Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

Autores
Marcuzzi, Olivia; Calcaterra, Francisco; Loza Vega, Ariel Jhonny; Ortega Masague, Maria Florencia; Armstrong, Eileen; Pereira Rico, Juan A.; Jara Tellechea, Eugenio Salvador; Olivera, L. Hernán; Peral Garcia, Pilar; Giovambattista, Guillermo
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.
Instituto de Investigación Animal del Chaco Semiárido
Fil: Marcuzzi, Olivia. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Marcuzzi, Olivia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Calcaterra, Francisco. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Calcaterra, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Loza Vega, Ariel Jhonny. Universidad Autónoma Gabriel René Moreno. Facultad de Ciencias Veterinarias; Bolivia
Fil: Ortega Masague, Maria Florencia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Animal del Chaco Semiárido; Argentina
Fil: Armstrong, Eileen. Universidad de la República. Facultad de Veterinaria. Unidad Académica Genética y Mejora Animal. Departamento de Producción Animal; Uruguay
Fil: Pereira Rico, Juan A. Universidad Autónoma Gabriel René Moreno. Facultad de Ciencias Veterinarias; Bolivia
Fil: Jara Tellechea, Eugenio Salvador. Universidad de la República. Facultad de Veterinaria. Unidad Académica Genética y Mejora Animal. Departamento de Producción Animal; Uruguay
Fil: Olivera, L. Hernán. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Olivera, L. Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Peral Garcia, Pilar. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Peral Garcia, Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Giovambattista, Guillermo. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria "Ing. Fernando N. Dulout”; Argentina
Fil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fuente
Animal Genetics 55 (4) : 527-539. (August 2024)
Materia
Ganado Bovino
Característica Genómica
Endogamia
Variación Genética
América del Sur
Cattle
Genomic Features
Inbreeding
Genetic Variation
South America
Genetic Resources Conservation
Conservación de Recursos Genéticos
Ganado Criollo
Creole Cattle
Nivel de accesibilidad
acceso restringido
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/23166
Acceder
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spelling Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South AmericaMarcuzzi, OliviaCalcaterra, FranciscoLoza Vega, Ariel JhonnyOrtega Masague, Maria FlorenciaArmstrong, EileenPereira Rico, Juan A.Jara Tellechea, Eugenio SalvadorOlivera, L. HernánPeral Garcia, PilarGiovambattista, GuillermoGanado BovinoCaracterística GenómicaEndogamiaVariación GenéticaAmérica del SurCattleGenomic FeaturesInbreedingGenetic VariationSouth AmericaGenetic Resources ConservationConservación de Recursos GenéticosGanado CriolloCreole CattleThe conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.Instituto de Investigación Animal del Chaco SemiáridoFil: Marcuzzi, Olivia. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaFil: Marcuzzi, Olivia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaFil: Calcaterra, Francisco. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaFil: Calcaterra, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaFil: Loza Vega, Ariel Jhonny. Universidad Autónoma Gabriel René Moreno. Facultad de Ciencias Veterinarias; BoliviaFil: Ortega Masague, Maria Florencia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Animal del Chaco Semiárido; ArgentinaFil: Armstrong, Eileen. Universidad de la República. Facultad de Veterinaria. Unidad Académica Genética y Mejora Animal. Departamento de Producción Animal; UruguayFil: Pereira Rico, Juan A. Universidad Autónoma Gabriel René Moreno. Facultad de Ciencias Veterinarias; BoliviaFil: Jara Tellechea, Eugenio Salvador. Universidad de la República. Facultad de Veterinaria. Unidad Académica Genética y Mejora Animal. Departamento de Producción Animal; UruguayFil: Olivera, L. Hernán. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaFil: Olivera, L. Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaFil: Peral Garcia, Pilar. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaFil: Peral Garcia, Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaFil: Giovambattista, Guillermo. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria "Ing. Fernando N. Dulout”; ArgentinaFil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; ArgentinaWiley2025-07-25T11:55:55Z2025-07-25T11:55:55Z2024-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/23166https://onlinelibrary.wiley.com/doi/10.1111/age.134350268-91461365-2052https://doi.org/10.1111/age.13435Animal Genetics 55 (4) : 527-539. (August 2024)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-29T13:47:26Zoai:localhost:20.500.12123/23166instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:47:26.387INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America
title Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America
spellingShingle Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America
Marcuzzi, Olivia
Ganado Bovino
Característica Genómica
Endogamia
Variación Genética
América del Sur
Cattle
Genomic Features
Inbreeding
Genetic Variation
South America
Genetic Resources Conservation
Conservación de Recursos Genéticos
Ganado Criollo
Creole Cattle
title_short Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America
title_full Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America
title_fullStr Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America
title_full_unstemmed Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America
title_sort Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America
dc.creator.none.fl_str_mv Marcuzzi, Olivia
Calcaterra, Francisco
Loza Vega, Ariel Jhonny
Ortega Masague, Maria Florencia
Armstrong, Eileen
Pereira Rico, Juan A.
