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PloS one2019; 14(1); e0210751; doi: 10.1371/journal.pone.0210751

A genome-wide scan for diversifying selection signatures in selected horse breeds.

Abstract: The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specific allele frequencies variation between populations, to detect selection signatures among six horse breeds maintained in Poland. These breeds can be classified into three major categories, including light, draft and primitive horses, selected mainly in terms of type (utility), exterior, performance, size, coat color and appearance. The analysis of the most pronounced selection signals found in this study allowed us to detect several genomic regions and genes connected with processes potentially important for breed phenotypic differentiation and associated with energy homeostasis during physical effort, heart functioning, fertility, disease resistance and motor coordination. Our results also confirmed previously described association of loci on ECA3 (spanning LCORL and NCAPG genes) and ECA11 (spanning LASP1 gene) with the regulation of body size in our draft and primitive (small size) horses. The efficiency of the applied FST-based approach was also confirmed by the identification of a robust selection signal in the blue dun colored Polish Konik horses at the locus of TBX3 gene, which was previously shown to be responsible for dun coat color dilution in other horse breeds. FST-based method showed to be efficient in detection of diversifying selection signatures in the analyzed horse breeds. Especially pronounced signals were observed at the loci responsible for fixed breed-specific features. Several candidate genes under selection were proposed in this study for traits selected in separate breeds and horse types, however, further functional and comparative studies are needed to confirm and explain their effect on the observed genetic diversity of the horse breeds.
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Publication Date: 2019-01-30 PubMed ID: 30699152PubMed Central: PMC6353161DOI: 10.1371/journal.pone.0210751Google 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 study investigates the level of genetic divergence among different horse breeds in Poland, using high throughput genotyping methods and the population differentiation index (FST). The results highlight various gene regions connected with traits such as energy balance during exercise, heart function, fertility, disease resistance, and motor coordination, which may contribute to the distinct characteristics of individual breeds.

Methodology

  • The research used techno-scientific advancements in genotyping methods to analyze the genetic variation in horse breeds. This approach allows more comprehensive studies of genetic differentiation at a genome-wide level.
  • The researchers used a measurable standard known as the population differentiation index (FST) to measure differences in allele frequencies between the different horse breeds.
  • The study focuses on six horse breeds, each representing a distinct category: light, draft, and primitive. These categories were selected based on factors such as utilization, exterior aesthetics, performance, size, coat color, and general appearance.

Findings

  • The results showed several gene regions that appeared to be associated with various traits. These traits include energy expenditure during physical effort, heart functioning, fertility, disease resistance, and motor coordination — all important factors in a horse’s phenotype or observable characteristics.
  • Two locations in the genome, known as loci (ECA3, which includes LCORL and NCAPG genes, and ECA11, which includes the LASP1 gene), were confirmed to be associated with regulation of body size in draft and primitive horses. These findings align with previous research.
  • The study also identified a potent selection signal in the blue dun colored Polish Konik horses at the locus of the TBX3 gene, previously associated with the dun coat color dilution in horses from other breeds.

Conclusion

  • The study demonstrated the efficacy of the FST-based approach, finding strong selection signals at loci responsible for breed-specific features.
  • The results contribute to the broader understanding of the genetic diversity in horse breeds. However, researchers highlight that further research is required to fully understand and explain the observed genetic diversity of distinct horse breeds and individual traits.

Cite This Article

APA
Gurgul A, Jasielczuk I, Semik-Gurgul E, Pawlina-Tyszko K, Stefaniuk-Szmukier M, Szmatoła T, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M. (2019). A genome-wide scan for diversifying selection signatures in selected horse breeds. PLoS One, 14(1), e0210751. https://doi.org/10.1371/journal.pone.0210751

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 14
Issue: 1
Pages: e0210751

Researcher Affiliations

Gurgul, Artur
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
Jasielczuk, Igor
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
Semik-Gurgul, Ewelina
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
Pawlina-Tyszko, Klaudia
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
Stefaniuk-Szmukier, Monika
  • Department of Horse Breeding, University of Agriculture in Kraków, al. Kraków, Poland.
Szmatoła, Tomasz
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
Polak, Grażyna
  • Department of Horse Breeding, National Research Institute of Animal Production, Balice, Poland.
Tomczyk-Wrona, Iwona
  • Department of Horse Breeding, National Research Institute of Animal Production, Balice, Poland.
Bugno-Poniewierska, Monika
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
  • Institute of Veterinary Sciences, University of Agriculture in Krakow, al. Kraków, Poland.

MeSH Terms

  • Animals
  • Chromosome Mapping
  • Female
  • Gene Frequency
  • Genetic Variation
  • Genetics, Population
  • Genome
  • Hair Color / genetics
  • Horses / anatomy & histology
  • Horses / genetics
  • Horses / physiology
  • Male
  • Phenotype
  • Poland
  • Polymorphism, Single Nucleotide
  • Selective Breeding

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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Citations

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