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
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/2818
Ver los metadatos del registro completo
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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/restrictedAccess2025-09-29T13:44:21Zoai: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:l2025-09-29 13:44:22.261INTA 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 |
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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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12.559606 |