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Stout TAE. WR 'Twink' Allen: A career revolutionising the study and practice of equine reproduction. Equine Vet J 2021; 54:5-10. [PMID: 34877708 DOI: 10.1111/evj.13525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Tom A E Stout
- Department of Clinical Sciences, Utrecht University, Utrecht, The Netherlands
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Beeson SK, Mickelson JR, McCue ME. Exploration of fine-scale recombination rate variation in the domestic horse. Genome Res 2019; 29:1744-1752. [PMID: 31434677 PMCID: PMC6771410 DOI: 10.1101/gr.243311.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/15/2019] [Indexed: 01/17/2023]
Abstract
Total genetic map length and local recombination landscapes typically vary within and across populations. As a first step to understanding the recombination landscape in the domestic horse, we calculated population recombination rates and identified likely recombination hotspots using approximately 1.8 million SNP genotypes for 485 horses from 32 distinct breeds. The resulting breed-averaged recombination map spans 2.36 Gb and accounts for 2939.07 cM. Recombination hotspots occur once per 23.8 Mb on average and account for ∼9% of the physical map length. Regions with elevated recombination rates in the entire cohort were enriched for genes in pathways involving interaction with the environment: immune system processes (specifically, MHC class I and class II genes), responses to stimuli, and serotonin receptor pathways. We found significant correlations between differences in local recombination rates and population differentiation quantified by F ST Analysis of breed-specific maps revealed thousands of hotspot regions unique to particular breeds, as well as unique "coldspots," regions where a particular breed showed below-average recombination, whereas all other breeds had evidence of a hotspot. Finally, we identified relative enrichment (P = 5.88 × 10-27) for the in silico-predicted recognition motif for equine PR/SET domain 9 (PRDM9) in recombination hotspots. These results indicate that selective pressures and PRDM9 function contribute to variation in recombination rates across the domestic horse genome.
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Affiliation(s)
- Samantha K Beeson
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - James R Mickelson
- Veterinary and Biomedical Sciences Department, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Molly E McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota 55108, USA
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3
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Finno CJ, Bannasch DL. Applied equine genetics. Equine Vet J 2014; 46:538-44. [PMID: 24802051 DOI: 10.1111/evj.12294] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/27/2014] [Indexed: 01/13/2023]
Abstract
Genome sequencing of the domestic horse and subsequent advancements in the field of equine genomics have led to an explosion in the development of tools for mapping traits and diseases and evaluating gene expression. The objective of this review is to discuss the current progress in the field of equine genomics, with specific emphasis on assembly and analysis of the reference sequence and subsequent sequencing of a Quarter Horse mare; the genomic tools currently available to researchers and their implications in genomic investigations in the horse; the genomics of Mendelian and non-Mendelian traits; the genomics of performance traits and considerations regarding genetic testing in the horse. The whole-genome sequencing of a Quarter Horse mare has provided additional variants within the equine genome that extend past single nucleotide polymorphisms to include insertions/deletions and copy number variants. Equine single nucleotide polymorphism arrays have allowed for the investigation of both simple and complex genetic traits while DNA microarrays have provided a tool for examining gene expression across various tissues and with certain disease conditions. Recently, next-generation sequencing has become more affordable and both whole-genome DNA sequencing and transcriptome-wide RNA sequencing are methodologies that are being applied to equine genomic research. Research in the field of equine genomics continues to expand rapidly as the cost of genotyping and sequencing decreases, resulting in a need for quality bioinformatics software and expertise to appropriately handle both the size and complexity of these data.
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Affiliation(s)
- C J Finno
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, USA
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5
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Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies. Mol Phylogenet Evol 2012; 65:573-81. [DOI: 10.1016/j.ympev.2012.07.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 05/18/2012] [Accepted: 07/14/2012] [Indexed: 11/19/2022]
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Abstract
The objective of this review is to introduce equine clinicians to the rapidly evolving field of clinical genomics with a vision of improving the health and welfare of the domestic horse. For 15 years a consortium of veterinary geneticists and clinicians has worked together under the umbrella of The Horse Genome Project. This group, encompassing 22 laboratories in 12 countries, has made rapid progress, developing several iterations of linkage, physical and comparative gene maps of the horse with increasing levels of detail. In early 2006, the research was greatly facilitated when the US National Human Genome Research Institute of the National Institutes of Health added the horse to the list of mammalian species scheduled for whole genome sequencing. The genome of the domestic horse has now been sequenced and is available to researchers worldwide in publicly accessible databases. This achievement creates the potential for transformative change within the horse industry, particularly in the fields of internal medicine, sports medicine and reproduction. The genome sequence has enabled the development of new genome-wide tools and resources for studying inherited diseases of the horse. To date, researchers have identified 11 mutations causing 10 clinical syndromes in the horse. Testing is commercially available for all but one of these diseases. Future research will probably identify the genetic bases for other equine diseases, produce new diagnostic tests and generate novel therapeutics for some of these conditions. This will enable equine clinicians to play a critical role in ensuring the thoughtful and appropriate application of this knowledge as they assist clients with breeding and clinical decision-making.
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Affiliation(s)
- M M Brosnahan
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, New York, USA
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7
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Lucas ZL, McLoughlin PD, Coltman DW, Barber C. Multiscale analysis reveals restricted gene flow and a linear gradient in heterozygosity for an island population of feral horses. CAN J ZOOL 2009. [DOI: 10.1139/z09-019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied the genetic (microsatellite) diversity of a feral population of horses ( Equus caballus L., 1758) on Sable Island, Nova Scotia, Canada (1983–2003), at two spatial scales: (1) for the island as a whole and (2) at the level of four equally sized subdivisions along the length of Sable Island, which is a long (42 km) and narrow (1.5 km) vegetated sand bar. At the island scale (n = 264 horses), observed heterozygosity over 10 loci was 0.647 ± 0.035 (mean ± 1 SE), while expected heterozygosity was 0.696 ± 0.029; we observed significant heterozygote deficiency with all loci considered (P < 0.0001). At the subdivision scale, observed heterozygosity ranged from 0.589 to 0.694 in a gradient from west to east. We observed a corresponding gradient in effective number of alleles and allelic richness. Pairwise values of FST were significant for most subdivision pairs, ranging as high as 0.067 from west to east. Western areas showed highest levels of inbreeding (FIS = 0.113) with outbreeding indicated in the east (FIS = –0.008). Our results suggest that for a large mammal that lives in polygynous social groups, like the feral horse, gene flow along linear habitats (corridors) may be restricted (relative to the dispersal capabilities of the species), even over short distances.
