Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse

Background: Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefcients have been historically estimated by using...

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Autores: Perdomo González, Davinia Isabel, Laseca, Nora, Demyda-Peyrás, Sebastián, Valera Córdoba, María Mercedes, Cervantes, Isabel, Molina, Antonio
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Recursos:Universidad de Sevilla (US)
Repositorio:idUS. Depósito de Investigación de la Universidad de Sevilla
OAI Identifier:oai:idus.us.es:11441/156610
Acesso em linha:https://hdl.handle.net/11441/156610
Access Level:acceso abierto
Palavra-chave:Genomic inbreeding
Horses
Pedigree inbreeding
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spelling Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horsePerdomo González, Davinia IsabelLaseca, NoraDemyda-Peyrás, SebastiánValera Córdoba, María MercedesCervantes, IsabelMolina, AntonioGenomic inbreedingHorsesPedigree inbreedingBackground: Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefcients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefcients have come to the forefront in this feld. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE popula‑ tion (344,718 horses) was used to estimate Classical (F), Ballou’s ancestral, Kalinowski’s ancestral, Kalinowski’s new and the ancestral history coefcient values. In addition, genotypic data from a selected population of 805 PRE individu‑ als was used to determine the individual inbreeding coefcient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefcients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estima‑ tions will give the data greater reliability. Results: The mean values of the pedigree-based inbreeding coefcients ranged from 0.01 (F for the last 3 genera‑ tions -F3-) to 0.44 (ancestral history coefcient) and the mean values of genomic-based inbreeding coefcients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Signifcant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreed‑ ing highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. Conclusions: Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigreebased genetic studies with very large efective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efciently and economi‑ cally than with massive genotyping.Premio Anual Publicación Científica Destacada de la US. Escuela Técnica Superior de Ingeniería AgronómicaSpringerAgronomía2022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttps://hdl.handle.net/11441/156610reponame:idUS. Depósito de Investigación de la Universidad de Sevillainstname:Universidad de Sevilla (US)InglésJournal of Animal Science and Biotechnology, 13 (127).info:eu-repo/semantics/openAccessoai:idus.us.es:11441/1566102026-06-17T12:51:07Z
dc.title.none.fl_str_mv Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse
title Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse
spellingShingle Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse
Perdomo González, Davinia Isabel
Genomic inbreeding
Horses
Pedigree inbreeding
title_short Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse
title_full Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse
title_fullStr Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse
title_full_unstemmed Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse
title_sort Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse
dc.creator.none.fl_str_mv Perdomo González, Davinia Isabel
Laseca, Nora
Demyda-Peyrás, Sebastián
Valera Córdoba, María Mercedes
Cervantes, Isabel
Molina, Antonio
author Perdomo González, Davinia Isabel
author_facet Perdomo González, Davinia Isabel
Laseca, Nora
Demyda-Peyrás, Sebastián
Valera Córdoba, María Mercedes
Cervantes, Isabel
Molina, Antonio
author_role author
author2 Laseca, Nora
Demyda-Peyrás, Sebastián
Valera Córdoba, María Mercedes
Cervantes, Isabel
Molina, Antonio
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Agronomía
dc.subject.none.fl_str_mv Genomic inbreeding
Horses
Pedigree inbreeding
topic Genomic inbreeding
Horses
Pedigree inbreeding
description Background: Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefcients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefcients have come to the forefront in this feld. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE popula‑ tion (344,718 horses) was used to estimate Classical (F), Ballou’s ancestral, Kalinowski’s ancestral, Kalinowski’s new and the ancestral history coefcient values. In addition, genotypic data from a selected population of 805 PRE individu‑ als was used to determine the individual inbreeding coefcient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefcients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estima‑ tions will give the data greater reliability. Results: The mean values of the pedigree-based inbreeding coefcients ranged from 0.01 (F for the last 3 genera‑ tions -F3-) to 0.44 (ancestral history coefcient) and the mean values of genomic-based inbreeding coefcients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Signifcant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreed‑ ing highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. Conclusions: Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigreebased genetic studies with very large efective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efciently and economi‑ cally than with massive genotyping.
publishDate 2022
dc.date.none.fl_str_mv 2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/11441/156610
url https://hdl.handle.net/11441/156610
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Journal of Animal Science and Biotechnology, 13 (127).
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:idUS. Depósito de Investigación de la Universidad de Sevilla
instname:Universidad de Sevilla (US)
instname_str Universidad de Sevilla (US)
reponame_str idUS. Depósito de Investigación de la Universidad de Sevilla
collection idUS. Depósito de Investigación de la Universidad de Sevilla
repository.name.fl_str_mv
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