Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle

Autores
Carignano, Hugo Adrián; Roldan, Dana L.; Beribe, María José; Raschia, Maria Agustina; Amadio, Ariel Fernando; Nani, Juan Pablo; Gutiérrez, Gerónimo; Alvarez, Irene; Trono, Karina Gabriela; Poli, Mario Andres; Miretti, Marcos Mateo
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral load (PVL) set-point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait. Results: We quantified anti-p24 response and total leukocytes count in peripheral blood from 1800 cows and used these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of the variance captured by all QC-passed SNPs represented 0.63 (SE±0.14) of the phenotypic variance for PVL and 0.56 (SE±0.15) for WBCs. Overall, significant associations (Bonferroni´s corrected -log10p>5.94) were shared for both phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium (LD) extent (r2=0.22±0.27 at inter-SNP distance of 25-50 kb). The SNPs and LD blocks indicated genes potentially associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF, IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D; ABT1, GCM1, PRRC2A). Conclusions: Data obtained represent a step forward to understand the biology of BLV-bovine interaction, and provide genetic information potentially applicable to selective breeding programs.
Fil: Carignano, Hugo Adrián. Instituto de Genética; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Roldan, Dana L.. Instituto de Genética; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Beribe, María José. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina
Fil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Instituto de Genética; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Amadio, Ariel Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina
Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Gutiérrez, Gerónimo. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Alvarez, Irene. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Trono, Karina Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina
Fil: Miretti, Marcos Mateo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
BOVINE LEUKEMIA VIRUS
LEVEL OF INFECTION
WHOLE GENOME ASSOCIATION STUDY
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:11336/91933
Acceder
id CONICETDig_9db6f0a4940708a5acd9001820102d44
oai_identifier_str oai:ri.conicet.gov.ar:11336/91933
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattleCarignano, Hugo AdriánRoldan, Dana L.Beribe, María JoséRaschia, Maria AgustinaAmadio, Ariel FernandoNani, Juan PabloGutiérrez, GerónimoAlvarez, IreneTrono, Karina GabrielaPoli, Mario AndresMiretti, Marcos MateoBOVINE LEUKEMIA VIRUSLEVEL OF INFECTIONWHOLE GENOME ASSOCIATION STUDYhttps://purl.org/becyt/ford/4.3https://purl.org/becyt/ford/4Background: Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral load (PVL) set-point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait. Results: We quantified anti-p24 response and total leukocytes count in peripheral blood from 1800 cows and used these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of the variance captured by all QC-passed SNPs represented 0.63 (SE±0.14) of the phenotypic variance for PVL and 0.56 (SE±0.15) for WBCs. Overall, significant associations (Bonferroni´s corrected -log10p>5.94) were shared for both phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium (LD) extent (r2=0.22±0.27 at inter-SNP distance of 25-50 kb). The SNPs and LD blocks indicated genes potentially associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF, IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D; ABT1, GCM1, PRRC2A). Conclusions: Data obtained represent a step forward to understand the biology of BLV-bovine interaction, and provide genetic information potentially applicable to selective breeding programs.Fil: Carignano, Hugo Adrián. Instituto de Genética; Argentina. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Roldan, Dana L.. Instituto de Genética; Argentina. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Beribe, María José. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; ArgentinaFil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Instituto de Genética; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Amadio, Ariel Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; ArgentinaFil: Gutiérrez, Gerónimo. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Alvarez, Irene. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Trono, Karina Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; ArgentinaFil: Miretti, Marcos Mateo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaBioMed Central2018-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/91933Carignano, Hugo Adrián; Roldan, Dana L.; Beribe, María José; Raschia, Maria Agustina; Amadio, Ariel Fernando; et al.; Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle; BioMed Central; BMC Genomics; 19; 142; 2-2018; 1-151471-2164CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4523-2info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-018-4523-2info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:19:21Zoai:ri.conicet.gov.ar:11336/91933instacron: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:34982025-10-15 15:19:21.453CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
title Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
spellingShingle Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
Carignano, Hugo Adrián
BOVINE LEUKEMIA VIRUS
LEVEL OF INFECTION
WHOLE GENOME ASSOCIATION STUDY
title_short Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
title_full Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
title_fullStr Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
title_full_unstemmed Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
title_sort Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
dc.creator.none.fl_str_mv Carignano, Hugo Adrián
Roldan, Dana L.
