BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds

Autores
Salim, Bashir; Takeshima, Shin‑nosuke; Nakao, Ryo; Moustafa, Mohamed A. M.; Ahmed, Mohamed‑Khair A.; Kambal, Sumaya; Mwacharo, Joram M.; Alkhaibari, Abeer M.; Giovambattista, Guillermo
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Autochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agroecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan’s harsh environment.
Instituto de Genética Veterinaria
Materia
Ciencias Veterinarias
Evolution
Genetics
Immunology
Molecular biology
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/130027

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network_name_str SEDICI (UNLP)
spelling BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breedsSalim, BashirTakeshima, Shin‑nosukeNakao, RyoMoustafa, Mohamed A. M.Ahmed, Mohamed‑Khair A.Kambal, SumayaMwacharo, Joram M.Alkhaibari, Abeer M.Giovambattista, GuillermoCiencias VeterinariasEvolutionGeneticsImmunologyMolecular biologyAutochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agroecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan’s harsh environment.Instituto de Genética Veterinaria2021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://sedici.unlp.edu.ar/handle/10915/130027enginfo:eu-repo/semantics/altIdentifier/issn/2045-2322info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-021-96330-7info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International (CC BY 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:32:41Zoai:sedici.unlp.edu.ar:10915/130027Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:32:42.184SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds
title BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds
spellingShingle BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds
Salim, Bashir
Ciencias Veterinarias
Evolution
Genetics
Immunology
Molecular biology
title_short BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds
title_full BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds
title_fullStr BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds
title_full_unstemmed BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds
title_sort BoLA‑DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds
dc.creator.none.fl_str_mv Salim, Bashir
Takeshima, Shin‑nosuke
Nakao, Ryo
Moustafa, Mohamed A. M.
Ahmed, Mohamed‑Khair A.
Kambal, Sumaya
Mwacharo, Joram M.
Alkhaibari, Abeer M.
Giovambattista, Guillermo
author Salim, Bashir
author_facet Salim, Bashir
Takeshima, Shin‑nosuke
Nakao, Ryo
Moustafa, Mohamed A. M.
Ahmed, Mohamed‑Khair A.
Kambal, Sumaya
Mwacharo, Joram M.
Alkhaibari, Abeer M.
Giovambattista, Guillermo
author_role author
author2 Takeshima, Shin‑nosuke
Nakao, Ryo
Moustafa, Mohamed A. M.
Ahmed, Mohamed‑Khair A.
Kambal, Sumaya
Mwacharo, Joram M.
Alkhaibari, Abeer M.
Giovambattista, Guillermo
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Ciencias Veterinarias
Evolution
Genetics
Immunology
Molecular biology
topic Ciencias Veterinarias
Evolution
Genetics
Immunology
Molecular biology
dc.description.none.fl_txt_mv Autochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agroecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan’s harsh environment.
Instituto de Genética Veterinaria
description Autochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agroecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan’s harsh environment.
publishDate 2021
dc.date.none.fl_str_mv 2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
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info:ar-repo/semantics/articulo
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status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/130027
url http://sedici.unlp.edu.ar/handle/10915/130027
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/2045-2322
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-021-96330-7
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/4.0/
Creative Commons Attribution 4.0 International (CC BY 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
Creative Commons Attribution 4.0 International (CC BY 4.0)
dc.format.none.fl_str_mv application/pdf
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collection SEDICI (UNLP)
instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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