Imputed genomes of historical horses provide insights into modern breeding
Evelyn T. Todd,
Aurore Fromentier,
Richard Sutcliffe,
Yvette Running Horse Collin,
Aude Perdereau,
Jean-Marc Aury,
Camille Èche,
Olivier Bouchez,
Cécile Donnadieu,
Patrick Wincker,
Ted Kalbfleisch,
Jessica L. Petersen,
Ludovic Orlando
Affiliations
Evelyn T. Todd
Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
Aurore Fromentier
Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
Richard Sutcliffe
Glasgow Museums Resource Centre, 200 Woodhead Road, Nitshill, G53 7NN Glasgow, UK
Yvette Running Horse Collin
Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
Aude Perdereau
Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
Jean-Marc Aury
Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
Camille Èche
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
Olivier Bouchez
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
Cécile Donnadieu
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
Patrick Wincker
Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
Ted Kalbfleisch
MH Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546-0091, USA
Jessica L. Petersen
Department of Animal Science, University of Nebraska-Lincoln, 3940 Fair St, Lincoln, NE 68583-0908, USA
Ludovic Orlando
Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France; Corresponding author
Summary: 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.