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Affiliation(s)
- Z. L. Lucas
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - P. D. McLoughlin
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - D. W. Coltman
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - C. Barber
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
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8
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Green RD. ASAS Centennial Paper: Future needs in animal breeding and genetics. J Anim Sci 2009; 87:793-800. [DOI: 10.2527/jas.2008-1406] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Report of the 3rd Havemeyer workshop on allergic diseases of the Horse, Hólar, Iceland, June 2007. Vet Immunol Immunopathol 2008; 126:351-61. [DOI: 10.1016/j.vetimm.2008.07.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 07/18/2008] [Accepted: 07/21/2008] [Indexed: 11/20/2022]
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Rexroad CE, Palti Y, Gahr SA, Vallejo RL. A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genet 2008; 9:74. [PMID: 19019240 PMCID: PMC2605456 DOI: 10.1186/1471-2156-9-74] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 11/19/2008] [Indexed: 11/14/2022] Open
Abstract
Background Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in this species in aquaculture and sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. We constructed a second generation genetic map for rainbow trout using microsatellite markers to facilitate the identification of quantitative trait loci for traits affecting aquaculture production efficiency and the extraction of comparative information from the genome sequences of model fish species. Results A genetic map ordering 1124 microsatellite loci spanning a sex-averaged distance of 2927.10 cM (Kosambi) and having 2.6 cM resolution was constructed by genotyping 10 parents and 150 offspring from the National Center for Cool and Cold Water Aquaculture (NCCCWA) reference family mapping panel. Microsatellite markers, representing pairs of loci resulting from an evolutionarily recent whole genome duplication event, identified 180 duplicated regions within the rainbow trout genome. Microsatellites associated with genes through expressed sequence tags or bacterial artificial chromosomes produced comparative assignments with tetraodon, zebrafish, fugu, and medaka resulting in assignments of homology for 199 loci. Conclusion The second generation NCCCWA genetic map provides an increased microsatellite marker density and quantifies differences in recombination rate between the sexes in outbred populations. It has the potential to integrate with cytogenetic and other physical maps, identifying paralogous regions of the rainbow trout genome arising from the evolutionarily recent genome duplication event, and anchoring a comparative map with the zebrafish, medaka, tetraodon, and fugu genomes. This resource will facilitate the identification of genes affecting traits of interest through fine mapping and positional cloning of candidate genes.
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Affiliation(s)
- Caird E Rexroad
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia, USA.
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Raudsepp T, Gustafson-Seabury A, Durkin K, Wagner ML, Goh G, Seabury CM, Brinkmeyer-Langford C, Lee EJ, Agarwala R, Stallknecht-Rice E, Schäffer AA, Skow LC, Tozaki T, Yasue H, Penedo MCT, Lyons LA, Khazanehdari KA, Binns MM, MacLeod JN, Distl O, Guérin G, Leeb T, Mickelson JR, Chowdhary BP. A 4,103 marker integrated physical and comparative map of the horse genome. Cytogenet Genome Res 2008; 122:28-36. [PMID: 18931483 DOI: 10.1159/000151313] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2008] [Indexed: 12/20/2022] Open
Abstract
A comprehensive second-generation whole genome radiation hybrid (RH II), cytogenetic and comparative map of the horse genome (2n = 64) has been developed using the 5000rad horse x hamster radiation hybrid panel and fluorescence in situ hybridization (FISH). The map contains 4,103 markers (3,816 RH; 1,144 FISH) assigned to all 31 pairs of autosomes and the X chromosome. The RH maps of individual chromosomes are anchored and oriented using 857 cytogenetic markers. The overall resolution of the map is one marker per 775 kilobase pairs (kb), which represents a more than five-fold improvement over the first-generation map. The RH II incorporates 920 markers shared jointly with the two recently reported meiotic maps. Consequently the two maps were aligned with the RH II maps of individual autosomes and the X chromosome. Additionally, a comparative map of the horse genome was generated by connecting 1,904 loci on the horse map with genome sequences available for eight diverse vertebrates to highlight regions of evolutionarily conserved syntenies, linkages, and chromosomal breakpoints. The integrated map thus obtained presents the most comprehensive information on the physical and comparative organization of the equine genome and will assist future assemblies of whole genome BAC fingerprint maps and the genome sequence. It will also serve as a tool to identify genes governing health, disease and performance traits in horses and assist us in understanding the evolution of the equine genome in relation to other species.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA.
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Chowdhary BP, Raudsepp T. The horse genome derby: racing from map to whole genome sequence. Chromosome Res 2008; 16:109-27. [PMID: 18274866 DOI: 10.1007/s10577-008-1204-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The map of the horse genome has undergone unprecedented expansion during the past six years. Beginning from a modest collection of approximately 300 mapped markers scattered on the 31 pairs of autosomes and the X chromosome in 2001, today the horse genome is among the best-mapped in domestic animals. Presently, high-resolution linearly ordered gene maps are available for all autosomes as well as the X and the Y chromosome. The approximately 4350 mapped markers distributed over the approximately 2.68 Gbp long equine genome provide on average 1 marker every 620 kb. Among the most remarkable developments in equine genome analysis is the availability of the assembled sequence (EquCab2) of the female horse genome and the generation approximately 1.5 million single nucleotide polymorphisms (SNPs) from diverse breeds. This has triggered the creation of new tools and resources like the 60K SNP-chip and whole genome expression microarrays that hold promise to study the equine genome and transcriptome in ways not previously envisaged. As a result of these developments it is anticipated that, during coming years, the genetics underlying important monogenic traits will be analyzed with improved accuracy and speed. Of larger interest will be the prospects of dissecting the genetic component of various complex/multigenic traits that are of vital significance for equine health and welfare. The number of investigations recently initiated to study a multitude of such traits hold promise for improved diagnostics, prevention and therapeutic approaches for horses.
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Affiliation(s)
- Bhanu P Chowdhary
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA.
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Chowdhary BP, Paria N, Raudsepp T. Potential applications of equine genomics in dissecting diseases and fertility. Anim Reprod Sci 2008; 107:208-18. [PMID: 18524508 DOI: 10.1016/j.anireprosci.2008.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Following the recent development of high-resolution gene maps and generation of several basic tools and resources to use them in analyzing traits that are economically important to horse owners, genome analysis in horses is witnessing a shift towards developing an ability to analyze complex traits. The likelihood of this happening in the very near future is great, mainly because of the recent availability of the whole genome sequence in the horse. The latter has triggered the development of novel tools like SNP-chip and expression arrays that will permit rapid genome-wide analysis. While these tools will be used for a range of multi-factorial disease traits, attempts are underway to develop focused tools that can target reproduction, fertility and sex determination. For this, a catalog of sex and reproduction related (SRR) genes is being developed in horses. A recently developed dense map of the horse Y chromosome will provide genes that are expressed exclusively in males and, therefore, have an impact on stallion fertility. Overall, these advances in equine genome analysis hold promise for improved diagnosis and treatment of various conditions in horses.