Beribe, María José
Raschia, Maria Agustina
Amadio, Ariel Fernando
Nani, Juan Pablo
Gutiérrez, Gerónimo
Alvarez, Irene
Trono, Karina Gabriela
Poli, Mario Andres
Miretti, Marcos Mateo
author Carignano, Hugo Adrián
author_facet Carignano, Hugo Adrián
Roldan, Dana L.
Beribe, María José
Raschia, Maria Agustina
Amadio, Ariel Fernando
Nani, Juan Pablo
Gutiérrez, Gerónimo
Alvarez, Irene
Trono, Karina Gabriela
Poli, Mario Andres
Miretti, Marcos Mateo
author_role author
author2 Roldan, Dana L.
Beribe, María José
Raschia, Maria Agustina
Amadio, Ariel Fernando
Nani, Juan Pablo
Gutiérrez, Gerónimo
Alvarez, Irene
Trono, Karina Gabriela
Poli, Mario Andres
Miretti, Marcos Mateo
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv BOVINE LEUKEMIA VIRUS
LEVEL OF INFECTION
WHOLE GENOME ASSOCIATION STUDY
topic BOVINE LEUKEMIA VIRUS
LEVEL OF INFECTION
WHOLE GENOME ASSOCIATION STUDY
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.3
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Background: Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral load (PVL) set-point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait. Results: We quantified anti-p24 response and total leukocytes count in peripheral blood from 1800 cows and used these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of the variance captured by all QC-passed SNPs represented 0.63 (SE±0.14) of the phenotypic variance for PVL and 0.56 (SE±0.15) for WBCs. Overall, significant associations (Bonferroni´s corrected -log10p>5.94) were shared for both phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium (LD) extent (r2=0.22±0.27 at inter-SNP distance of 25-50 kb). The SNPs and LD blocks indicated genes potentially associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF, IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D; ABT1, GCM1, PRRC2A). Conclusions: Data obtained represent a step forward to understand the biology of BLV-bovine interaction, and provide genetic information potentially applicable to selective breeding programs.
Fil: Carignano, Hugo Adrián. Instituto de Genética; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Roldan, Dana L.. Instituto de Genética; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Beribe, María José. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina
Fil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Instituto de Genética; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Amadio, Ariel Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina
Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Gutiérrez, Gerónimo. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Alvarez, Irene. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Trono, Karina Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina
Fil: Miretti, Marcos Mateo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Background: Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral load (PVL) set-point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait. Results: We quantified anti-p24 response and total leukocytes count in peripheral blood from 1800 cows and used these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of the variance captured by all QC-passed SNPs represented 0.63 (SE±0.14) of the phenotypic variance for PVL and 0.56 (SE±0.15) for WBCs. Overall, significant associations (Bonferroni´s corrected -log10p>5.94) were shared for both phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium (LD) extent (r2=0.22±0.27 at inter-SNP distance of 25-50 kb). The SNPs and LD blocks indicated genes potentially associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF, IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D; ABT1, GCM1, PRRC2A). Conclusions: Data obtained represent a step forward to understand the biology of BLV-bovine interaction, and provide genetic information potentially applicable to selective breeding programs.
publishDate 2018
dc.date.none.fl_str_mv 2018-02
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/11336/91933
Carignano, Hugo Adrián; Roldan, Dana L.; Beribe, María José; Raschia, Maria Agustina; Amadio, Ariel Fernando; et al.; Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle; BioMed Central; BMC Genomics; 19; 142; 2-2018; 1-15
1471-2164
CONICET Digital
CONICET
url http://hdl.handle.net/11336/91933
identifier_str_mv Carignano, Hugo Adrián; Roldan, Dana L.; Beribe, María José; Raschia, Maria Agustina; Amadio, Ariel Fernando; et al.; Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle; BioMed Central; BMC Genomics; 19; 142; 2-2018; 1-15
1471-2164
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://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4523-2
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-018-4523-2
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
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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
_version_ 1846083342446886912
score 13.22299

Publicaciones similares