Genome-wide association study for somatic cell score in Argentinean dairy cattle
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...
| Autores principales: | , , , , |
|---|---|
| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
| Publicado: |
2018
|
| Materias: | |
| Acceso en línea: | 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 |
| _version_ | 1855035031958847488 |
|---|---|
| author | Nani, Juan Pablo Raschia, Maria Agustina Poli, Mario Andres Calvinho, Luis Fernando Amadio, Ariel |
| author_browse | Amadio, Ariel Calvinho, Luis Fernando Nani, Juan Pablo Poli, Mario Andres Raschia, Maria Agustina |
| author_facet | Nani, Juan Pablo Raschia, Maria Agustina Poli, Mario Andres Calvinho, Luis Fernando Amadio, Ariel |
| author_sort | Nani, Juan Pablo |
| collection | INTA Digital |
| 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. |
| format | info:ar-repo/semantics/artículo |
| id | INTA2818 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| record_format | dspace |
| spelling | INTA28182018-07-18T17:30:29Z Genome-wide association study for somatic cell score in Argentinean dairy cattle Nani, Juan Pablo Raschia, Maria Agustina Poli, Mario Andres Calvinho, Luis Fernando Amadio, Ariel Ganado de Leche Genética Genomas Células Somáticas Dairy Cattle Genetics Genomes Somatic Cells Argentina 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 2018-07-18T17:26:40Z 2018-07-18T17:26:40Z 2015-05 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng info:eu-repo/semantics/restrictedAccess application/pdf Livestock Science 175 : 1-9 (May 2015) |
| spellingShingle | Ganado de Leche Genética Genomas Células Somáticas Dairy Cattle Genetics Genomes Somatic Cells Argentina Nani, Juan Pablo Raschia, Maria Agustina Poli, Mario Andres Calvinho, Luis Fernando Amadio, Ariel 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 |
| 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_short | 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 |
| topic | Ganado de Leche Genética Genomas Células Somáticas Dairy Cattle Genetics Genomes Somatic Cells Argentina |
| 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 |
| work_keys_str_mv | AT nanijuanpablo genomewideassociationstudyforsomaticcellscoreinargentineandairycattle AT raschiamariaagustina genomewideassociationstudyforsomaticcellscoreinargentineandairycattle AT polimarioandres genomewideassociationstudyforsomaticcellscoreinargentineandairycattle AT calvinholuisfernando genomewideassociationstudyforsomaticcellscoreinargentineandairycattle AT amadioariel genomewideassociationstudyforsomaticcellscoreinargentineandairycattle |