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iScience2023; 26(7); 107104; doi: 10.1016/j.isci.2023.107104

Imputed genomes of historical horses provide insights into modern breeding.

Abstract: Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski's horse following a century of captive breeding.
© 2023 The Authors.
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Publication Date: 2023-06-14 PubMed ID: 37416458PubMed Central: PMC10319840DOI: 10.1016/j.isci.2023.107104Google 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 investigates the historical genomes of horses to better understand the genetic changes that have led to the development of modern breeds. It provides insights into the history and evolution of Clydesdale, Thoroughbred, and the endangered Przewalski’s horse breeds, as well as highlighting the increased inbreeding in recent times.

Genomic Variations Analysis Context

  • The study embarks on the process of characterizing 8.7 million genomic variants. This information was obtained from a panel of 430 horses belonging to 73 breeds. Distinct in the panel, genomes from 20 Clydesdales and 10 Shire horses were newly sequenced.
  • The modern genomic variants thus obtained were used to impute, or predict, the genomes of four historically important horse breeds. These include 2 Przewalski’s horses, a Thoroughbred, and a newly sequenced Clydesdale. This essentially entails using known genetic data to estimate unknown genetic data.

Connecting Historical and Modern Genomes

  • Using the imputed historical genomes, the researchers identified modern horses that showed higher genetic similarity to past horses. This information is valuable in breed preservation or phenotype prediction efforts, thereby helping breeders in making informed decisions.
  • The team also found evidence of increased inbreeding in recent times. Inbreeding could lead to decreased genetic diversity, which can have detrimental effects on a breed’s health and resilience.

Discovering Unknown Characteristics

  • The researchers genotyped variants associated with appearance and behavior. Genotyping refers to determining the genetic constitution of an individual by examining their DNA sequence. This helped to reveal previously unknown characteristics of these historically significant horses.
  • These insights could help in managing breeding choices for specific traits and ensuring the health and vitality of future horse populations.

Conclusion of the Study

  • The study provides valuable insights into the history and development of the Thoroughbred and Clydesdale horse breeds. These could be utilized in efforts aimed at preserving or recreating specific breed traits.
  • The study also throws light on genomic changes in the endangered Przewalski’s horse following a century of captive breeding. This knowledge could contribute to future conservation efforts.

Cite This Article

APA
Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T, Petersen JL, Orlando L. (2023). Imputed genomes of historical horses provide insights into modern breeding. iScience, 26(7), 107104. https://doi.org/10.1016/j.isci.2023.107104

Publication

iScience
ISSN: 2589-0042
NlmUniqueID: 101724038
Country: United States
Language: English
Volume: 26
Issue: 7
Pages: 107104
PII: 107104

Researcher Affiliations

Todd, Evelyn T
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France.
Fromentier, Aurore
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France.
Sutcliffe, Richard
  • Glasgow Museums Resource Centre, 200 Woodhead Road, Nitshill, G53 7NN Glasgow, UK.
Running Horse Collin, Yvette
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France.
Perdereau, Aude
  • Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, 91042 Evry, France.
Aury, Jean-Marc
  • Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, 91042 Evry, France.
Èche, Camille
  • GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, 31326 Castanet-Tolosan Cedex, France.
Bouchez, Olivier
  • GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, 31326 Castanet-Tolosan Cedex, France.
Donnadieu, Cécile
  • GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, 31326 Castanet-Tolosan Cedex, France.
Wincker, Patrick
  • Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, 91042 Evry, France.
Kalbfleisch, Ted
  • MH Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546-0091, USA.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska-Lincoln, 3940 Fair St, Lincoln, NE 68583-0908, USA.
Orlando, Ludovic
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France.

Conflict of Interest Statement

The authors declare no competing interests.

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