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
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 10 kb the average r2 was 0.40. Between 40 and 50 kb the average r2 was 0.25 and 0.18 for 100 kb 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.
EEA Rafaela
Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Calvinho, Luis Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Amadio, Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
Livestock Science 175 : 1-9 (May 2015)
Materia
Ganado de Leche
Genética
Genomas
Células Somáticas
Dairy Cattle
Genetics
Genomes
Somatic Cells
Argentina
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/2818
Acceder
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oai_identifier_str oai:localhost:20.500.12123/2818
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling Genome-wide association study for somatic cell score in Argentinean dairy cattleNani, Juan PabloRaschia, Maria AgustinaPoli, Mario AndresCalvinho, Luis FernandoAmadio, ArielGanado de LecheGenéticaGenomasCélulas SomáticasDairy CattleGeneticsGenomesSomatic CellsArgentinaThis 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 10 kb the average r2 was 0.40. Between 40 and 50 kb the average r2 was 0.25 and 0.18 for 100 kb 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.EEA RafaelaFil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; ArgentinaFil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Calvinho, Luis Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; ArgentinaFil: Amadio, Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina2018-07-18T17:26:40Z2018-07-18T17:26:40Z2015-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://www.sciencedirect.com/science/article/pii/S1871141315000955http://hdl.handle.net/20.500.12123/28181871-1413https://doi.org/10.1016/j.livsci.2015.02.007Livestock Science 175 : 1-9 (May 2015)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-10-30T11:22:46Zoai:localhost:20.500.12123/2818instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-30 11:22:47.284INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
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
Ganado de Leche
Genética
Genomas
Células Somáticas
Dairy Cattle
Genetics
Genomes
Somatic Cells
Argentina
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
author Nani, Juan Pablo
author_facet Nani, Juan Pablo
Raschia, Maria Agustina
Poli, Mario Andres
Calvinho, Luis Fernando
Amadio, Ariel
author_role author
author2 Raschia, Maria Agustina
Poli, Mario Andres
Calvinho, Luis Fernando
Amadio, Ariel
author2_role author
author
author
author
dc.subject.none.fl_str_mv Ganado de Leche
Genética
Genomas
Células Somáticas
Dairy Cattle
Genetics
Genomes
Somatic Cells
Argentina
topic Ganado de Leche
Genética
Genomas
Células Somáticas
Dairy Cattle
Genetics
Genomes
Somatic Cells
Argentina
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 10 kb the average r2 was 0.40. Between 40 and 50 kb the average r2 was 0.25 and 0.18 for 100 kb 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.
EEA Rafaela
Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Calvinho, Luis Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina
Fil: Amadio, Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; 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 10 kb the average r2 was 0.40. Between 40 and 50 kb the average r2 was 0.25 and 0.18 for 100 kb 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
2018-07-18T17:26:40Z
2018-07-18T17:26:40Z
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 https://www.sciencedirect.com/science/article/pii/S1871141315000955
http://hdl.handle.net/20.500.12123/2818
1871-1413
https://doi.org/10.1016/j.livsci.2015.02.007
url https://www.sciencedirect.com/science/article/pii/S1871141315000955
http://hdl.handle.net/20.500.12123/2818
https://doi.org/10.1016/j.livsci.2015.02.007
identifier_str_mv 1871-1413
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv Livestock Science 175 : 1-9 (May 2015)
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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score 12.573905

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