Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares

Autores
Laseca, Nora; Molina, Antonio; Ramón, Manuel; Valera, Mercedes; Azcona, Florencia; Encina, Ana; Demyda-peyrás, Sebastian
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (FROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.
Fil: Laseca, Nora. Universidad de Córdoba; España
Fil: Molina, Antonio. Universidad de Córdoba; España
Fil: Ramón, Manuel. Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal Castilla La Mancha; España
Fil: Valera, Mercedes. Universidad de Sevilla; España
Fil: Azcona, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Encina, Ana. Universidad de Sevilla; España
Fil: Demyda-peyrás, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
FERTILITY
GENOMICS
INBREEDING
MARES
REPRODUCTIVE EFFICIENCY
ROHI
RUNS OF HOMOZYGOSITY
SNP
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/192270
Acceder
id CONICETDig_eb7a1644cd27613d33001366c33ba1ff
oai_identifier_str oai:ri.conicet.gov.ar:11336/192270
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in MaresLaseca, NoraMolina, AntonioRamón, ManuelValera, MercedesAzcona, FlorenciaEncina, AnaDemyda-peyrás, SebastianFERTILITYGENOMICSINBREEDINGMARESREPRODUCTIVE EFFICIENCYROHIRUNS OF HOMOZYGOSITYSNPhttps://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (FROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.Fil: Laseca, Nora. Universidad de Córdoba; EspañaFil: Molina, Antonio. Universidad de Córdoba; EspañaFil: Ramón, Manuel. Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal Castilla La Mancha; EspañaFil: Valera, Mercedes. Universidad de Sevilla; EspañaFil: Azcona, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Encina, Ana. Universidad de Sevilla; EspañaFil: Demyda-peyrás, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFrontiers Media2022-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/192270Laseca, Nora; Molina, Antonio; Ramón, Manuel; Valera, Mercedes; Azcona, Florencia; et al.; Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares; Frontiers Media; Frontiers in Veterinary Science; 9; 2-2022; 1-92297-1769CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.frontiersin.org/articles/10.3389/fvets.2022.754028/fullinfo:eu-repo/semantics/altIdentifier/doi/10.3389/fvets.2022.754028info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:01:04Zoai:ri.conicet.gov.ar:11336/192270instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:01:04.93CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares
title Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares
spellingShingle Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares
Laseca, Nora
FERTILITY
GENOMICS
INBREEDING
MARES
REPRODUCTIVE EFFICIENCY
ROHI
RUNS OF HOMOZYGOSITY
SNP
title_short Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares
title_full Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares
title_fullStr Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares
title_full_unstemmed Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares
title_sort Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares
dc.creator.none.fl_str_mv Laseca, Nora
Molina, Antonio
Ramón, Manuel
Valera, Mercedes
Azcona, Florencia
Encina, Ana
Demyda-peyrás, Sebastian
author Laseca, Nora
author_facet Laseca, Nora
Molina, Antonio
Ramón, Manuel
Valera, Mercedes
Azcona, Florencia
Encina, Ana
Demyda-peyrás, Sebastian
author_role author
author2 Molina, Antonio
Ramón, Manuel
Valera, Mercedes
Azcona, Florencia
Encina, Ana
Demyda-peyrás, Sebastian
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv FERTILITY
GENOMICS
INBREEDING
MARES
REPRODUCTIVE EFFICIENCY
ROHI
RUNS OF HOMOZYGOSITY
SNP
topic FERTILITY
GENOMICS
INBREEDING
MARES
REPRODUCTIVE EFFICIENCY
ROHI
RUNS OF HOMOZYGOSITY
SNP
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (FROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.
Fil: Laseca, Nora. Universidad de Córdoba; España
Fil: Molina, Antonio. Universidad de Córdoba; España
Fil: Ramón, Manuel. Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal Castilla La Mancha; España
Fil: Valera, Mercedes. Universidad de Sevilla; España
Fil: Azcona, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Encina, Ana. Universidad de Sevilla; España
Fil: Demyda-peyrás, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (FROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.
publishDate 2022
dc.date.none.fl_str_mv 2022-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/192270
Laseca, Nora; Molina, Antonio; Ramón, Manuel; Valera, Mercedes; Azcona, Florencia; et al.; Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares; Frontiers Media; Frontiers in Veterinary Science; 9; 2-2022; 1-9
2297-1769
CONICET Digital
CONICET
url http://hdl.handle.net/11336/192270
identifier_str_mv Laseca, Nora; Molina, Antonio; Ramón, Manuel; Valera, Mercedes; Azcona, Florencia; et al.; Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares; Frontiers Media; Frontiers in Veterinary Science; 9; 2-2022; 1-9
2297-1769
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.frontiersin.org/articles/10.3389/fvets.2022.754028/full
info:eu-repo/semantics/altIdentifier/doi/10.3389/fvets.2022.754028
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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