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 agro-ecosystems. 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.
Fil: Salim, Bashir. University of Khartoum; Sudán
Fil: Takeshima, Shin nosuke. Jumonji University; Japón
Fil: Nakao, Ryo. Hokkaido University; Japón
Fil: Moustafa, Mohamed A. M.. Hokkaido University; Japón
Fil: Ahmed, Mohamed Khair A.. University of Khartoum; Sudán
Fil: Kambal, Sumaya. National University Biomedical Research Institute; Sudán
Fil: Mwacharo, Joram M.. International Centre for Agricultural Research in the Dry Areas; Líbano
Fil: Alkhaibari, Abeer M.. University of Tabuk; Arabia Saudita
Fil: Giovambattista, Guillermo. 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
Materia
BOLA-DRB3
GENETIC DIVERSITY
BAGGARA
KENANA
BUTANA
SEQUENCE-BASED TYPING
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:11336/158090
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/158090
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
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, GuillermoBOLA-DRB3GENETIC DIVERSITYBAGGARAKENANABUTANASEQUENCE-BASED TYPINGhttps://purl.org/becyt/ford/4.3https://purl.org/becyt/ford/4Autochthonous 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 agro-ecosystems. 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.Fil: Salim, Bashir. University of Khartoum; SudánFil: Takeshima, Shin nosuke. Jumonji University; JapónFil: Nakao, Ryo. Hokkaido University; JapónFil: Moustafa, Mohamed A. M.. Hokkaido University; JapónFil: Ahmed, Mohamed Khair A.. University of Khartoum; SudánFil: Kambal, Sumaya. National University Biomedical Research Institute; SudánFil: Mwacharo, Joram M.. International Centre for Agricultural Research in the Dry Areas; LíbanoFil: Alkhaibari, Abeer M.. University of Tabuk; Arabia SauditaFil: Giovambattista, Guillermo. 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; ArgentinaNature Publishing Group2021-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/158090Salim, Bashir; Takeshima, Shin nosuke; Nakao, Ryo; Moustafa, Mohamed A. M.; Ahmed, Mohamed Khair A.; et al.; BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds; Nature Publishing Group; Scientific Reports; 11; 17202; 8-2021; 1-152045-2322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-021-96330-7info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-021-96330-7info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:14:41Zoai:ri.conicet.gov.ar:11336/158090instacron: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:34982025-09-29 10:14:42.231CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
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
BOLA-DRB3
GENETIC DIVERSITY
BAGGARA
KENANA
BUTANA
SEQUENCE-BASED TYPING
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 BOLA-DRB3
GENETIC DIVERSITY
BAGGARA
KENANA
BUTANA
SEQUENCE-BASED TYPING
topic BOLA-DRB3
GENETIC DIVERSITY
BAGGARA
KENANA
BUTANA
SEQUENCE-BASED TYPING
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.3
https://purl.org/becyt/ford/4
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 agro-ecosystems. 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.
Fil: Salim, Bashir. University of Khartoum; Sudán
Fil: Takeshima, Shin nosuke. Jumonji University; Japón
Fil: Nakao, Ryo. Hokkaido University; Japón
Fil: Moustafa, Mohamed A. M.. Hokkaido University; Japón
Fil: Ahmed, Mohamed Khair A.. University of Khartoum; Sudán
Fil: Kambal, Sumaya. National University Biomedical Research Institute; Sudán
Fil: Mwacharo, Joram M.. International Centre for Agricultural Research in the Dry Areas; Líbano
Fil: Alkhaibari, Abeer M.. University of Tabuk; Arabia Saudita
Fil: Giovambattista, Guillermo. 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
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 agro-ecosystems. 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 2021-08
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/11336/158090
Salim, Bashir; Takeshima, Shin nosuke; Nakao, Ryo; Moustafa, Mohamed A. M.; Ahmed, Mohamed Khair A.; et al.; BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds; Nature Publishing Group; Scientific Reports; 11; 17202; 8-2021; 1-15
2045-2322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/158090
identifier_str_mv Salim, Bashir; Takeshima, Shin nosuke; Nakao, Ryo; Moustafa, Mohamed A. M.; Ahmed, Mohamed Khair A.; et al.; BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds; Nature Publishing Group; Scientific Reports; 11; 17202; 8-2021; 1-15
2045-2322
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.nature.com/articles/s41598-021-96330-7
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-021-96330-7
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 Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
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 13.070432

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