Genome-wide association study for somatic cell score in Argentinean dairy cattle

Autores
Nani, Juan Pablo; Raschia, Maria Agustina; Poli, Mario Andres; Calvinho, Luis Fernando; Amadio, Ariel Fernando
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
This study aimed to understand the genomic architecture of Argentinean dairy herds by measuring linkage disequilibrium (LD) and identifying loci associated with parameters calculated from somatic cell count (SCC). Phenotypic data consisted of 3530 SCC records from 544 Holstein and Holstein x Jersey cows owned by a single dairy company located in the Central dairy area of Argentina. SCC was recorded every 40 days. After quality control, genotypic data consisted in 38,872 single nucleotide polymorphisms (SNP). The squared correlation of the alleles at two loci (r2) was computed for all SNP pairs on each chromosome. At marker distances less than 10kb the average r2 was 0.40. Between 40 and 50kb the average r2 was 0.25 and 0.18 for 100kb apart. Three different variables were calculated from the somatic cell score (SCS): the arithmetic mean (AM), the maximum value (MAX) and the arithmetic mean of the top 3 values (TOP3). Few significant SNP associations were found. As expected, polygenic traits such as SCC are influenced by multiple loci throughout the genome, each with a relatively small effect. AM on one side and TOP3 and MAX on the other, showed different SNP associated showing that they capture different aspects of mastitis response. AM was significantly associated with two SNP: ARS-BFGL-NGS-114608 (BTA1) and Hapmap60306-rs29023088 (BTA5). MAX and TOP3 were significantly associated with four SNP: ARS-BFGL-NGS-107594, ARS-BFGL-NGS-104220 (BTA10), BTA-43543-no-rs (BTA18) and ARS-BFGL-NGS-109705 (BTA26). MAX and TOP3 were equivalent phenotypic variables to be used in a GWAS. These results contribute to gain insight into the genomic regions influencing the SCC in Argentinean herds.
Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina
Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; Argentina
Fil: Calvinho, Luis Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Amadio, Ariel Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina
Materia
GWAS
MASTITIS
MILK
RESISTANCE
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:11336/180105
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/180105
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genome-wide association study for somatic cell score in Argentinean dairy cattleNani, Juan PabloRaschia, Maria AgustinaPoli, Mario AndresCalvinho, Luis FernandoAmadio, Ariel FernandoGWASMASTITISMILKRESISTANCEhttps://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4This study aimed to understand the genomic architecture of Argentinean dairy herds by measuring linkage disequilibrium (LD) and identifying loci associated with parameters calculated from somatic cell count (SCC). Phenotypic data consisted of 3530 SCC records from 544 Holstein and Holstein x Jersey cows owned by a single dairy company located in the Central dairy area of Argentina. SCC was recorded every 40 days. After quality control, genotypic data consisted in 38,872 single nucleotide polymorphisms (SNP). The squared correlation of the alleles at two loci (r2) was computed for all SNP pairs on each chromosome. At marker distances less than 10kb the average r2 was 0.40. Between 40 and 50kb the average r2 was 0.25 and 0.18 for 100kb apart. Three different variables were calculated from the somatic cell score (SCS): the arithmetic mean (AM), the maximum value (MAX) and the arithmetic mean of the top 3 values (TOP3). Few significant SNP associations were found. As expected, polygenic traits such as SCC are influenced by multiple loci throughout the genome, each with a relatively small effect. AM on one side and TOP3 and MAX on the other, showed different SNP associated showing that they capture different aspects of mastitis response. AM was significantly associated with two SNP: ARS-BFGL-NGS-114608 (BTA1) and Hapmap60306-rs29023088 (BTA5). MAX and TOP3 were significantly associated with four SNP: ARS-BFGL-NGS-107594, ARS-BFGL-NGS-104220 (BTA10), BTA-43543-no-rs (BTA18) and ARS-BFGL-NGS-109705 (BTA26). MAX and TOP3 were equivalent phenotypic variables to be used in a GWAS. These results contribute to gain insight into the genomic regions influencing the SCC in Argentinean herds.Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; ArgentinaFil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; ArgentinaFil: Calvinho, Luis Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; ArgentinaFil: Amadio, Ariel Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; ArgentinaElsevier Science2015-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/180105Nani, Juan Pablo; Raschia, Maria Agustina; Poli, Mario Andres; Calvinho, Luis Fernando; Amadio, Ariel Fernando; Genome-wide association study for somatic cell score in Argentinean dairy cattle; Elsevier Science; Livestock Science; 175; 5-2015; 1-91871-1413CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1871141315000955info:eu-repo/semantics/altIdentifier/doi/10.1016/j.livsci.2015.02.007info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:43:36Zoai:ri.conicet.gov.ar:11336/180105instacron: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 09:43:36.651CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genome-wide association study for somatic cell score in Argentinean dairy cattle
title Genome-wide association study for somatic cell score in Argentinean dairy cattle
spellingShingle Genome-wide association study for somatic cell score in Argentinean dairy cattle
Nani, Juan Pablo
GWAS
MASTITIS
MILK
RESISTANCE
title_short Genome-wide association study for somatic cell score in Argentinean dairy cattle
