A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers.
Abstract: To generate a domestic horse genome map we integrated synteny information for markers screened on a somatic cell hybrid (SCH) panel with published information for markers physically assigned to chromosomes. The mouse-horse SCH panel was established by fusing pSV2neo transformed primary horse fibroblasts to either RAG or LMTk mouse cells, followed by G418 antibiotic selection. For each of the 108 cell lines of the panel, we defined the presence or absence of 240 genetic markers by PCR, including 58 random amplified polymorphic DNA (RAPD) markers and 182 microsatellites. Thirty-three syntenic groups were defined, comprised of two to 26 markers with correlation coefficient (r) values ranging from 0.70 to 1.0. Based on significant correlation values with physically mapped microsatellite (type II) or gene (type I) markers, 22 syntenic groups were assigned to horse chromosomes (1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 15, 18, 19, 20, 21, 22, 23, 24, 26, 30, X and Y). The other 11 syntenic groups were provisionally assigned to the remaining chromosomes based on information provided by heterologous species painting probes and work in progress with type I markers.
Publication Date: 1999-03-02 PubMed ID: 10050277DOI: 10.1046/j.1365-2052.1999.00377.xGoogle Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The study outlines the process and results of creating a synteny map for the genome of a domestic horse. This involved the collection of synteny information for selected markers on a somatic cell hybrid (SCH) panel and markers physically assigned to chromosomes. This resulted in the definition of 33 syntenic groups and their subsequent assignment to particular horse chromosomes.
Mapping the Horse Genome
- The researchers embarked on a project to create a synteny map for the domestic horse. This means they sought to identify the physical locations of genetic markers within the horse’s chromosomes.
- The first step was to establish a mouse-horse somatic cell hybrid (SCH) panel. This was done by fusing transformed primary horse fibroblasts with either RAG or LMTk mouse cells, and then administering an antibiotic selection procedure.
- On each of the panel’s 108 cell lines, the presence or absence of 240 genetic markers were defined through the use of PCR. The markers comprised 58 random amplified polymorphic DNA (RAPD) markers and 182 microsatellites.
Creating Syntenic Groups
- The research identified 33 syntenic groups within the horse genome. These groups, which are sets of genetic markers located on the same chromosome, comprised between two to 26 markers each. Correlation coefficient values for these groups ranged between 0.70 and 1.0.
- The researchers were able to assign 22 of the syntenic groups to specific horse chromosomes due to significant correlation values with physically mapped microsatellite markers (type II) or gene markers (type I). These chromosomes numbered: 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 15, 18, 19, 20, 21, 22, 23, 24, 26, 30, X and Y.
- The remaining 11 syntenic groups were provisionally assigned to the outstanding chromosomes. This was based on the information gathered from heterologous species painting probes and ongoing work with type I markers.
Significance of the Study
- This research provides significant groundwork for the further exploration of the horse genome. Creating a synteny map of the genome facilitates the investigation of the chromosomal location of specific genes, the study of genetic linkage, and the understanding of genetic diseases in horses.
- The study also helps in further development and establishment of comparative genomics, by enhancing our understanding the organization and evolution of mammalian genomes through comparisons with the genomes of other species.
Cite This Article
APA
Shiue YL, Bickel LA, Caetano AR, Millon LV, Clark RS, Eggleston ML, Michelmore R, Bailey E, Guérin G, Godard S, Mickelson JR, Valberg SJ, Murray JD, Bowling AT.
(1999).
A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers.
Anim Genet, 30(1), 1-9.
https://doi.org/10.1046/j.1365-2052.1999.00377.x Publication
Researcher Affiliations
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis 95616-8744, USA.
MeSH Terms
- Animals
- Cell Fusion
- Cell Transformation, Viral
- Cells, Cultured
- Chromosome Mapping / veterinary
- Female
- Genetic Markers
- Genome
- Horses / genetics
- Male
- Mice
- Microsatellite Repeats
- Random Amplified Polymorphic DNA Technique / veterinary
- Simian virus 40
Citations
This article has been cited 8 times.- Finno CJ, Bannasch DL. Applied equine genetics. Equine Vet J 2014 Sep;46(5):538-44.
- Brinkmeyer-Langford C, Raudsepp T, Lee EJ, Goh G, Schäffer AA, Agarwala R, Wagner ML, Tozaki T, Skow LC, Womack JE, Mickelson JR, Chowdhary BP. A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals. Mamm Genome 2005 Aug;16(8):631-49.
- 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. The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res 2003 Apr;13(4):742-51.
- Lindgren G, Breen M, Godard S, Bowling A, Murray J, Scavone M, Skow L, Sandberg K, Guérin G, Binns M, Ellegren H. Mapping of 13 horse genes by fluorescence in-situ hybridization (FISH) and somatic cell hybrid analysis. Chromosome Res 2001;9(1):53-9.
- Shiue Y-L, Millon LV, Skow LC, Honeycutt D, Murray JD, Bowling AT. Synteny and regional marker order assignment of 26 type I and microsatellite markers to the horse X- and Y-chromosomes. Chromosome Res 2000;8(1):45-55.
- Caetano AR, Shiue YL, Lyons LA, O'Brien SJ, Laughlin TF, Bowling AT, Murray JD. A comparative gene map of the horse (Equus caballus). Genome Res 1999 Dec;9(12):1239-49.
- Birkhead TR, Martínez JG, Burke T, Froman DP. Sperm mobility determines the outcome of sperm competition in the domestic fowl. Proc Biol Sci 1999 Sep 7;266(1430):1759-64.
- Lindgren G, Sandberg K, Persson H, Marklund S, Breen M, Sandgren B, Carlstén J, Ellegren H. A primary male autosomal linkage map of the horse genome. Genome Res 1998 Sep;8(9):951-66.
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