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Animals : an open access journal from MDPI2022; 12(23); 3293; doi: 10.3390/ani12233293

Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types.

Abstract: The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ROH islands, which may be signals of recent selection events. Eight to fourteen ROH islands were identified per breed, which spanned multiple genes. Many were involved in important horse breed characteristics, including , , , , , , , and the zinc finger protein family. Regions of the genome with zero ROH occurrences were also of major interest in specific populations. Depending on the breed, we detected between 2 to 57 no-ROH regions and identified 27 genes in these regions that were common for five breeds. These genes were involved in, e.g., muscle contractility () and muscle development (, , ). To sum up, the obtained results can be furthered analyzed in the topic of identification of markers unique for specific horse breed characteristics.
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Publication Date: 2022-11-25 PubMed ID: 36496815PubMed Central: PMC9736150DOI: 10.3390/ani12233293Google 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 analyzes the distribution of runs of homozygosity (ROH) in the genomes of six horse breeds to understand differences between the breeds and types of horses. The information drawn from these analyses can be used to identify unique markers for specific horse breed characteristics.

Understanding Runs of Homozygosity (ROH)

  • ROH are stretches in the genome where the two copies of the chromosome are identical.
  • The study aims to explore the length, quantity, and frequency of these ROH characteristics in the genome.
  • Analyzed were genomes of six horse breeds: a total of 571 horses. These breeds come from three types: primitive, light, and draft horses.
  • The data was garnered using a 65k Equine BeadChip assay that is used to analyze the genotype of a horse.

Findings of the Study

  • The results show noticeable differences in the number, length and distribution of ROH between the different breeds.
  • In addition, differences were observed in genomic inbreeding coefficients i.e. the probability where both alleles of a gene come from the same ancestor.

Regions of Interest in the Genome

  • The study also investigated areas in the genome with a high occurrence of ROH, called ROH islands, often indicative of recent selection events.
  • Depending on the breed, between 8 to 14 ROH islands were identified. These islands span several genes and many are related to characteristics unique to horse breeds.

Regions with No-ROH Occurrences

  • The regions of the genome with no ROH occurrences also pose significant interest. Depending on the breed, there were 2 to 57 such regions detected.
  • Twenty-seven genes within these no-ROH regions were common for five breeds.
  • These genes are believed to be involved in functions such as muscle contractility and development.

Implications of the Research

  • Through these analyses, specific markers for distinctive horse breed characteristics can be identified.
  • This can be used in future studies and applications for equine genetic characterization and enhancement.

Cite This Article

APA
Szmatoła T, Gurgul A, Jasielczuk I, Oclon E, Ropka-Molik K, Stefaniuk-Szmukier M, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M. (2022). Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types. Animals (Basel), 12(23), 3293. https://doi.org/10.3390/ani12233293

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 12
Issue: 23
PII: 3293

Researcher Affiliations

Szmatoła, Tomasz
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland.
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Gurgul, Artur
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland.
Jasielczuk, Igor
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland.
Oclon, Ewa
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland.
Ropka-Molik, Katarzyna
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Stefaniuk-Szmukier, Monika
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Polak, Grazyna
  • Office of the Director for Scientific Affairs, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Tomczyk-Wrona, Iwona
  • Department of Horse Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Bugno-Poniewierska, Monika
  • Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059 Kraków, Poland.

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

This article has been cited 2 times.
  1. Dementieva N, Nikitkina E, Shcherbakov Y, Nikolaeva O, Mitrofanova O, Ryabova A, Atroshchenko M, Makhmutova O, Zaitsev A. The Genetic Diversity of Stallions of Different Breeds in Russia.. Genes (Basel) 2023 Jul 24;14(7).
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  2. Gmel AI, Brem G, Neuditschko M. New genomic insights into the conformation of Lipizzan horses.. Sci Rep 2023 Jun 2;13(1):8990.
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