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Affiliation(s)
- Bhanu P Chowdhary
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458, USA.
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Wittwer C, Löhring K, Drögemüller C, Hamann H, Rosenberger E, Distl O. Mapping quantitative trait loci for osteochondrosis in fetlock and hock joints and palmar/plantar osseus fragments in fetlock joints of South German Coldblood horses. Anim Genet 2007; 38:350-7. [PMID: 17559552 DOI: 10.1111/j.1365-2052.2007.01610.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aim of this study was to identify quantitative trait loci (QTL) for osteochondrosis (OC) and palmar/plantar osseous fragments (POF) in fetlock joints in a whole-genome scan of 219 South German Coldblood horses. Symptoms of OC and POF were checked by radiography in 117 South German Coldblood horses at a mean age of 17 months. The radiographic examination comprised the fetlock and hock joints of all limbs. The genome scan included 157 polymorphic microsatellite markers. All microsatellite markers were equally spaced over the 31 autosomes and the X chromosome, with an average distance of 17.7 cM and a mean polymorphism information content (PIC) of 63%. Sixteen chromosomes harbouring putative QTL regions were further investigated by genotyping the animals with 93 additional markers. QTL that had chromosome-wide significance by non-parametric Z-means and LOD scores were found on 10 chromosomes. This included seven QTL for fetlock OC and one QTL on ECA18 associated with hock OC and fetlock OC. Significant QTL for POF in fetlock joints were located on equine chromosomes 1, 4, 8, 12 and 18. This genome scan is an important step towards the identification of genes responsible for OC in horses.
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Affiliation(s)
- C Wittwer
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany
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Diesterbeck US, Hertsch B, Distl O. Genome-wide search for microsatellite markers associated with radiologic alterations in the navicular bone of Hanoverian warmblood horses. Mamm Genome 2007; 18:373-81. [PMID: 17551792 DOI: 10.1007/s00335-007-9021-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Revised: 03/30/2007] [Accepted: 04/03/2007] [Indexed: 10/23/2022]
Abstract
The aim of this study was to identify quantitative trait loci (QTLs) for pathologic changes in the navicular bone in Hanoverian warmblood horses. Seventeen paternal half-sib groups comprising 192 individuals were analyzed in a whole-genome scan. These families included 144 progeny and grandchildren, which were randomly chosen from the Hanoverian warmblood. Three different traits were considered: deformed canales sesamoidales and radiographic changes in the contour and in the structure of the navicular bone. The genome scan included in total 214 highly polymorphic microsatellite markers. The putatively linked genomic regions on equine chromosomes (ECA) 2, 3, 10, and 15 were refined using 53 additional microsatellites. Chromosome-wide significant QTLs were located on five different equine chromosomes (ECA2, 3, 4, 10, and 26). Genome-wide significant QTLs were on ECA2 at 48 cM and on ECA10 from 45.5 to 49.8 cM. This study was a first step to get more insight into the molecular genetic determination of radiologic changes in the equine navicular bone.
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Affiliation(s)
- Ulrike S Diesterbeck
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany
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Tozaki T, Swinburne J, Hirota KI, Hasegawa T, Ishida N, Tobe T. Improved resolution of the comparative horse–human map: Investigating markers with in silico and linkage mapping approaches. Gene 2007; 392:181-6. [PMID: 17306472 DOI: 10.1016/j.gene.2006.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 10/27/2006] [Accepted: 12/15/2006] [Indexed: 11/16/2022]
Abstract
Genetic maps are extremely important tools for tracing the genes that govern economically significant traits, and microsatellites are a significant component of these. In this study, we isolated 2346 novel horse microsatellites as resources for the construction of high-density horse genetic maps. Of these 2346 markers, 339 (14.5%) horse sequences showed sequence homology to DNA sequences in the human genome, demonstrating that microsatellites as type II markers are valuable resources for developing linkage maps and that they have a potential equal to that of type I markers for developing comparative maps. Of the 339 markers, 206 (60.8%) were assigned to horse chromosomes using the Animal Health Trust (AHT) full-sib reference family, and 195 (94.6%) of these localized to the expected syntenic locations on the human genome. These results confirmed the high level of accuracy of in silico mapping. Thus, the 339 markers that exhibited homology to the human genome increased the density of markers on the horse-human comparative map. The resulting comparative map will facilitate the use of horse microsatellites as genetic markers for the identification of quantitative trait loci (QTL) that have been mapped on the human genome. In addition, although the in silico and linkage mapping data did not agree for the other 11 (5.4%) of the assigned 206 markers, these may represent new putative regions of horse-human synteny.
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Affiliation(s)
- Teruaki Tozaki
- Department of Molecular Genetics, Laboratory of Racing Chemistry, 1731-2, Tsurutamachi, Utsunomiya, Tochigi 320-0851, Japan.
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17
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Dranchak PK, Valberg SJ, Onan GW, Gallant EM, Binns MM, Swinburne JE, Mickelson JR. Exclusion of linkage of theRYR1, CACNA1S, andATP2A1genes to recurrent exertional rhabdomyolysis in Thoroughbreds. Am J Vet Res 2006; 67:1395-400. [PMID: 16881852 DOI: 10.2460/ajvr.67.8.1395] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether there was genetic linkage between the recurrent exertional rhabdomyolysis (RER) trait in Thoroughbred horse pedigrees and DNA markers in genes (the sarcoplasmic reticulum calcium release channel [RYR1] gene, the sarcoplasmic reticulum calcium ATPase [ATP2A1] gene, and the transverse tubule dihydropyridine receptor-voltage sensor [CACNA1S] gene) that are important in myoplasmic calcium regulation. ANIMALS 34 horses in the University of Minnesota RER resource herd and 62 Thoroughbreds from 3 families of Thoroughbreds outside of the university in which RER-affected status was assigned after 2 or more episodes of ER had been observed. PROCEDURES Microsatellite DNA markers from the RYR1, ATP2A1, and CACNA1S gene loci on equine chromosomes 10, 13, and 30 were identified. Genotypes were obtained for all horses in the 4 families affected by RER, and data were used to test for linkage of these 3 loci to the RER phenotype. RESULTS Analysis of the RYR1, CACNA1S, and ATP2A1 microsatellites excluded a link between those markers and the RER trait. CONCLUSIONS AND CLINICAL RELEVANCE It is likely that the heritable alterations in muscle contractility that are characteristic of RER are caused by a gene that is not yet known to cause related muscle disease in other species.
