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Home / Equine Research Bank / BMC Genomics / Whole-genome sequencing and genetic variant analysis of a Qu...
BMC genomics2012; 13; 78; doi: 10.1186/1471-2164-13-78

Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

Abstract: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. Results: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. Conclusions: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.
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Publication Date: 2012-02-17 PubMed ID: 22340285PubMed Central: PMC3309927DOI: 10.1186/1471-2164-13-78Google Scholar: Lookup
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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 article discusses the identification of genetic variants in the genome of a Quarter Horse mare using next-generation sequencing technologies. The study identified millions of new, single nucleotide polymorphisms, insertion/deletion polymorphisms, and copy number variants, highlighting the genome’s enrichment in sensory perception, signal transduction, and immunity and defense pathways.

Methodology

  • The researchers used massively parallel paired-end sequencing to generate 59.6 Gb of DNA sequence from a Quarter Horse mare. This resulted in an average sequence coverage of 24.7X.
  • These sequences were then mapped to approximately 97% of the reference Thoroughbred genome.
  • The remaining unmapped reads were de novo assembled, resulting in 19.1 Mb of new genomic sequence in the horse.

Findings

  • With a stringent filtering method, the researchers identified 3.1 million single nucleotide polymorphisms (SNPs), 193 thousand insertion/deletion polymorphisms (INDELs), and 282 copy number variants (CNVs).
  • The genetic variants were annotated to establish their effect on gene structure and function.
  • Additionally, the team genotyped the Quarter Horse for mutations related to known diseases and variants associated with certain traits.
  • Functional clustering analysis revealed that most of the genetic variation in the Quarter Horse’s genome was enriched in sensory perception, signal transduction, and immunity and defense pathways.

Conclusion and Future Implications

  • This study marked the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare.
  • The discovered genetic variants have significantly expanded the catalog of genetic variants for use in equine genomics.
  • The detailed information about novel SNPs, INDELs, and CNVs will serve as a useful resource for future research on genetic variation regulating performance traits and diseases in equids.

Cite This Article

APA
Doan R, Cohen ND, Sawyer J, Ghaffari N, Johnson CD, Dindot SV. (2012). Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare. BMC Genomics, 13, 78. https://doi.org/10.1186/1471-2164-13-78

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 13
Pages: 78

Researcher Affiliations

Doan, Ryan
  • Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA.
Cohen, Noah D
    Sawyer, Jason
      Ghaffari, Noushin
        Johnson, Charlie D
          Dindot, Scott V

            MeSH Terms

            • Animals
            • DNA Copy Number Variations
            • Female
            • Genome
            • Genomics / methods
            • Genotype
            • Horse Diseases / genetics
            • Horses / genetics
            • Molecular Sequence Annotation
            • Mutation
            • Polymorphism, Single Nucleotide
            • Quantitative Trait Loci
            • Sequence Analysis, DNA
            • Signal Transduction

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