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The Journal of heredity2018; 109(4); 384-392; doi: 10.1093/jhered/esx114

Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse.

Abstract: Within the scope of current genetic diversity analyses, population structure and homozygosity measures are independently analyzed and interpreted. To enhance analytical power, we combined the visualization of recently described high-resolution population networks with runs of homozygosity (ROH). In this study, we demonstrate that this approach enabled us to reveal important aspects of the breeding history of the Haflinger horse. We collected high-density genotype information of 531 horses originating from 7 populations which were involved in the formation of the Haflinger, namely 32 Italian Haflingers, 78 Austrian Haflingers, 190 Noriker, 23 Bosnian Mountain Horses, 20 Gidran, 33 Shagya Arabians, and 155 Purebred Arabians. Model-based cluster analysis identified substructures within Purebred Arabian, Haflinger, and Noriker that reflected distinct genealogy (Purebred Arabian), geographic origin (Haflinger), and coat color patterns (Noriker). Analysis of ROH revealed that the 2 Arabian populations (Purebred and Shagya Arabians), Gidran and the Bosnian Mountain Horse had the highest genome proportion covered by ROH segments (306-397 Mb). The Noriker and the Austrian Haflinger showed the lowest ROH coverage (228, 282 Mb). Our combined visualization approach made it feasible to clearly identify outbred (admixture) and inbred (ROH segments) horses. Genomic inbreeding coefficients (FROH) ranged from 10.1% (Noriker) to 17.7% (Purebred Arabian). Finally it could be demonstrated, that the Austrian Haflinger sample has a lack of longer ROH segments and a deviating ROH spectrum, which is associated with past bottleneck events and the recent mating strategy favoring out-crosses within the breed.
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Publication Date: 2018-01-03 PubMed ID: 29294044DOI: 10.1093/jhered/esx114Google 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.

The research presents a study that combines population structure and homozygosity measures using high-resolution population networks with runs of homozygosity (ROH) to investigate the breeding history of the Haflinger horse. Using a dataset of more than 500 horses, the researchers were able to identify substructures reflecting breed origin, geographic origin, and coat color patterns.

Research Methodology

  • The researchers collected high-density genotype information from 531 horses from 7 populations involved in the formation of the Haflinger horse. These were divided between Italian Haflingers, Austrian Haflingers, Noriker, Bosnian Mountain Horses, Gidran, Shagya Arabians, and Purebred Arabians.
  • They utilized model-based cluster analysis to identify substructures. These substructures correlated with distinct genealogy (Purebred Arabian), geographic origin (Haflinger), and coat color patterns (Noriker).
  • Analysis was also performed on ROH to determine the genome proportion covered by ROH segments.
  • The combination of population networks with ROH enabled the identification of outbred (admixture) and inbred (ROH segments) horses.

Major Findings

  • The study revealed that the two Arabian populations (Purebred and Shagya Arabians), Gidran and the Bosnian Mountain Horse had the highest genome proportion covered by ROH segments (306-397 Mb).
  • Noriker and the Austrian Haflinger showed the lowest coverage of ROH (228, 282 Mb).
  • Genomic inbreeding coefficients (FROH) varied across breeds, with 10.1% (Noriker) to 17.7% (Purebred Arabian).
  • A key finding was that the Austrian Haflinger sample showed a lack of longer ROH segments and a deviating ROH spectrum. This suggests past bottleneck events and a recent mating strategy that favours out-crosses within the breed.

Implication of the Research

  • The findings contribute to the understanding of the Haflinger horse’s breeding history. It also offers valuable insights into the population structure and homozygosity of the horse breeds involved in the formation of the Haflinger.
  • The combined implementation of population networks with ROH, as demonstrated in this study, could be an efficient approach for future genetic diversity analyses.

Cite This Article

APA
Druml T, Neuditschko M, Grilz-Seger G, Horna M, Ricard A, Mesaric M, Cotman M, Pausch H, Brem G. (2018). Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse. J Hered, 109(4), 384-392. https://doi.org/10.1093/jhered/esx114

Publication

The Journal of heredity
ISSN: 1465-7333
NlmUniqueID: 0375373
Country: United States
Language: English
Volume: 109
Issue: 4
Pages: 384-392

Researcher Affiliations

Druml, Thomas
  • Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria.
Neuditschko, Markus
  • Agroscope, Swiss National Stud Farm, Avenches, Switzerland.
Grilz-Seger, Gertrud
  • Pöckau, Arnoldstein, Austria.
Horna, Michaela
  • Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Nitra-Chrenová, Slovak Republic.
Ricard, Anne
  • Institut National de la Recherche Agronomique, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
  • Institut Français du Cheval et de l'Equitation, Recherche et Innovation, Exmes, France.
Mesaric, Matjaz
  • Clinic for Reproduction and Large Animals, Veterinary Faculty, University of Lubljana, Cesta v Mestni log, Ljubljana, Slovenia.
Cotman, Marco
  • Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Cesta v Mestni log, Ljubljana, Slovenia.
Pausch, Hubert
  • Animal Genomics, ETH Zürich, Zürich, Switzerland.
Brem, Gottfried
  • Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria.

MeSH Terms

  • Animals
  • Breeding
  • Female
  • Genetic Variation
  • Genetics, Population
  • Genome / genetics
  • Genomics
  • Genotype
  • Homozygote
  • Horses / classification
  • Horses / genetics
  • Inbreeding
  • Male
  • Polymorphism, Single Nucleotide / genetics

Citations

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