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Affiliation(s)
- Patricia K Dranchak
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, 55108, USA
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Wagner ML, Raudsepp T, Goh G, Agarwala R, Schaffer AA, Dranchak PK, Brinkmeyer-Langford C, Skow LC, Chowdhary BP, Mickelson JR. A 1.3-Mb interval map of equine homologs of HSA2. Cytogenet Genome Res 2006; 112:227-34. [PMID: 16484777 DOI: 10.1159/000089875] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Accepted: 08/21/2005] [Indexed: 11/19/2022] Open
Abstract
A comparative approach that utilizes information from more densely mapped or sequenced genomes is a proven and efficient means to increase our knowledge of the structure of the horse genome. Human chromosome 2 (HSA2), the second largest human chromosome, comprising 243 Mb, and containing 1246 known genes, corresponds to all or parts of three equine chromosomes. This report describes the assignment of 140 new markers (78 genes and 62 microsatellites) to the equine radiation hybrid (RH) map, and the anchoring of 24 of these markers to horse chromosomes by FISH. The updated equine RH maps for ECA6p, ECA15, and ECA18 resulting from this work have one, two, and three RH linkage groups, respectively, per chromosome/chromosome-arm. These maps have a three-fold increase in the number of mapped markers compared to previous maps of these chromosomes, and an increase in the average marker density to one marker per 1.3 Mb. Comparative maps of ECA6p, ECA15, and ECA18 with human, chimpanzee, dog, mouse, rat, and chicken genomes reveal blocks of conserved synteny across mammals and vertebrates.
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Affiliation(s)
- M L Wagner
- Department of Veterinary Biosciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
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Pielberg G, Mikko S, Sandberg K, Andersson L. Comparative linkage mapping of the Grey coat colour gene in horses. Anim Genet 2006; 36:390-5. [PMID: 16167981 DOI: 10.1111/j.1365-2052.2005.01334.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Grey horses are born coloured, turn progressively grey and often develop melanomas late in life. Grey shows an autosomal dominant inheritance and the locus has previously been mapped to horse chromosome 25 (ECA25), around the TXN gene. We have now developed eight new single nucleotide polymorphisms (SNPs) associated with genes on ECA25 using information on the linear order of genes on human chromosome 9q, as well as the human and mouse coding sequences. These SNPs were mapped in relation to the Grey locus using more than 300 progeny from matings between two Swedish Warmblood grey stallions and non-grey mares. Grey was firmly assigned to an interval with flanking markers NANS and ABCA1. This corresponds to a region of approximately 6.9 Mb on human chromosome 9q. Furthermore, no recombination was observed between Grey, TGFBR1 and TMEFF1, the last two being 1.4 Mb apart in human. There are no obvious candidate genes in this region and none of the genes has been associated with pigmentation disorders or melanoma development, suggesting that the grey phenotype is caused by a mutation in a novel gene.
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Affiliation(s)
- G Pielberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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20
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Krüger K, Gaillard C, Stranzinger G, Rieder S. Phylogenetic analysis and species allocation of individual equids using microsatellite data. J Anim Breed Genet 2005; 122 Suppl 1:78-86. [PMID: 16130461 DOI: 10.1111/j.1439-0388.2005.00505.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The taxonomic status of all equid species is not completely unravelled. This is of practical relevance for conservation initiatives of endangered, fragmented equid populations, such as the Asiatic wild asses (in particular Equus hemionus onager and E. hemionus kulan). In this study, a marker panel consisting of 31 microsatellite loci was used to assess species demarcation and phylogeny, as well as allocation of individuals (n = 120) to specific populations of origin (n = 11). Phylogenetic analysis revealed coalescence times comparable with those previously published from fossil records and mtDNA data. Using Bayesian approaches, it was possible to distinguish between the studied equids, although individual assignment levels varied. The observed results support the maintenance of separate captive conservation herds for E. hemionus onager and E. hemionus kulan. The first molecular genetic results for E. hemionus luteus remained contradictory, as they unexpectedly indicated a closer genetic relationship between E. hemionus luteus and E. kiang holderi compared with the other hemiones.
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Affiliation(s)
- K Krüger
- Institute of Animal Science, Swiss Federal Institute of Technology, Zürich, Switzerland
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21
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Abstract
Genome research in animals used in agriculture has progressed rapidly in recent years, moving from rudimentary genome maps to trait maps to gene discovery. These advances are the result of animal genome projects following closely in the footsteps of the Human Genome Project, which has opened the door to genome research in farm animals. In return, genome research in livestock species is contributing to our understanding of chromosome evolution and to informing the human genome. Enhancement of these contributions plus the much anticipated application of DNA-based tools to animal health and production can be expected as livestock genomics enters its sequencing era.
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Affiliation(s)
- James E Womack
- Department of Veterinary Pathobiology, Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas 77843-4467, USA.
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22
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Swinburne JE, Boursnell M, Hill G, Pettitt L, Allen T, Chowdhary B, Hasegawa T, Kurosawa M, Leeb T, Mashima S, Mickelson JR, Raudsepp T, Tozaki T, Binns M. Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families. Genomics 2005; 87:1-29. [PMID: 16314071 DOI: 10.1016/j.ygeno.2005.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Revised: 08/19/2005] [Accepted: 09/03/2005] [Indexed: 11/30/2022]
Abstract
A genetic linkage map of the horse consisting of 742 markers, which comprises a single linkage group for each of the autosomes and the X chromosome, is presented. The map has been generated from two three-generation full-sibling reference families, sired by the same stallion, in which there are 61 individuals in the F2 generation. Each linkage group has been assigned to a chromosome and oriented with reference to markers mapped by fluorescence in situ hybridization. The average interval between markers is 3.7 cM and the linkage groups collectively span 2772 cM. The 742 markers comprise 734 microsatellite and 8 gene-based markers. The utility of the microsatellite markers for comparative mapping has been significantly enhanced by comparing their flanking sequences with the human genome sequence; this enabled conserved segments between human and horse to be identified. The new map provides a valuable resource for genetically mapping traits of interest in the horse.
