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Genes2019; 10(7); 491; doi: 10.3390/genes10070491

Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds.

Abstract: Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated. In the entire dataset, 180 ROH islands were identified, whilst 100 islands were breed specific, all other overlapped in 36 genomic regions with at least one ROH island of another breed. Furthermore, two ROH hot spots were determined at horse chromosome 3 (ECA3) and ECA11. Besides the confirmation of previously documented target genes involved in selection for coat color (, , ), body size (, , , ), racing ability (), behavioral traits (, ) and gait patterns (), several putative target genes related to embryonic morphogenesis (), energy metabolism (, -), hair follicle morphogenesis (, , ) and autophagy () were highlighted. Furthermore, genes were pinpointed which might be involved in environmental adaptation of specific habitats (, , , , ).
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Publication Date: 2019-06-28 PubMed ID: 31261764PubMed Central: PMC6679042DOI: 10.3390/genes10070491Google 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 study is about investigating genetic variation among European horse breeds through findings obtained from 1476 horses across 12 breeds using runs of homozygosity to analyse the loss of genetic diversity in the horse breeds.

Methodology

  • A total of 1476 horses belonging to 12 different European and Near Eastern breeds were studied. The breeds chosen for the study represent a wide spectrum of selection goals ranging from coat color to agility traits.
  • The process called runs of homozygosity (ROH) was used. ROH is essentially the unbroken sequence of identical markers inherited from both parents, indicating possible regions of the horse’s genome where selection might have taken place.
  • A genotyping array that features 670,000 single nucleotide polymorphisms (SNPs) or genetic markers was used to screen the horses. SNPs represent variations at a single position in a DNA sequence among individuals.

Findings

  • In all, 180 overlapping homozygous regions (referred to as ROH islands) were identified, which could potentially indicate areas of selection.
  • Out of these, 100 ROH islands were unique to certain breeds, while the rest were common to at least two different breeds.
  • Two notable ROH hot spots were observed on horse chromosome 3 (ECA3) and 11 (ECA11).

Genes Influencing Traits

  • The findings corroborated earlier studies on target genes influencing coat color, body size, racing ability, behavioral traits, and gait patterns.
  • Genes potentially influencing embryonic morphogenesis (early developmental stage), energy metabolism (processing of food for energy), hair follicle morphogenesis (development of hair follicles), and autophagy (cell’s self-destruction mechanism) were highlighted in this study.
  • Interestingly, the study also pointed out genes that might be connected with the ability of the horse breeds to adapt to specific environments or habitats.

Implications

  • The genetic signature of selection observed in these horse breeds, determined by overlapping areas of homozygosity, provides valuable insights into how natural and artificial selection can shape the genetic diversity within animals species.
  • This information could be vital for genetic conservation of these breeds and understanding genetic predisposition to certain traits and diseases. It can also contribute to the fundamental understanding of the action of selection on the equine genome.

Cite This Article

APA
Grilz-Seger G, Neuditschko M, Ricard A, Velie B, Lindgren G, Mesarič M, Cotman M, Horna M, Dobretsberger M, Brem G, Druml T. (2019). Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds. Genes (Basel), 10(7), 491. https://doi.org/10.3390/genes10070491

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 10
Issue: 7
PII: 491

Researcher Affiliations

Grilz-Seger, Gertrud
  • Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria. gertrud.grilz@vetmeduni.ac.at.
Neuditschko, Markus
  • Agroscope, Swiss National Stud Farm, Les Longs Prés, CH-1580 Avenches, Switzerland. markus.neuditschko@agroscope.admin.ch.
Ricard, Anne
  • UMR 1313 Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, Domaine de Vilvert, Bat 211, 78352 Jouy-en-Josas, France. anne.ricard@inra.fr.
Velie, Brandon
  • Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 750 07 Uppsala, Sweden. brandon.velie@sydney.edu.au.
  • School of Life and Environmental Sciences, University of Sydney, Eastern Ave, 2006 NSW Sydney, Australia. brandon.velie@sydney.edu.au.
Lindgren, Gabriella
  • Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 750 07 Uppsala, Sweden. gabriella.lindgren@slu.se.
  • Livestock Genetics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium. gabriella.lindgren@slu.se.
Mesarič, Matjaz
  • Clinic for Reproduction and Large Animals, University of Ljubljana, Veterinary, Faculty, Cesta v Mestni log 47, 1000 Ljubljana, Slovenia. Matjaz.Mesaric@vf.uni-lj.si.
Cotman, Marko
  • Institute for Preclinical Sciences, University of Ljubljana, Veterinary Faculty, Gerbičeva 60, 1000 Ljubljana, Slovenia. marko.cotman@vf.uni-lj.si.
Horna, Michaela
  • Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia. michaela.horna@post.sk.
Dobretsberger, Max
  • Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria. maximilian.dobretsberger@vetmeduni.ac.at.
Brem, Gottfried
  • Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria. gottfried.brem@vetmeduni.ac.at.
Druml, Thomas
  • Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria. thomas.druml@vetmeduni.ac.at.

MeSH Terms

  • Agouti Signaling Protein / genetics
  • Animals
  • Basic-Leucine Zipper Transcription Factors / genetics
  • Breeding
  • Carrier Proteins / genetics
  • Cell Adhesion Molecules / genetics
  • Cytoskeletal Proteins / genetics
  • Gene Ontology
  • Genome
  • HMGA2 Protein / genetics
  • Homeodomain Proteins / genetics
  • Homozygote
  • Horses / genetics
  • Insulin-Like Growth Factor Binding Proteins / genetics
  • Keratins, Hair-Specific / genetics
  • Membrane Proteins / genetics
  • Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha / genetics
  • Polymorphism, Single Nucleotide
  • Repressor Proteins / genetics
  • Transcription Factors / genetics
  • Vesicular Transport Proteins / genetics
  • ral GTP-Binding Proteins / genetics

Conflict of Interest Statement

Data Availability: The primary data of this study are owned by different research groups. Primary data of the breeds Lipizzan, Noriker, Haflinger, Akhal Teke, Shagya Arabian, Gidran, Bosnian Mountain Horse and Posavina are available from project consortium FFG project number 843464, Veterinary University Vienna, Xenogenetik, five European state stud farms and the Austrian and Slovenian Horse breeders Association, but restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of project consortium, FFG project number 843464, Veterinary University Vienna, Xenogenetik and partners. Genotype data for the Exmoor Pony breed will be provided by contacting authors Lindgren/Velie or for a larger data set via the following reference: Velie, B.D.; Shrestha, M.; Franҫois, L.; Schurink, A.; Tesfayonas, Y.G.; Stinckens, A.; Blott, S.; Ducro, B.J.; Mikko, S.; Thomas, R.; Swinburne, J.E.; Sundqvist, M.; Eriksson, S.; Buys, N.; Lindgren, G. Using an inbred horse breed in a high density genome-wide scan for genetic risk factors of insect bite hypersensitivity (IBH). PLoS One. 2016, 11, e0152966.

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