Jara Tellechea, Eugenio Salvador
Olivera, L. Hernán
Peral Garcia, Pilar
Giovambattista, Guillermo
author Marcuzzi, Olivia
author_facet Marcuzzi, Olivia
Calcaterra, Francisco
Loza Vega, Ariel Jhonny
Ortega Masague, Maria Florencia
Armstrong, Eileen
Pereira Rico, Juan A.
Jara Tellechea, Eugenio Salvador
Olivera, L. Hernán
Peral Garcia, Pilar
Giovambattista, Guillermo
author_role author
author2 Calcaterra, Francisco
Loza Vega, Ariel Jhonny
Ortega Masague, Maria Florencia
Armstrong, Eileen
Pereira Rico, Juan A.
Jara Tellechea, Eugenio Salvador
Olivera, L. Hernán
Peral Garcia, Pilar
Giovambattista, Guillermo
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Ganado Bovino
Característica Genómica
Endogamia
Variación Genética
América del Sur
Cattle
Genomic Features
Inbreeding
Genetic Variation
South America
Genetic Resources Conservation
Conservación de Recursos Genéticos
Ganado Criollo
Creole Cattle
topic Ganado Bovino
Característica Genómica
Endogamia
Variación Genética
América del Sur
Cattle
Genomic Features
Inbreeding
Genetic Variation
South America
Genetic Resources Conservation
Conservación de Recursos Genéticos
Ganado Criollo
Creole Cattle
dc.description.none.fl_txt_mv The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.
Instituto de Investigación Animal del Chaco Semiárido
Fil: Marcuzzi, Olivia. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Marcuzzi, Olivia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Calcaterra, Francisco. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Calcaterra, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Loza Vega, Ariel Jhonny. Universidad Autónoma Gabriel René Moreno. Facultad de Ciencias Veterinarias; Bolivia
Fil: Ortega Masague, Maria Florencia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Animal del Chaco Semiárido; Argentina
Fil: Armstrong, Eileen. Universidad de la República. Facultad de Veterinaria. Unidad Académica Genética y Mejora Animal. Departamento de Producción Animal; Uruguay
Fil: Pereira Rico, Juan A. Universidad Autónoma Gabriel René Moreno. Facultad de Ciencias Veterinarias; Bolivia
Fil: Jara Tellechea, Eugenio Salvador. Universidad de la República. Facultad de Veterinaria. Unidad Académica Genética y Mejora Animal. Departamento de Producción Animal; Uruguay
Fil: Olivera, L. Hernán. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Olivera, L. Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Peral Garcia, Pilar. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Peral Garcia, Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
Fil: Giovambattista, Guillermo. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria "Ing. Fernando N. Dulout”; Argentina
Fil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Genética Veterinaria ‘Ing. Fernando N. Dulout’; Argentina
description The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.
publishDate 2024
dc.date.none.fl_str_mv 2024-08
2025-07-25T11:55:55Z
2025-07-25T11:55:55Z
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/20.500.12123/23166
https://onlinelibrary.wiley.com/doi/10.1111/age.13435
0268-9146
1365-2052
https://doi.org/10.1111/age.13435
url http://hdl.handle.net/20.500.12123/23166
https://onlinelibrary.wiley.com/doi/10.1111/age.13435
https://doi.org/10.1111/age.13435
identifier_str_mv 0268-9146
1365-2052
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv restrictedAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
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 Animal Genetics 55 (4) : 527-539. (August 2024)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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