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23
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Penedo MCT, Millon LV, Bernoco D, Bailey E, Binns M, Cholewinski G, Ellis N, Flynn J, Gralak B, Guthrie A, Hasegawa T, Lindgren G, Lyons LA, Røed KH, Swinburne JE, Tozaki T. International Equine Gene Mapping Workshop Report: a comprehensive linkage map constructed with data from new markers and by merging four mapping resources. Cytogenet Genome Res 2005; 111:5-15. [PMID: 16093715 DOI: 10.1159/000085664] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2004] [Accepted: 08/26/2004] [Indexed: 11/19/2022] Open
Abstract
A comprehensive male linkage map was generated by adding 359 new, informative microsatellites to the International Equine Gene Map half-sibling reference families and by combining genotype data from three independent mapping resources: a full sibling family created at the Animal Health Trust in Newmarket, United Kingdom, eight half-sibling families from Sweden and two half-sibling families from the University of California, Davis. Because the combined data were derived primarily from half-sibling families, only autosomal markers were analyzed. The map was constructed from a total of 766 markers distributed on the 31 equine chromosomes. It has a higher marker density than that of previously reported maps, with 626 markers linearly ordered and 140 other markers assigned to a chromosomal region. Fifty-nine markers (7%) failed to meet the criteria for statistical evidence of linkage and remain unassigned. The map spans 3,740 cM with an average distance of 6.3 cM between markers. Fifty-five percent of the intervals are < or = 5 cM and only 3% > or = 20 cM. The present map demonstrates the cohesiveness of the different data sets and provides a single resource for genome scan analyses and integration with the radiation hybrid map.
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Affiliation(s)
- M C T Penedo
- School of Veterinary Medicine, University of California, Davis, CA, USA.
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24
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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; 16:631-49. [PMID: 16180145 DOI: 10.1007/s00335-005-0023-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Accepted: 04/28/2005] [Indexed: 11/25/2022]
Abstract
A high-resolution (1 marker/700 kb) physically ordered radiation hybrid (RH) and comparative map of 122 loci on equine homologs of human Chromosome 19 (HSA19) shows a variant evolution of these segments in equids/Perissodactyls compared with other mammals. The segments include parts of both the long and the short arm of horse Chromosome 7 (ECA7), the proximal part of ECA21, and the entire short arm of ECA10. The map includes 93 new markers, of which 89 (64 gene-specific and 25 microsatellite) were genotyped on a 5000-rad horse x hamster RH panel, and 4 were mapped exclusively by FISH. The orientation and alignment of the map was strengthened by 21 new FISH localizations, of which 15 represent genes. The approximately sevenfold-improved map resolution attained in this study will prove extremely useful for candidate gene discovery in the targeted equine chromosomal regions. The highlight of the comparative map is the fine definition of homology between the four equine chromosomal segments and corresponding HSA19 regions specified by physical coordinates (bp) in the human genome sequence. Of particular interest are the regions on ECA7 and ECA21 that correspond to the short arm of HSA19-a genomic rearrangement discovered to date only in equids/Perissodactyls as evidenced through comparative Zoo-FISH analysis of the evolution of ancestral HSA19 segments in eight mammalian orders involving about 50 species.
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Affiliation(s)
- Candice Brinkmeyer-Langford
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, USA
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25
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Hillyer LL, Pettitt LA, Debenham SL, Swinburne JE, Binns MM, Price JS. Equine microsatellites associated with the COMP, LRP5 and COL1A1 genes. Anim Genet 2005; 36:261-2. [PMID: 15932412 DOI: 10.1111/j.1365-2052.2005.01272.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L L Hillyer
- Department of Veterinary Basic Sciences, Royal Veterinary College, London, UK.
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26
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Milenkovic D, Mariat D, Swinburne J, Chadi-Taourit S, Binns M, Guérin G. Characterization and localization of 17 microsatellites derived from BACs in the horse. Anim Genet 2005; 36:164-6. [PMID: 15771732 DOI: 10.1111/j.1365-2052.2004.01235.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D Milenkovic
- Institut national de la recherche agronomique, Centre de Recherches de Jouy, Laboratoire de Génétique biochimique et de Cytogénétique, Département de Génétique animale, 78352 Jouy-en-Josas Cedex, France
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27
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Mickelson JR, Wagner ML, Goh G, Wu JT, Morrison LY, Alexander LJ, Raudsepp T, Skow LC, Chowdhary BP, Swinburne JE, Binns MM. Thirty-five new equine microsatellite loci assigned to genetic linkage and radiation hybrid maps. Anim Genet 2005; 35:481-4. [PMID: 15566482 DOI: 10.1111/j.1365-2052.2004.01206.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J R Mickelson
- Department of Veterinary Biosciences, College of Veterinary Medicine, University of Minnesota, 295 AS/VM, 1988 Fitch Ave., St Paul, MN 55108, USA
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28
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Wagner ML, Goh G, Wu JT, Morrison LY, Alexander LJ, Raudsepp T, Skow LC, Chowdhary BP, Mickelson JR. Sixty-seven new equine microsatellite loci assigned to the equine radiation hybrid map. Anim Genet 2005; 35:484-6. [PMID: 15566483 DOI: 10.1111/j.1365-2052.2004.01205.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M L Wagner
- Department of Veterinary Biosciences, College of Veterinary Medicine, University of Minnesota, 295 AS/VM, 1988 Fitch Ave., St Paul, MN 55108, USA
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29
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Gustafson-Seabury A, Raudsepp T, Goh G, Kata SR, Wagner ML, Tozaki T, Mickelson JR, Womack JE, Skow LC, Chowdhary BP. High-resolution RH map of horse chromosome 22 reveals a putative ancestral vertebrate chromosome. Genomics 2005; 85:188-200. [PMID: 15676277 DOI: 10.1016/j.ygeno.2004.10.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Accepted: 10/22/2004] [Indexed: 11/28/2022]
Abstract
High-resolution gene maps of individual equine chromosomes are essential to identify genes governing traits of economic importance in the horse. In pursuit of this goal we herein report the generation of a dense map of horse chromosome 22 (ECA22) comprising 83 markers, of which 52 represent specific genes and 31 are microsatellites. The map spans 831 cR over an estimated 64 Mb of physical length of the chromosome, thus providing markers at approximately 770 kb or 10 cR intervals. Overall, the resolution of the map is to date the densest in the horse and is the highest for any of the domesticated animal species for which annotated sequence data are not yet available. Comparative analysis showed that ECA22 shares remarkable conservation of gene order along the entire length of dog chromosome 24, something not yet found for an autosome in evolutionarily diverged species. Comparison with human, mouse, and rat homologues shows that ECA22 can be traced as two conserved linkage blocks, each related to individual arms of the human homologue-HSA20. Extending the comparison to the chicken genome showed that one of the ECA22 blocks that corresponds to HSA20q shares synteny conservation with chicken chromosome 20, suggesting the segment to be ancestral in mammals and birds.
