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Home / Equine Research Bank / Mol Genet Genomics / Whole-genome linkage disequilibrium screening for complex tr...
Molecular genetics and genomics : MGG2007; 277(6); 663-672; doi: 10.1007/s00438-007-0216-2

Whole-genome linkage disequilibrium screening for complex traits in horses.

Abstract: The identification of candidate genes for significant traits is crucial. In this study, we developed and tested effective and systematic methods based on linkage disequilibrium (LD) for the identification of candidate regions for genes with Mendelian inheritance and those associated with complex traits. Our approach entailed the combination of primary screening using pooled DNA samples based on DeltaTAC, secondary screening using an individual typing method and tertiary screening using a permutation test based on the differences in the haplotype frequency between two neighbouring microsatellites. This series of methods was evaluated using horse coat colour traits (chestnut/non-chestnut) as a simple Mendelian inheritance model. In addition, the methods were evaluated using a complex trait model constructed by mixing samples from chestnut and non-chestnut horses. Using both models, the methods could detect the expected regions for the horse coat colour trait. The results revealed that LD extends up to several centimorgans in horses, indicating that whole-genome LD screening in horses could be performed systematically and efficiently by combining the above-mentioned methods. Since genetic maps based on microsatellites have been constructed for many other species, the approaches present here could have wide applicability.
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Publication Date: 2007-02-22 PubMed ID: 17318585DOI: 10.1007/s00438-007-0216-2Google 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 research investigates a systematic method based on linkage disequilibrium (LD) for identifying genes associated with complex traits in horses, using horse coat color as a model. The research shows that the proposed methodology can effectively detect key gene regions and suggests that the approach could be applied to many other species.

Methodology

  • The research is based on a systematic set of methods that use LD to identify candidate regions for genes.
  • The procedure starts with primary screening of pooled DNA samples, using a process called DeltaTAC, which is aimed at identifying regions of the genome that are likely to contain genes of interest.
  • The second stage, or secondary screening, involves individual typing.
  • The final stage, or tertiary screening, uses a permutation test based on the frequency differences between two neighboring microsatellites, which are repeating sequences of DNA.

Model Traits

  • The approach was tested using two models: the horse coat colour trait (chestnut or non-chestnut), and a complex trait model constructed by mixing samples from chestnut and non-chestnut horses.
  • The purpose of this step was to see if the screening methodology could accurately identify the relevant regions based on these straightforward and complex models respectively.

Results and Implications

  • The results showed that the proposed methods could effectively detect the expected regions for the horse coat colour trait in both models.
  • This indicated that LD extends up to several centimorgans in horses, which means that whole-genome LD screening in horses could be carried out systematically and efficiently using the combination of these methods.
  • Since genetic maps based on microsatellites have already been developed for many species, the approach could potentially be applicable in a wide range of contexts.

Cite This Article

APA
Tozaki T, Hirota K, Hasegawa T, Ishida N, Tobe T. (2007). Whole-genome linkage disequilibrium screening for complex traits in horses. Mol Genet Genomics, 277(6), 663-672. https://doi.org/10.1007/s00438-007-0216-2

Publication

Molecular genetics and genomics : MGG
ISSN: 1617-4615
NlmUniqueID: 101093320
Country: Germany
Language: English
Volume: 277
Issue: 6
Pages: 663-672

Researcher Affiliations

Tozaki, Teruaki
  • Department of Molecular Genetics, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi 320-0851, Japan. ttozaki@lrc.or.jp
Hirota, Kei-ichi
    Hasegawa, Telhisa
      Ishida, Nobushige
        Tobe, Takashi

          MeSH Terms

          • Animals
          • Chromosome Mapping
          • Genome
          • Haplotypes
          • Horses / genetics
          • Linkage Disequilibrium
          • Microsatellite Repeats
          • Phenotype

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          Citations

          This article has been cited 1 times.
          1. Gu J, Orr N, Park SD, Katz LM, Sulimova G, MacHugh DE, Hill EW. A genome scan for positive selection in thoroughbred horses. PLoS One 2009 Jun 2;4(6):e5767.
            doi: 10.1371/journal.pone.0005767pubmed: 19503617google scholar: lookup
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