Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed

In autochthonous livestock breeds with small populations, such as the Rubia Galega from Galicia (Spain), mating between relatives is common and can lead to inbreeding depression. Genomic inbreeding coefficients were estimated for 4984 animals using~63,000 SNPs to assess inbreeding depression in four...

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Autores: Mejuto Vázquez, Nicolás, Hervás Rivero, Carlos, Rodríguez Bermúdez, Ruth, López Carbonell, David, Hermida Prieto, Miguel, Martínez Portela, Paulino, Varona, Luis
Formato: artículo
Fecha de publicación:2025
País:España
Recursos:Universidad de Santiago de Compostela (USC)
Repositorio:Minerva. Repositorio Institucional de la Universidad de Santiago de Compostela
Idioma:inglés
OAI Identifier:oai:minerva.usc.gal:10347/44936
Acesso em linha:https://hdl.handle.net/10347/44936
Access Level:acceso abierto
Palavra-chave:BLUP
indigenous
mstn
run of homozygosity
SNP
240111 Patología animal
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spelling Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle BreedMejuto Vázquez, NicolásHervás Rivero, CarlosRodríguez Bermúdez, RuthLópez Carbonell, DavidHermida Prieto, MiguelMartínez Portela, PaulinoVarona, LuisBLUPindigenousmstnrun of homozygositySNP240111 Patología animalIn autochthonous livestock breeds with small populations, such as the Rubia Galega from Galicia (Spain), mating between relatives is common and can lead to inbreeding depression. Genomic inbreeding coefficients were estimated for 4984 animals using~63,000 SNPs to assess inbreeding depression in four key traits: age at first calving (AFC) with 3503 records, calving interval (CI) with 3315 records, birth weight (BW) with 4878 records and weight at 210 days (W210) with 3285 records. Runs of homozygosity were sorted by length ([1,2], (2,4], (4,8], (8,16], > 16 Mb), and the corresponding inbreeding coefficients (FROH>1, FROH>2, FROH>4, FROH>8, FROH>16) were calculated using the consecutiveRUNs R package. A Genomic BLUP (GBLUP) was conducted for each FROH estimate using the BLUPF90+ programs. The results revealed significant inbreeding depression for AFC and CI, whereas W210 and BW exhibited similar inbreeding trends, but the effects of inbreeding on these traits were not statistically significant. To further explore the genetic basis of inbreeding depression, SNPs located within ROHs were tested, though a t-test, for their association with phenotypic traits. Genes located in significant regions (−log(p-value) > 3 from t-test) were annotated using EnsemblBioMart within a ± 0.5 Mb window. Recent inbreeding (ROH > 8 Mb) showed significant negative effects on reproductive traits, and key genomic regions—particularly on chromosome 2 involving MSTN, NAB1, and COL5A2—were linked to increased AFC and reduced BW and W210; ROH-based inbreeding estimates proved effective in detecting inbreeding depression in this native breed. Overall, ROH-based analyses revealed genomic regions and candidate genes, notably MSTN, contributing to inbreeding depression and key production traits in Rubia Galega cattle.WileyUniversidade de Santiago de Compostela. Departamento de Anatomía, Produción Animal e Ciencias Clínicas VeterinariasUniversidade de Santiago de Compostela. Departamento de Xenética20252025-12-1620252025-12-16journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10347/44936reponame:Minerva. Repositorio Institucional de la Universidad de Santiago de Compostelainstname:Universidad de Santiago de Compostela (USC)InglésengAxencia Galega de Innovación Not available ED431C 2022%2F33open accesshttp://purl.org/coar/access_right/c_abf2© 2025 The Author(s). Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:minerva.usc.gal:10347/449362026-06-15T12:47:27Z
dc.title.none.fl_str_mv Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed
title Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed
spellingShingle Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed
Mejuto Vázquez, Nicolás
BLUP
indigenous
mstn
run of homozygosity
SNP
240111 Patología animal
title_short Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed
title_full Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed
title_fullStr Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed
title_full_unstemmed Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed
title_sort Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed
dc.creator.none.fl_str_mv Mejuto Vázquez, Nicolás
Hervás Rivero, Carlos
Rodríguez Bermúdez, Ruth
López Carbonell, David
Hermida Prieto, Miguel
Martínez Portela, Paulino
Varona, Luis
author Mejuto Vázquez, Nicolás
author_facet Mejuto Vázquez, Nicolás
Hervás Rivero, Carlos
Rodríguez Bermúdez, Ruth
López Carbonell, David
Hermida Prieto, Miguel
Martínez Portela, Paulino
Varona, Luis
author_role author
author2 Hervás Rivero, Carlos
Rodríguez Bermúdez, Ruth
López Carbonell, David
Hermida Prieto, Miguel
Martínez Portela, Paulino
Varona, Luis
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade de Santiago de Compostela. Departamento de Anatomía, Produción Animal e Ciencias Clínicas Veterinarias
Universidade de Santiago de Compostela. Departamento de Xenética
dc.subject.none.fl_str_mv BLUP
indigenous
mstn
run of homozygosity
SNP
240111 Patología animal
topic BLUP
indigenous
mstn
run of homozygosity
SNP
240111 Patología animal
description In autochthonous livestock breeds with small populations, such as the Rubia Galega from Galicia (Spain), mating between relatives is common and can lead to inbreeding depression. Genomic inbreeding coefficients were estimated for 4984 animals using~63,000 SNPs to assess inbreeding depression in four key traits: age at first calving (AFC) with 3503 records, calving interval (CI) with 3315 records, birth weight (BW) with 4878 records and weight at 210 days (W210) with 3285 records. Runs of homozygosity were sorted by length ([1,2], (2,4], (4,8], (8,16], > 16 Mb), and the corresponding inbreeding coefficients (FROH>1, FROH>2, FROH>4, FROH>8, FROH>16) were calculated using the consecutiveRUNs R package. A Genomic BLUP (GBLUP) was conducted for each FROH estimate using the BLUPF90+ programs. The results revealed significant inbreeding depression for AFC and CI, whereas W210 and BW exhibited similar inbreeding trends, but the effects of inbreeding on these traits were not statistically significant. To further explore the genetic basis of inbreeding depression, SNPs located within ROHs were tested, though a t-test, for their association with phenotypic traits. Genes located in significant regions (−log(p-value) > 3 from t-test) were annotated using EnsemblBioMart within a ± 0.5 Mb window. Recent inbreeding (ROH > 8 Mb) showed significant negative effects on reproductive traits, and key genomic regions—particularly on chromosome 2 involving MSTN, NAB1, and COL5A2—were linked to increased AFC and reduced BW and W210; ROH-based inbreeding estimates proved effective in detecting inbreeding depression in this native breed. Overall, ROH-based analyses revealed genomic regions and candidate genes, notably MSTN, contributing to inbreeding depression and key production traits in Rubia Galega cattle.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025-12-16
2025
2025-12-16
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/10347/44936
url https://hdl.handle.net/10347/44936
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Axencia Galega de Innovación Not available ED431C 2022%2F33
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv reponame:Minerva. Repositorio Institucional de la Universidad de Santiago de Compostela
instname:Universidad de Santiago de Compostela (USC)
instname_str Universidad de Santiago de Compostela (USC)
reponame_str Minerva. Repositorio Institucional de la Universidad de Santiago de Compostela
collection Minerva. Repositorio Institucional de la Universidad de Santiago de Compostela
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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