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Affiliation(s)
- Ashley Gustafson-Seabury
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
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30
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Tozaki T, Hirota KI, Hasegawa T, Tomita M, Kurosawa M. Prospects for whole genome linkage disequilibrium mapping in thoroughbreds. Gene 2005; 346:127-32. [PMID: 15716058 DOI: 10.1016/j.gene.2004.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Revised: 09/09/2004] [Accepted: 10/14/2004] [Indexed: 11/29/2022]
Abstract
Linkage disequilibrium (LD) mapping is often used in searches for genes governing economically significant traits and diseases. The D' coefficient is a commonly used measure of the extent of LD between all possible pairs of alleles at two markers. This study aimed to test the utility of the D' coefficient for LD mapping of a trait in a thoroughbred population. Microsatellite genotype data and grey coat colour as a trait model in a thoroughbred population were used to assess the extent of LD. We demonstrated that LD mapping was a reasonable approach for initial genome-wide scans in a thoroughbred population. Significant LD was demonstrated at approximately 7 cM, implying that roughly 430 appropriately spaced microsatellites were needed for systematic whole-genome LD mapping in this model. LD mapping methods using D' in a thoroughbred population were useful for identifying the chromosomal regions for diseases and economic trait loci (ETL). It was suggested that a thoroughbred population represented a population particularly suitable for LD mapping.
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Affiliation(s)
- Teruaki Tozaki
- Department of Molecular Genetics, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi 320-0851, Japan.
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31
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Mau C, Poncet PA, Bucher B, Stranzinger G, Rieder S. Genetic mapping of dominant white (W), a homozygous lethal condition in the horse (Equus caballus). J Anim Breed Genet 2004. [DOI: 10.1111/j.1439-0388.2004.00481.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Lee EJ, Raudsepp T, Kata SR, Adelson D, Womack JE, Skow LC, Chowdhary BP. A 1.4-Mb interval RH map of horse chromosome 17 provides detailed comparison with human and mouse homologues. Genomics 2004; 83:203-15. [PMID: 14706449 DOI: 10.1016/j.ygeno.2003.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Comparative genomics has served as a backbone for the rapid development of gene maps in domesticated animals. The integration of this approach with radiation hybrid (RH) analysis provides one of the most direct ways to obtain physically ordered comparative maps across evolutionarily diverged species. We herein report the development of a detailed RH and comparative map for horse chromosome 17 (ECA17). With markers distributed at an average interval of every 1.4 Mb, the map is currently the most informative among the equine chromosomes. It comprises 75 markers (56 genes and 19 microsatellites), of which 50 gene specific and 5 microsatellite markers were generated in this study and typed to our 5000-rad horse x hamster whole genome RH panel. The markers are dispersed over six RH linkage groups and span 825 cR(5000). The map is among the most comprehensive whole chromosome comparative maps currently available for domesticated animals. It finely aligns ECA17 to human and mouse homologues (HSA13 and MMU1, 3, 5, 8, and 14, respectively) and homologues in other domesticated animals. Comparisons provide insight into their relative organization and help to identify evolutionarily conserved segments. The new ECA17 map will serve as a template for the development of clusters of BAC contigs in regions containing genes of interest. Sequencing of these regions will help to initiate studies aimed at understanding the molecular mechanisms for various diseases and inherited disorders in horse as well as human.
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Affiliation(s)
- Eun-Joon Lee
- Department of Veterinary Anatomy & Public Health, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
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33
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Aberle KS, Hamann H, Drögemüller C, Distl O. Genetic diversity in German draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers. Anim Genet 2004; 35:270-7. [PMID: 15265065 DOI: 10.1111/j.1365-2052.2004.01166.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We compared the genetic diversity and distance among six German draught horse breeds to wild (Przewalski's Horse), primitive (Icelandic Horse, Sorraia Horse, Exmoor Pony) or riding horse breeds (Hanoverian Warmblood, Arabian) by means of genotypic information from 30 microsatellite loci. The draught horse breeds included the South German Coldblood, Rhenish German Draught Horse, Mecklenburg Coldblood, Saxon Thuringa Coldblood, Black Forest Horse and Schleswig Draught Horse. Despite large differences in population sizes, the average observed heterozygosity (H(o)) differed little among the heavy horse breeds (0.64-0.71), but was considerably lower than in the Hanoverian Warmblood or Icelandic Horse population. The mean number of alleles (N(A)) decreased more markedly with declining population sizes of German draught horse breeds (5.2-6.3) but did not reach the values of Hanoverian Warmblood (N(A) = 6.7). The coefficient of differentiation among the heavy horse breeds showed 11.6% of the diversity between the heavy horse breeds, as opposed to 21.2% between the other horse populations. The differentiation test revealed highly significant genetic differences among all draught horse breeds except the Mecklenburg and Saxon Thuringa Coldbloods. The Schleswig Draught Horse was the most distinct draught horse breed. In conclusion, the study demonstrated a clear distinction among the German draught horse breeds and even among breeds with a very short history of divergence like Rhenish German Draught Horse and its East German subpopulations Mecklenburg and Saxon Thuringa Coldblood.
