Prospects for whole genome linkage disequilibrium mapping in thoroughbreds.
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.
Publication Date: 2005-01-22 PubMed ID: 15716058DOI: 10.1016/j.gene.2004.10.011Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research article presents a study that explores the potential for whole genome linkage disequilibrium mapping in thoroughbreds using the D’ coefficient. This method is often deployed for discovering genes linked to economically significant traits and diseases.
Overview of Linkage Disequilibrium (LD)
- Linkage Disequilibrium (LD) is a concept which refers to the non-random association of alleles at two or more loci and is often used in identifying genes responsible for certain economically significant traits and diseases.
- The D’ coefficient is a measure often used in determining the extent of LD between all possible pairs of alleles at two markers.
D’ Coefficient and LD Mapping in Thoroughbreds
- This study evaluates the efficacy of the D’ coefficient in LD mapping, specifically researching a trait in a thoroughbred horse population.
- The researchers used the data that includes the microsatellite genotype and grey coat colour as a trait model in their thoroughbred subjects to evaluate LD. A microsatellite genotype refers to a short DNA sequence repeated many times in a row.
- The study found LD mapping to be a viable method for preliminary genome-wide scans in a thoroughbred population.
Findings of the Study
- Significant Linkage Disequilibrium was demonstrated at a distance of approximately 7 cM (centimorgans, a unit of measurement for genetic linkage).
- This means that around 430 accurately spaced microsatellites would be required for systematic whole-genome LD mapping in this horse breed, based on their model.
- The LD mapping methods using the D’ coefficient in thoroughbred horses were found to be effective in identifying chromosomal regions for diseases and Economic Trait Loci (ETL).
Utility of the Thoroughbred Population for LD Mapping
- The researchers surmise that the Thoroughbred horse breed offers a particularly suitable population for LD mapping due to its unique breeding history, high inbreeding rate and several controlled characteristics that make them ideal for genetic studies.
Cite This Article
APA
Tozaki T, Hirota K, Hasegawa T, Tomita M, Kurosawa M.
(2005).
Prospects for whole genome linkage disequilibrium mapping in thoroughbreds.
Gene, 346, 127-132.
https://doi.org/10.1016/j.gene.2004.10.011 Publication
Researcher Affiliations
- Department of Molecular Genetics, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi 320-0851, Japan. ttozaki@nyc.odn.ne.jp
MeSH Terms
- Animals
- Base Sequence
- DNA Primers
- Genome
- Horses / genetics
- Linkage Disequilibrium
- Polymerase Chain Reaction
Citations
This article has been cited 6 times.- Whiteley AR, Bhat A, Martins EP, Mayden RL, Arunachalam M, Uusi-Heikkilä S, Ahmed AT, Shrestha J, Clark M, Stemple D, Bernatchez L. Population genomics of wild and laboratory zebrafish (Danio rerio). Mol Ecol 2011 Oct;20(20):4259-76.
- Khatkar MS, Nicholas FW, Collins AR, Zenger KR, Cavanagh JA, Barris W, Schnabel RD, Taylor JF, Raadsma HW. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 2008 Apr 24;9:187.
- Khatkar MS, Zenger KR, Hobbs M, Hawken RJ, Cavanagh JA, Barris W, McClintock AE, McClintock S, Thomson PC, Tier B, Nicholas FW, Raadsma HW. A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle. Genetics 2007 Jun;176(2):763-72.
- Tozaki T, Hirota K, Hasegawa T, Ishida N, Tobe T. Whole-genome linkage disequilibrium screening for complex traits in horses. Mol Genet Genomics 2007 Jun;277(6):663-72.
- Khatkar MS, Collins A, Cavanagh JA, Hawken RJ, Hobbs M, Zenger KR, Barris W, McClintock AE, Thomson PC, Nicholas FW, Raadsma HW. A first-generation metric linkage disequilibrium map of bovine chromosome 6. Genetics 2006 Sep;174(1):79-85.
- Yokomori T, Tozaki T, Segawa T, Itou T. Genomic regions and candidate genes associated with forehead whorl positioning in Thoroughbred horses. J Equine Sci 2025;36(1):11-18.
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