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Genome research2003; 13(4); 742-751; doi: 10.1101/gr.917503

The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes.

Abstract: A first-generation radiation hybrid (RH) map of the equine (Equus caballus) genome was assembled using 92 horse x hamster hybrid cell lines and 730 equine markers. The map is the first comprehensive framework map of the horse that (1) incorporates type I as well as type II markers, (2) integrates synteny, cytogenetic, and meiotic maps into a consensus map, and (3) provides the most detailed genome-wide information to date on the organization and comparative status of the equine genome. The 730 loci (258 type I and 472 type II) included in the final map are clustered in 101 RH groups distributed over all equine autosomes and the X chromosome. The overall marker retention frequency in the panel is approximately 21%, and the possibility of adding any new marker to the map is approximately 90%. On average, the mapped markers are distributed every 19 cR (4 Mb) of the equine genome--a significant improvement in resolution over previous maps. With 69 new FISH assignments, a total of 253 cytogenetically mapped loci physically anchor the RH map to various chromosomal segments. Synteny assignments of 39 gene loci complemented the RH mapping of 27 genes. The results added 12 new loci to the horse gene map. Lastly, comparison of the assembly of 447 equine genes (256 linearly ordered RH-mapped and additional 191 FISH-mapped) with the location of draft sequences of their human and mouse orthologs provides the most extensive horse-human and horse-mouse comparative map to date. We expect that the foundation established through this map will significantly facilitate rapid targeted expansion of the horse gene map and consequently, mapping and positional cloning of genes governing traits significant to the equine industry.
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Publication Date: 2003-04-03 PubMed ID: 12671008PubMed Central: PMC430160DOI: 10.1101/gr.917503Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research involves the construction of a first-generation radiation hybrid (RH) map of the horse (Equus caballus) genome, encompassing type I and II markers and integrating various other maps to offer detailed insights into the organization and comparative status of the equine genome, thus promoting further mapping and genes’ positional cloning.

Research Background and Methodology

  • This study created a radiation hybrid (RH) map, a tool used for locating existing genes and discovering new ones, for the equine (Equus caballus) genome. This was done using 92 hybrid cell lines, formed by fusing horse and hamster cells, and 730 markers relevant to horse genetics.
  • This research constitutes the first comprehensive framework map for the horse genome. The map incorporates type I (those related to characteristics expressed in the phenotype) and type II (those related to DNA sequence variations) markers.
  • The map integrates synteny (the physical co-localization of genetic loci on the same chromosome within an individual or species), cytogenetic (study of chromosomes), and meiotic (cell division that halves the number of chromosomes in reproductive cells) maps into a consensus map.

Results and Findings

  • The 730 loci, or fixed positions on the horse genome, included in the map are spread across all the horse’s autosomes (non-sex chromosomes) and the X chromosome.
  • The overall retention of markers in the panel is around 21%, which implies that the likelihood of adding any new marker to the map is about 90%.
  • On average, marker distribution is every 19 cR (centiRay; a measure of distance between genes) or 4 Mb of the equine genome. This is a considerable upgrade in resolution compared to earlier maps.
  • A total of 253 cytogenetically mapped loci, including 69 new Fluorescent in Situ Hybridization (FISH) assignments, physically anchor the RH map to various chromosomal segments.
  • Synteny assignments of 39 gene loci combined with the RH mapping of 27 genes add 12 new loci to the horse gene map.
  • The assembly comparison of 447 horse genes alongside draft sequences of their human and mouse equivalents provides an extensive comparative map, enriching our understanding of the genetic similarities and differences across these species.

Implications and Future Research

  • The foundation established by this map is expected to greatly boost the rapid targeted expansion of the horse gene map. This will facilitate mapping and positional cloning of genes, which involves identifying the location of disease-related genes based on their position in the genome.
  • The research could also potentially affect the understanding and manipulation of traits significant to the equine industry.

Cite This Article

APA
Chowdhary BP, Raudsepp T, Kata SR, Goh G, Millon LV, Allan V, Piumi F, Guérin G, Swinburne J, Binns M, Lear TL, Mickelson J, Murray J, Antczak DF, Womack JE, Skow LC. (2003). The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res, 13(4), 742-751. https://doi.org/10.1101/gr.917503

Publication

Genome research
ISSN: 1088-9051
NlmUniqueID: 9518021
Country: United States
Language: English
Volume: 13
Issue: 4
Pages: 742-751

Researcher Affiliations

Chowdhary, Bhanu P
  • Department of Veterinary Anatomy and Public Health, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA. bchowdhary@cvm.tamu.edu
Raudsepp, Terje
    Kata, Srinivas R
      Goh, Glenda
        Millon, Lee V
          Allan, Veronica
            Piumi, François
              Guérin, Gérard
                Swinburne, June
                  Binns, Matthew
                    Lear, Teri L
                      Mickelson, Jim
                        Murray, James
                          Antczak, Douglas F
                            Womack, James E
                              Skow, Loren C

                                MeSH Terms

                                • Animals
                                • Cell Line
                                • Conserved Sequence / genetics
                                • Cricetinae
                                • Genetic Markers / genetics
                                • Genetic Markers / radiation effects
                                • Genome
                                • Genome, Human
                                • Horses / genetics
                                • Humans
                                • Hybrid Cells
                                • In Situ Hybridization, Fluorescence / methods
                                • In Situ Hybridization, Fluorescence / statistics & numerical data
                                • In Situ Hybridization, Fluorescence / veterinary
                                • Mice
                                • Microsatellite Repeats / genetics
                                • Microsatellite Repeats / radiation effects
                                • Molecular Sequence Data
                                • Radiation Hybrid Mapping / methods
                                • Radiation Hybrid Mapping / statistics & numerical data
                                • Radiation Hybrid Mapping / veterinary
                                • Sequence Alignment / methods
                                • Sequence Alignment / statistics & numerical data
                                • Sequence Alignment / veterinary
                                • Statistical Distributions
                                • Synteny / genetics
                                • Synteny / radiation effects

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