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Affiliation(s)
- K S Aberle
- Institute of Animal Breeding and Genetics, School of Veterinary Medicine Hannover, Hannover, Germany
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34
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Wagner ML, Goh G, Wu JT, Raudsepp T, Morrison LY, Alexander LJ, Skow LC, Chowdhary BP, Mickelson JR. Radiation hybrid mapping of 63 previously unreported equine microsatellite loci. Anim Genet 2004; 35:159-62. [PMID: 15025590 DOI: 10.1111/j.1365-2052.2004.01109.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- M L Wagner
- Department of Veterinary PathoBiology, College of Veterinary Medicine, University of Minnesota, 1988 Fitch Ave., St Paul, MN 55108, USA
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35
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Terry RB, Archer S, Brooks S, Bernoco D, Bailey E. Assignment of the appaloosa coat colour gene (LP) to equine chromosome 1. Anim Genet 2004; 35:134-7. [PMID: 15025575 DOI: 10.1111/j.1365-2052.2004.01113.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A single autosomal dominant locus, leopard complex (LP) controls the presence of appaloosa pigmentation patterns in the horse. The causative gene for LP is unknown. This study was undertaken to map LP in the horse. Two paternal half sib families segregating for the LP locus and including a total of 47 offspring were used to perform a genome scan which localized LP to horse chromosome 1 (ECA1). LP was linked to ASB08 (LOD = 9.99 at Theta = 0.02) and AHT21 (LOD = 5.03 at Theta = 0.14). To refine the map position of LP, eight microsatellite markers on ECA1 (UM041, LEX77, 1CA41, TKY374, COR046, 1CA32, 1CA43, and TKY002) were analysed in the two half sib families. Results from this linkage analysis showed LP was located in the interval between ASB08 and 1CA43. Tight junction protein (TJP1), which lies within the LP interval on ECA1, was used to determine the homologous chromosomes in humans (HSA15) and mice (mouse chromosome 7). We propose that the pink eyed dilution (p) gene and transient receptor potential cation channel subfamily M, member 1 (TRPM1) are positional candidate genes for LP.
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Affiliation(s)
- R B Terry
- Department of Biology, University of Tampa, Tampa, FL 33606, USA.
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36
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Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res 2004; 14:528-38. [PMID: 15059993 PMCID: PMC383296 DOI: 10.1101/gr.1970304] [Citation(s) in RCA: 364] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2003] [Accepted: 02/09/2004] [Indexed: 11/24/2022]
Abstract
Levels of recombination vary among species, among chromosomes within species, and among regions within chromosomes in mammals. This heterogeneity may affect levels of diversity, efficiency of selection, and genome composition, as well as have practical consequences for the genetic mapping of traits. We compared the genetic maps to the genome sequence assemblies of rat, mouse, and human to estimate local recombination rates across these genomes. Humans have greater overall levels of recombination, as well as greater variance. In rat and mouse, the size of the chromosome and proximity to telomere have less effect on local recombination rate than in human. At the chromosome level, rat and mouse X chromosomes have the lowest recombination rates, whereas human chromosome X does not show the same pattern. In all species, local recombination rate is significantly correlated with several sequence variables, including GC%, CpG density, repetitive elements, and the neutral mutation rate, with some pronounced differences between species. Recombination rate in one species is not strongly correlated with the rate in another, when comparing homologous syntenic blocks of the genome. This comparative approach provides additional insight into the causes and consequences of genomic heterogeneity in recombination.
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Affiliation(s)
- Michael I Jensen-Seaman
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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37
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Raudsepp T, Lee EJ, Kata SR, Brinkmeyer C, Mickelson JR, Skow LC, Womack JE, Chowdhary BP. Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping. Proc Natl Acad Sci U S A 2004; 101:2386-91. [PMID: 14983019 PMCID: PMC356960 DOI: 10.1073/pnas.0308513100] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Development of a dense map of the horse genome is key to efforts aimed at identifying genes controlling health, reproduction, and performance. We herein report a high-resolution gene map of the horse (Equus caballus) X chromosome (ECAX) generated by developing and typing 116 gene-specific and 12 short tandem repeat markers on the 5,000-rad horse x hamster whole-genome radiation hybrid panel and mapping 29 gene loci by fluorescence in situ hybridization. The human X chromosome sequence was used as a template to select genes at 1-Mb intervals to develop equine orthologs. Coupled with our previous data, the new map comprises a total of 175 markers (139 genes and 36 short tandem repeats, of which 53 are fluorescence in situ hybridization mapped) distributed on average at approximately 880-kb intervals along the chromosome. This is the densest and most uniformly distributed chromosomal map presently available in any mammalian species other than humans and rodents. Comparison of the horse and human X chromosome maps shows remarkable conservation of gene order along the entire span of the chromosomes, including the location of the centromere. An overview of the status of the horse map in relation to mouse, livestock, and companion animal species is also provided. The map will be instrumental for analysis of X linked health and fertility traits in horses by facilitating identification of targeted chromosomal regions for isolation of polymorphic markers, building bacterial artificial chromosome contigs, or sequencing.
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Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Anatomy and Public Health, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
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38
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Guérin G, Bailey E, Bernoco D, Anderson I, Antczak DF, Bell K, Biros I, Bjørnstad G, Bowling AT, Brandon R, Caetano AR, Cholewinski G, Colling D, Eggleston M, Ellis N, Flynn J, Gralak B, Hasegawa T, Ketchum M, Lindgren G, Lyons LA, Millon LV, Mariat D, Murray J, Neau A, Røed K, Sandberg K, Skow LC, Tammen I, Tozaki T, Van Dyk E, Weiss B, Young A, Ziegle J. The second generation of the International Equine Gene Mapping Workshop half-sibling linkage map. Anim Genet 2003; 34:161-8. [PMID: 12755815 DOI: 10.1046/j.1365-2052.2003.00973.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A low-density, male-based linkage map was constructed as one of the objectives of the International Equine Gene Mapping Workshop. Here we report the second generation map based on testing 503 half-sibling offspring from 13 sire families for 344 informative markers using the CRIMAP program. The multipoint linkage analysis localized 310 markers (90%) with 257 markers being linearly ordered. The map included 34 linkage groups representing all 31 autosomes and spanning 2262 cM with an average interval between loci of 10.1 cM. This map is a milestone in that it is the first map with linkage groups assigned to each of the 31 automosomes and a single linkage group to all but three chromosomes.
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Affiliation(s)
- G Guérin
- Centre de Recherche de Jouy, Jouy-en-Josas, France
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39
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Mau C, Stranzinger G, Rieder S. Polymorphisms in the equine WNT1 gene allow linkage mapping to ECA6q. Anim Genet 2003; 34:148-9. [PMID: 12648100 DOI: 10.1046/j.1365-2052.2003.00965_2.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- C Mau
- Institute of Animal Science, Breeding Biology, Swiss Federal Institute of Technology, Zurich, Switzerland
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40
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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; 13:742-51. [PMID: 12671008 PMCID: PMC430160 DOI: 10.1101/gr.917503] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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Affiliation(s)
- Bhanu P Chowdhary
- Department of Veterinary Anatomy and Public Health, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA.
