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

doi:10.1016/j.isci.2023.107104

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

Producción científica: Article › revisión exhaustiva

16 Citas (Scopus)

Resumen

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.

Idioma original	English
Número de artículo	107104
Publicación	iScience
Volumen	26
N.º	7
DOI	https://doi.org/10.1016/j.isci.2023.107104
Estado	Published - jul 21 2023

Nota bibliográfica

Publisher Copyright:
© 2023 The Authors

Financiación

The Genoscope sequencing platform is partly funded by the France Génomique National infrastructure, is part of the BUCEPHALE project and was funded by the French Government “Investissement d'Avenir” managed by Agence Nationale pour la Recherche (ANR-10-INBS-09). This work was supported by CNRS and Université Paul Sabatier (AnimalFarm International Research Program, IRP), the France Génomique “Grands Projets” program (BUCEPHALE and MARENGO), and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 681605 - PEGASUS). Dr Yvette Running Horse Collin was supported by the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement 890702 (MethylRIDE). The bone sample of Baron O'Buchylverie was collected with thanks to BBC Scotland, The Canadian Film for Video Production Tax Credit, The Canadian Media Fund, Clyde Vet Group, Creative Scotland, Glasgow Life, Graven, Infield Fly Productions, Ontario Creates, Rogers Cable Network Fund, and Stream Scotland. Conceptualization, L.O.; Methodology, E.T.T. L.O.; Formal Analysis, E.T.T. L.O.; Visualization, E.T.T.; Resources, A.F. R.S. Y.R.H.C. A.P. J-M.A. C.E. O.B. C.D. P.W. T.K. J.L.P. L.O.; Writing- Original Draft, L.O. E.T.T. Writing – Review and Editing, L.O. E.T.T. with input from J.L.P. and Y.R.H.C. and all co-authors. The authors declare no competing interests. The Genoscope sequencing platform is partly funded by the France Génomique National infrastructure , is part of the BUCEPHALE project and was funded by the French Government “Investissement d’Avenir” managed by Agence Nationale pour la Recherche ( ANR-10-INBS-09 ). This work was supported by CNRS and Université Paul Sabatier (AnimalFarm International Research Program, IRP), the France Génomique “Grands Projets” program (BUCEPHALE and MARENGO), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 681605 - PEGASUS ). Dr Yvette Running Horse Collin was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement 890702 (MethylRIDE).

Financiadores	Número del financiador
AnimalFarm International Research Program
Canadian Film for Video Production Tax Credit
Canadian Media Fund
Clyde Vet Group
Stream Scotland
Université Paul Sabatier
Horizon 2020 Framework Programme
H2020 Marie Skłodowska-Curie Actions	890702
Institute for Research on Poverty
H2020 European Research Council
French Agence Nationale de la Recherche	ANR-10-INBS-09
CNRS Centre National de la Recherche Scientifique
Horizon 2020	681605 - PEGASUS

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title = "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.",

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AU - Sutcliffe, Richard

AU - Running Horse Collin, Yvette

AU - Perdereau, Aude

AU - Aury, Jean Marc

AU - Èche, Camille

AU - Bouchez, Olivier

AU - Donnadieu, Cécile

AU - Wincker, Patrick

AU - Kalbfleisch, Ted

AU - Petersen, Jessica L.

AU - Orlando, Ludovic

PY - 2023/7/21

Y1 - 2023/7/21

N2 - 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.

AB - 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.

KW - Equine genetics

KW - Genomics

KW - Phylogenetics

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Imputed genomes of historical horses provide insights into modern breeding

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