 27–30.
Breen, M., Jouquand, S., Renier, C., et al. (2001) Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/ linkage map of the domestic dog genome to all chromosomes. Genome Res. 11, 1784–1795.
Guyon, R., Lorentzen, T. D., Hitte, C., et al. (2003) A 1-Mb resolution radiation hybrid map of the canine genome. Proc. Natl Acad. Sci. USA 100, 5296–5301.
Guyon, R., Kirkness, E. F., Lorentzen, T. D., et al. (2003) Building comparative maps using 1.5× sequence coverage: human chromosome 1p and the canine genome. Cold Spring Harb. Symp. Quant. Biol. 68, 171–177.
Breen, M., Hitte, C., Lorentzen, T. D., et al. (2004) An integrated 4249 marker FISH/RH map of the canine genome. BMC Genomics 5, 1–11.
Hitte, C., Madeoy, J., Kirkness, E. F., et al. (2005) Survey sequencing combined with dense radiation hybrid gene mapping facilitates genome navigation. Nat. Rev. Genet. 6, 643–648.
Vignaux, F., Priat, C., Jouquand, S., et al. (1999) Toward a dog radiation hybrid map. J. Hered. 90, 62–67.
Matise, T. C., Perlin, M., and Chakravarti, A. (1994) Automated construction of genetic linkage maps using an expert system (MultiMap): a human genome linkage map. Nat. Genet. 6, 384–390.
Agarwala, R., Applegate, D. L., Maglott, D., Schuler, G. D., and Schaffer, A. A. (2000) A fast and scalable radiation hybrid map construction and integration strategy. Genome Res. 10, 350–364.
Hitte, C., Lorentzen, T., Guyon, R., et al. (2003) Comparison of the MultiMap and TSP/CONCORDE packages for constructing radiation hybrid maps. J. Hered. 94, 9–13.
Kirkness, E. F., Bafna, V., Halpern, A. L., et al. (2003) The dog genome: survey sequencing and comparative analysis. Science 301, 1898–1903.
Lindblad-Toh, K., Wade, C. M., Mikkelsen, T., et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803–819.
Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.
Margulies, E. H., Maduro, V. V., Thomas, P. J., et al. (2005) Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. Proc. Natl Acad. Sci. USA 102, 3354–3359.
Thomas, E. E. (2005) Short, local duplications in eukaryotic genomes. Curr. Opin. Genet. Dev. 15, 640–644.
Hardison, R. C. (2003) Comparative genomics. PLoS Biol. 1(2).
Senger, F., Priat, C., Hitte, C., et al. (2006) The first radiation hybrid map of a perch-like fish: The gilthead seabream (Sparus aurata L). Genomics 87, 793–800.
O’Brien, S. J., Womack, J. E., Lyons, L. A., et al. (1993) Anchored reference loci for comparative genome mapping in mammals. Nat. Genet. 3, 103–112.
Murphy, W. J., Larkin, D. M., Everts-van der Wind, A., et al. (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309, 613–617.
Boehnke, M., Lange, K., and Cox, D. R. (1991) Statistical methods for multipoint radiation hybrid mapping. Am. J. Hum. Genet. 49, 1174–1188.
Soderlund, C., Lau, T., and Deloukas, P. (1998) Z extensions to the RHMAPPER package. Bioinformatics 14, 538–539.
Schiex, T. and Gaspin, C. (1997) CARTHAGENE: constructing and joining maximum likelihood genetic maps. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5, 258–267.
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Hitte, C., Kirkness, E.F., Ostrander, E.A., Galibert, F. (2008). Survey Sequencing and Radiation Hybrid Mapping to Construct Comparative Maps. In: Murphy, W.J. (eds) Phylogenomics. Methods in Molecular Biology™, vol 422. Humana Press. https://doi.org/10.1007/978-1-59745-581-7_5
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DOI: https://doi.org/10.1007/978-1-59745-581-7_5
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