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41
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Swinburne JE, Turner A, Alexander LJ, Mickleson JR, Binns MM. Characterization and linkage map assignments for 61 new horse microsatellite loci (AHT49-109). Anim Genet 2003; 34:65-8. [PMID: 12580791 DOI: 10.1046/j.1365-2052.2003.00951_1.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- J E Swinburne
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, UK
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42
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Mickelson JR, Wu JT, Morrison LY, Swinburne JE, Binns MM, Reed KM, Alexander LJ. Eighty-three previously unreported equine microsatellite loci. Anim Genet 2003; 34:71-4. [PMID: 12580794 DOI: 10.1046/j.1365-2052.2003.00951_4.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- J R Mickelson
- Department of Veterinary PathoBiology, College of Veterinary Medicine, University of Minnesota, MN, USA.
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43
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Blechynden LM, Hilbert BJ, Swinburne JE, Binns MM, Laing NG. Four type I equine microsatellites associated with the MITF, KIT, ATP2A1 and GDAP1 genes. Anim Genet 2002; 33:387-8. [PMID: 12354153 DOI: 10.1046/j.1365-2052.2002.00896_7.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- L M Blechynden
- Australian Equine Neuromuscular Research Group, Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
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44
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Swinburne JE, Hopkins A, Binns MM. Assignment of the horse grey coat colour gene to ECA25 using whole genome scanning. Anim Genet 2002; 33:338-42. [PMID: 12354141 DOI: 10.1046/j.1365-2052.2002.00895.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The dominant grey coat colour gene of horses has been mapped using a whole genome scanning approach. Samples from a large half-sibling pedigree of Thoroughbred horses were utilized in order to map the grey coat colour locus, G. Multiplex groups of microsatellite markers were developed and used to efficiently screen the horse genome at a resolution of approximately 22 cM, based on an estimated map length for the horse genome of 2720 cM. The grey gene was assigned to chromosome 25 (ECA25), one of the smaller acrocentric horse chromosomes. Based on the current state of knowledge of conserved synteny and coat colour genetics in other mammalian species, there are no obvious candidate genes for the grey gene in the region.
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Affiliation(s)
- June E Swinburne
- Animal Health Trust, Lanwades Hall, Kentford, Newmarket, Suffolk CB8 7UU, UK.
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45
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Locke MM, Penedo MCT, Bricker SJ, Millon LV, Murray JD. Linkage of the grey coat colour locus to microsatellites on horse chromosome 25. Anim Genet 2002; 33:329-37. [PMID: 12354140 DOI: 10.1046/j.1365-2052.2002.00885.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The progressive loss of colour in the hair of grey horses is controlled by a dominantly inherited allele at the Grey locus (GG). In this study, two paternal Quarter Horse (QH) families segregating for the GG allele were genotyped with a set of 101 microsatellite markers spanning the 31 autosomes and the X chromosome. This genome scan demonstrated linkage of Grey to COR018 (RF=0.02, LOD=12.04) on horse chromosome 25 (ECA25). Further chromosome-specific analysis of seven total QH families confirmed the linkage of Grey to a group of ECA25 markers and the map order of NVHEQ43-(0.24)-UCDEQ405-(0.09)-COR080-(0.05)-GREY-(0.14)-UCDEQ464 was produced. Although G was found to be linked to TXN and COR018 in the chromosome-specific analysis, the data were not sufficiently informative to place either marker on our ECA25 map with significant LODs. Our results excluded the equine tyrosinase related protein 1 (TYRP1) and melanocyte protein 17 (Pmel17) genes as possible candidates for the grey phenotype in horses.
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Affiliation(s)
- M M Locke
- Veterinary Genetics Laboratory School of veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA 95616-8744, USA
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46
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Murray JD. Horse genomics and reproduction. Theriogenology 2002. [DOI: 10.1016/s0093-691x(02)00910-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Pascual I, Dhar AK, Fan Y, Paradis MR, Arruga MV, Alcivar-Warren A. Isolation of expressed sequence tags from a Thoroughbred horse (Equus caballus) 5'-RACE cDNA library. Anim Genet 2002; 33:231-2. [PMID: 12030932 DOI: 10.1046/j.1365-2052.2002.t01-2-00876.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- I Pascual
- Department of Environmental and Population Health, Tufts University School of Veterinary Medicine, North Grafton, MA 01536, USA
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48
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Breen M. Equine clinical cytogenetics--human chromosomes sitting on horse chromosomes. Equine Vet J 2002; 34:110-1. [PMID: 11902753 DOI: 10.2746/042516402776767141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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49
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Raudsepp T, Kata SR, Piumi F, Swinburne J, Womack JE, Skow LC, Chowdhary BP. Conservation of gene order between horse and human X chromosomes as evidenced through radiation hybrid mapping. Genomics 2002; 79:451-7. [PMID: 11863376 DOI: 10.1006/geno.2002.6723] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A radiation hybrid (RH) map of the equine X chromosome (ECAX) was obtained using the recently produced 5000(rad) horse x hamster hybrid panel. The map comprises 34 markers (16 genes and 18 microsatellites) and spans a total of 676 cR(5000), covering almost the entire length of ECAX. Cytogenetic alignment of the RH map was improved by fluorescent in situ hybridization mapping of six of the markers. The map integrates and refines the currently available genetic linkage, syntenic, and cytogenetic maps, and adds new loci. Comparison of the physical location of the 16 genes mapped in this study with the human genome reveals similarity in the order of the genes along the entire length of the two X chromosomes. This degree of gene order conservation across evolutionarily distantly related species has up to now been reported only between human and cat. The ECAX RH map provides a framework for the generation of a high-density map for this chromosome. The map will serve as an important tool for positional cloning of X-linked diseases/conditions in the horse.
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Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Anatomy, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
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50
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Locke MM, Ruth LS, Millon LV, Penedo MC, Murray JD, Bowling AT. The cream dilution gene, responsible for the palomino and buckskin coat colours, maps to horse chromosome 21. Anim Genet 2001; 32:340-3. [PMID: 11736803 DOI: 10.1046/j.1365-2052.2001.00806.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The colour locus historically referred to as C in the horse is linked to microsatellites markers on horse chromosome 21. Preliminary results demonstrated linkage of Ccr, thought to be the cream dilution variant of the C locus, to HTG10. An analysis of horse chromosome 21 using additional families confirmed and established a group of markers linked to Ccr. This work also improved the resolution of previously reported linkage maps for this chromosome. Linkage analysis unambiguously produced the map order: SGCV16-(19.1 cM)-HTG10-(3.8 cM)-LEX60/COR73-(1.3 cM)-COR68-(4.5 cM)- Ccr-(11.9 cM)-LEX31. Comparative and synteny data suggested that the horse C locus is not tyrosinase (TYR).
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Affiliation(s)
- M M Locke
- Veterinary Genetics Laboratory, University of California, Davis, CA, USA.
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