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PloS one2020; 15(4); e0230899; doi: 10.1371/journal.pone.0230899

Whole genome detection of sequence and structural polymorphism in six diverse horses.

Abstract: The domesticated horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of horse. To enrich the current collection of genetic variants in the horse, we sequenced whole genomes from six horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse, and mapped them to EquCab3.0 genome. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six horses with coverage between 15x to 24x per horse. After applying rigorous filtration, we identified and functionally annotated 17,514,723 Single Nucleotide Polymorphisms (SNPs), and 1,923,693 Insertions/Deletions (INDELs), as well as an average of 1,540 Copy Number Variations (CNVs) and 3,321 Structural Variations (SVs) per horse. Our results revealed putative functional variants including genes associated with size variation like LCORL gene (found in all horses), ZFAT in the Arabian, American Miniature and Percheron horses and ANKRD1 in the Native Mongolian Chakouyi horse. We detected a copy number variation in the Latherin gene that may be the result of evolutionary selection impacting thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the horse.
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Publication Date: 2020-04-09 PubMed ID: 32271776PubMed Central: PMC7144971DOI: 10.1371/journal.pone.0230899Google 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 paper presents the use of whole genome sequencing to detect sequence and structural polymorphisms in six different breeds of horses. With this process, a more comprehensive collection of genetic variations within the horse species was attained which can contribute to identify the genetic underpinnings of various physiological adaptations of different horse breeds.

Study Methodology

The study selected six horses from six different breeds: American Miniature, Percheron, Arabian, Mangalarga Marchador, Native Mongolian Chakouyi, and Tennessee Walking Horse. These breeds, chosen due to their unique physiological adaptations and geographical diversity, were subjected to whole genome sequencing. The sequences generated were then mapped to the EquCab 3.0 horse reference genome.

  • A total of 1.3 billion reads were generated and each horse test subject had coverage between 15x to 24x.
  • Extensive filtration protocols were used to identify the gene variations within the sequences.
  • These included Single Nucleotide Polymorphisms (SNPs), Insertions/Deletions (INDELs), Copy Number Variations (CNVs), and Structural Variations (SVs).

Study Findings

The study resulted in the identification of a considerable amount of previously unknown gene variations among the six horse breeds.

  • They found 17,514,723 Single Nucleotide Polymorphisms (SNPs), 1,923,693 Insertions/Deletions (INDELs), and an average of 1,540 Copy Number Variations (CNVs) and 3,321 Structural Variations (SVs) per horse.
  • The researchers were able to identify genes responsible for size variations among breeds, such as the LCORL gene (found in all horses), the ZFAT gene in the Arabian, American Miniature and Percheron horses, and the ANKRD1 gene in the Native Mongolian Chakouyi horse.
  • A significant finding was the detection of a variant in the Latherin gene, which is associated with an evolutionary adaptation in thermoregulation through sweating, a pivotal factor in athletic performance and heat tolerance.

Implications of the Study

This study has significantly enriched the known collection of genetic variations in horses. These results represent an important resource for future genetic studies in horses.

  • The new variants provide insight into the genetic reasons behind the diverse phenotypes seen in various horse breeds.
  • The database can be utilized to better understand genetic adaptations to different climates, as well as the relationship between horses and humans.
  • Ultimately, the findings will help to better identify and utilize the genetic potential of horses in various areas such as agriculture, sport, and therapy.

Cite This Article

APA
Al Abri MA, Holl HM, Kalla SE, Sutter NB, Brooks SA. (2020). Whole genome detection of sequence and structural polymorphism in six diverse horses. PLoS One, 15(4), e0230899. https://doi.org/10.1371/journal.pone.0230899

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 15
Issue: 4
Pages: e0230899

Researcher Affiliations

Al Abri, Mohammed Ali
  • Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Al Khod, Muscat, Oman.
Holl, Heather Marie
  • Department of Animal Science, Cornell University, Ithaca, NY, United States of America.
Kalla, Sara E
  • Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America.
Sutter, Nathan B
  • Department of Biology, La Sierra University, Riverwalk Parkway, Riverside, CA, United States of America.
Brooks, Samantha A
  • Department of Animal Sciences, University of Florida Genetics Institute, University of Florida, Gainesville, FL, United States of America.

MeSH Terms

  • Animals
  • Body Size / genetics
  • DNA Copy Number Variations
  • Fatty Acid-Binding Proteins / genetics
  • Genetic Variation
  • Genome
  • Horses / genetics
  • INDEL Mutation
  • Molecular Sequence Annotation
  • Polymorphism, Single Nucleotide
  • Whole Genome Sequencing

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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