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Home / Equine Research Bank / Mol Biol Rep / Gametic phase disequilibrium between the syntenic multiallel...
Molecular biology reports2011; 39(2); 1447-1452; doi: 10.1007/s11033-011-0881-4

Gametic phase disequilibrium between the syntenic multiallelic HTG4 and HMS3 markers widely used for parentage testing in Thoroughbred horses.

Abstract: Validation of parentage and horse breed registries through DNA typing relies on estimates of random match probabilities with DNA profiles generated from multiple polymorphic loci. Of the twenty-seven microsatellite loci recommended by the International Society for Animal Genetics for parentage testing in Thoroughbred horses, eleven are located on five chromosomes. An important aspect in determining combined exclusion probabilities is the ascertainment of the genetic linkage status of syntenic markers, which may affect reliable use of the product rule in estimating random match probabilities. In principle, linked markers can be in gametic phase disequilibrium (GD). We aimed at determining the extent, by frequency and strength, of GD between the HTG4 and HMS3 multiallelic loci, syntenic on chromosome 9. We typed the qualified offspring (n (1) = 27; n (2) = 14) of two Quarter Bred stallions (registered by the Brazilian Association of Quarter Horse Breeders) and 121 unrelated horses from the same breed. In the 41 informative meioses analyzed, the frequency of recombination between the HTG4 and HMS3 loci was 0.27. Consistent with genetic map distances, this recombination rate does not fit to the theoretical distribution for independently segregated markers. We estimated sign-based D' coefficients as a measure of GD, and showed that the HTG4 and HMS3 loci are in significant, yet partial and weak, disequilibrium, with two allele pairs involved (HTG4 M/HMS3 P, D'(+) = 0.6274; and HTG4 K/HMS3 P, D'(-) = -0.6096). These results warn against the inadequate inclusion of genetically linked markers in the calculation of combined power of discrimination for Thoroughbred parentage validation.
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Publication Date: 2011-05-24 PubMed ID: 21607619DOI: 10.1007/s11033-011-0881-4Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

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.

This study investigated the reliability of two genetic markers used for DNA typing in Thoroughbred parentage testing. The research found that these markers are not as reliably independent as previously thought, which could affect the accuracy of parentage testing.

Introduction and Background

  • This research focuses on the genetic linkage status of two markers (HTG4 and HMS3) used for Thoroughbred horse parentage testing. These markers’ genetic linkage and independence are crucial for estimating random match probabilities and combined exclusion probabilities, both critical to validate parentage accurately.
  • These two markers are syntenic, meaning they are found on the same chromosome (chromosome 9 in this case). The two markers are suspected of being in gametic phase disequilibrium (GD), meaning they do not assort independently during the production of gametes.

Methodology

  • The research team assessed the degree, by frequency and strength, of GD between the HTG4 and HMS3 loci. They did this by typing the offspring of two Quarter Bred stallions and 121 unrelated horses from the same breed.
  • They also analyzed 41 ‘informative meioses’ – instances of cell division forming gametes or spores in which chromosome numbers are halved – to determine the frequency of recombination between the HTG4 and HMS3 loci.

Results

  • The frequency of recombination between the HTG4 and HMS3 loci was 0.27, meaning these loci do not fully obey Mendel’s law of independent assortment. The deviation from expected recombination puts these markers out of step with the theoretical distribution for independently segregated markers.
  • The team used the sign-based D’ coefficient as an additional measure of GD. The HTG4 and HMS3 loci showed considerable, albeit partial and weak, disequilibrium. Two specific allele pairs (HTG4 M/HMS3 P and HTG4 K/HMS3 P) were involved in this disequilibrium.
  • These results challenge the notion of full independence in these markers, suggesting a need for caution in using them for calculating the combined power of discrimination in Thoroughbred parentage validation.

Cite This Article

APA
Machado FB, de Vasconcellos Machado L, Bydlowski CR, Bydlowski SP, Medina-Acosta E. (2011). Gametic phase disequilibrium between the syntenic multiallelic HTG4 and HMS3 markers widely used for parentage testing in Thoroughbred horses. Mol Biol Rep, 39(2), 1447-1452. https://doi.org/10.1007/s11033-011-0881-4

Publication

Molecular biology reports
ISSN: 1573-4978
NlmUniqueID: 0403234
Country: Netherlands
Language: English
Volume: 39
Issue: 2
Pages: 1447-1452

Researcher Affiliations

Machado, Filipe Brum
  • Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, SP, CEP 14049-900, Brazil.
de Vasconcellos Machado, Luana
    Bydlowski, Cynthia Rachid
      Bydlowski, Sergio Paulo
        Medina-Acosta, Enrique

          MeSH Terms

          • Alleles
          • Animals
          • Brazil
          • Gene Frequency / genetics
          • Genetic Markers / genetics
          • Genotype
          • Horses / genetics
          • Linkage Disequilibrium / genetics
          • Microsatellite Repeats / genetics
          • Pedigree
          • Polymerase Chain Reaction / veterinary
          • Synteny / genetics

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          Citations

          This article has been cited 1 times.
          1. Ywasaki Lima J, Machado FB, Farro APC, Barbosa LA, da Silveira LS, Medina-Acosta E. Population genetic structure of Guiana dolphin (Sotalia guianensis) from the southwestern Atlantic coast of Brazil.. PLoS One 2017;12(8):e0183645.
            doi: 10.1371/journal.pone.0183645pubmed: 28837691google scholar: lookup
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