title_full Genome-wide association study for somatic cell score in Argentinean dairy cattle
title_fullStr Genome-wide association study for somatic cell score in Argentinean dairy cattle
title_full_unstemmed Genome-wide association study for somatic cell score in Argentinean dairy cattle
title_sort Genome-wide association study for somatic cell score in Argentinean dairy cattle
dc.creator.none.fl_str_mv Nani, Juan Pablo
Raschia, Maria Agustina
Poli, Mario Andres
Calvinho, Luis Fernando
Amadio, Ariel Fernando
author Nani, Juan Pablo
author_facet Nani, Juan Pablo
Raschia, Maria Agustina
Poli, Mario Andres
Calvinho, Luis Fernando
Amadio, Ariel Fernando
author_role author
author2 Raschia, Maria Agustina
Poli, Mario Andres
Calvinho, Luis Fernando
Amadio, Ariel Fernando
author2_role author
author
author
author
dc.subject.none.fl_str_mv GWAS
MASTITIS
MILK
RESISTANCE
topic GWAS
MASTITIS
MILK
RESISTANCE
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv This study aimed to understand the genomic architecture of Argentinean dairy herds by measuring linkage disequilibrium (LD) and identifying loci associated with parameters calculated from somatic cell count (SCC). Phenotypic data consisted of 3530 SCC records from 544 Holstein and Holstein x Jersey cows owned by a single dairy company located in the Central dairy area of Argentina. SCC was recorded every 40 days. After quality control, genotypic data consisted in 38,872 single nucleotide polymorphisms (SNP). The squared correlation of the alleles at two loci (r2) was computed for all SNP pairs on each chromosome. At marker distances less than 10kb the average r2 was 0.40. Between 40 and 50kb the average r2 was 0.25 and 0.18 for 100kb apart. Three different variables were calculated from the somatic cell score (SCS): the arithmetic mean (AM), the maximum value (MAX) and the arithmetic mean of the top 3 values (TOP3). Few significant SNP associations were found. As expected, polygenic traits such as SCC are influenced by multiple loci throughout the genome, each with a relatively small effect. AM on one side and TOP3 and MAX on the other, showed different SNP associated showing that they capture different aspects of mastitis response. AM was significantly associated with two SNP: ARS-BFGL-NGS-114608 (BTA1) and Hapmap60306-rs29023088 (BTA5). MAX and TOP3 were significantly associated with four SNP: ARS-BFGL-NGS-107594, ARS-BFGL-NGS-104220 (BTA10), BTA-43543-no-rs (BTA18) and ARS-BFGL-NGS-109705 (BTA26). MAX and TOP3 were equivalent phenotypic variables to be used in a GWAS. These results contribute to gain insight into the genomic regions influencing the SCC in Argentinean herds.
Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina
Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; Argentina
Fil: Calvinho, Luis Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Amadio, Ariel Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina
description This study aimed to understand the genomic architecture of Argentinean dairy herds by measuring linkage disequilibrium (LD) and identifying loci associated with parameters calculated from somatic cell count (SCC). Phenotypic data consisted of 3530 SCC records from 544 Holstein and Holstein x Jersey cows owned by a single dairy company located in the Central dairy area of Argentina. SCC was recorded every 40 days. After quality control, genotypic data consisted in 38,872 single nucleotide polymorphisms (SNP). The squared correlation of the alleles at two loci (r2) was computed for all SNP pairs on each chromosome. At marker distances less than 10kb the average r2 was 0.40. Between 40 and 50kb the average r2 was 0.25 and 0.18 for 100kb apart. Three different variables were calculated from the somatic cell score (SCS): the arithmetic mean (AM), the maximum value (MAX) and the arithmetic mean of the top 3 values (TOP3). Few significant SNP associations were found. As expected, polygenic traits such as SCC are influenced by multiple loci throughout the genome, each with a relatively small effect. AM on one side and TOP3 and MAX on the other, showed different SNP associated showing that they capture different aspects of mastitis response. AM was significantly associated with two SNP: ARS-BFGL-NGS-114608 (BTA1) and Hapmap60306-rs29023088 (BTA5). MAX and TOP3 were significantly associated with four SNP: ARS-BFGL-NGS-107594, ARS-BFGL-NGS-104220 (BTA10), BTA-43543-no-rs (BTA18) and ARS-BFGL-NGS-109705 (BTA26). MAX and TOP3 were equivalent phenotypic variables to be used in a GWAS. These results contribute to gain insight into the genomic regions influencing the SCC in Argentinean herds.
publishDate 2015
dc.date.none.fl_str_mv 2015-05
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/11336/180105
Nani, Juan Pablo; Raschia, Maria Agustina; Poli, Mario Andres; Calvinho, Luis Fernando; Amadio, Ariel Fernando; Genome-wide association study for somatic cell score in Argentinean dairy cattle; Elsevier Science; Livestock Science; 175; 5-2015; 1-9
1871-1413
CONICET Digital
CONICET
url http://hdl.handle.net/11336/180105
identifier_str_mv Nani, Juan Pablo; Raschia, Maria Agustina; Poli, Mario Andres; Calvinho, Luis Fernando; Amadio, Ariel Fernando; Genome-wide association study for somatic cell score in Argentinean dairy cattle; Elsevier Science; Livestock Science; 175; 5-2015; 1-9
1871-1413
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1871141315000955
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.livsci.2015.02.007
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
dc.publisher.none.fl_str_mv Elsevier Science
publisher.none.fl_str_mv Elsevier Science
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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