Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle
The purpose of this study was to identify genomic regions explaining a major proportion of the genetic variance in milk production and milk fat and protein content on a commercial herd of Holstein and Holstein x Jersey crossbred cattle bred in an extensive grazing system. We analyzed 305-day cumulat...
| Autores principales: | , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier
2020
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| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12123/8109 https://www.sciencedirect.com/science/article/abs/pii/S187114132030281X https://doi.org/10.1016/j.livsci.2020.104294 |
| _version_ | 1855484135381925888 |
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| author | Raschia, Maria Agustina Nani, Juan Pablo Carignano, Hugo Adrian Amadio, Ariel Maizon, Daniel Omar Poli, Mario Andres |
| author_browse | Amadio, Ariel Carignano, Hugo Adrian Maizon, Daniel Omar Nani, Juan Pablo Poli, Mario Andres Raschia, Maria Agustina |
| author_facet | Raschia, Maria Agustina Nani, Juan Pablo Carignano, Hugo Adrian Amadio, Ariel Maizon, Daniel Omar Poli, Mario Andres |
| author_sort | Raschia, Maria Agustina |
| collection | INTA Digital |
| description | The purpose of this study was to identify genomic regions explaining a major proportion of the genetic variance in milk production and milk fat and protein content on a commercial herd of Holstein and Holstein x Jersey crossbred cattle bred in an extensive grazing system. We analyzed 305-day cumulative milk production records from 18876 cows at first lactation, of which 16907 and 16735 had milk fat and protein content records during the same period. After data quality control, genotypes from 998 animals on 40417 SNPs included in the Illumina Bovine SNP50 v2 BeadChip were available. Weighted single-step genome-wide association studies were conducted for milk yield (MY), fat content (FC) and protein content (PC). Windows of 10 adjacent single nucleotide polymorphisms explaining more than 0.31% of the genetic variance were considered relevant. Protein-coding genes located within those windows were retrieved, their functional relevance was assessed, the main functional categories and biological processes represented by them were identified, and an overrepresentation test was performed. Relevant windows for MY, FC and PC were 52, 57 and 56, and harbored 304, 293 and 269 proteincoding genes, respectively. The proteins encoded by those genes were mainly involved in cellular, metabolic and
biological regulation processes. Cellular response to cytokine stimulus, GTPase activity and GTP binding, and heterotrimeric G-protein were the main overrepresented biological process, molecular functions, and protein class, respectively. Among the candidate genes found, some previously reported genes associated with milk traits, such as CDH2, DGAT1, GRINA, LIPA, PGR, RPGRIP1L, VPS28, MAF1, and FTO were identified. However, novel candidate genes related to transcriptional regulation and transporter activity were also found. These results contribute to a better understanding of the loci influencing milk traits in the main dairy cattle breeds in Argentina. |
| format | Artículo |
| id | INTA8109 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | INTA81092020-10-22T16:44:32Z Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle Raschia, Maria Agustina Nani, Juan Pablo Carignano, Hugo Adrian Amadio, Ariel Maizon, Daniel Omar Poli, Mario Andres Crossbreds Dairy Cattle Milk Fat Milk Protein Milk Yield Genomes Genetic Variance Productos del Cruzamiento Ganado de Leche Grasa de la Leche Proteínas de la Leche Rendimiento Lechero Genomas Varianza Genética Raza Holstein Raza Holstein x Jersey The purpose of this study was to identify genomic regions explaining a major proportion of the genetic variance in milk production and milk fat and protein content on a commercial herd of Holstein and Holstein x Jersey crossbred cattle bred in an extensive grazing system. We analyzed 305-day cumulative milk production records from 18876 cows at first lactation, of which 16907 and 16735 had milk fat and protein content records during the same period. After data quality control, genotypes from 998 animals on 40417 SNPs included in the Illumina Bovine SNP50 v2 BeadChip were available. Weighted single-step genome-wide association studies were conducted for milk yield (MY), fat content (FC) and protein content (PC). Windows of 10 adjacent single nucleotide polymorphisms explaining more than 0.31% of the genetic variance were considered relevant. Protein-coding genes located within those windows were retrieved, their functional relevance was assessed, the main functional categories and biological processes represented by them were identified, and an overrepresentation test was performed. Relevant windows for MY, FC and PC were 52, 57 and 56, and harbored 304, 293 and 269 proteincoding genes, respectively. The proteins encoded by those genes were mainly involved in cellular, metabolic and biological regulation processes. Cellular response to cytokine stimulus, GTPase activity and GTP binding, and heterotrimeric G-protein were the main overrepresented biological process, molecular functions, and protein class, respectively. Among the candidate genes found, some previously reported genes associated with milk traits, such as CDH2, DGAT1, GRINA, LIPA, PGR, RPGRIP1L, VPS28, MAF1, and FTO were identified. However, novel candidate genes related to transcriptional regulation and transporter activity were also found. These results contribute to a better understanding of the loci influencing milk traits in the main dairy cattle breeds in Argentina. Instituto de Genética Fil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina Fil: Carignano, Hugo Adrian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Amadio, Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Maizon, Daniel Omar. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil; Argentina Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina 2020-10-22T16:32:30Z 2020-10-22T16:32:30Z 2020-12 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/8109 https://www.sciencedirect.com/science/article/abs/pii/S187114132030281X 1871-1413 https://doi.org/10.1016/j.livsci.2020.104294 eng info:eu-repograntAgreement/INTA/PNBIO-1131033/AR./Genómica y biotecnología aplicada a la cría animal. info:eu-repograntAgreement/INTA/PNBIO-1131043/AR./Bioinformática y Estadística Genómica. info:eu-repograntAgreement/INTA/2019-PE-E6-I145-001/2019-PE-E6-I145-001/AR./Mejora genética objetiva para aumentar la eficiencia de los sistemas de producción animal. info:eu-repo/semantics/restrictedAccess application/pdf Elsevier Livestock Science 242 : 104294 (Diciembre 2020) |
| spellingShingle | Crossbreds Dairy Cattle Milk Fat Milk Protein Milk Yield Genomes Genetic Variance Productos del Cruzamiento Ganado de Leche Grasa de la Leche Proteínas de la Leche Rendimiento Lechero Genomas Varianza Genética Raza Holstein Raza Holstein x Jersey Raschia, Maria Agustina Nani, Juan Pablo Carignano, Hugo Adrian Amadio, Ariel Maizon, Daniel Omar Poli, Mario Andres Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle |
| title | Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle |
| title_full | Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle |
| title_fullStr | Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle |
| title_full_unstemmed | Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle |
| title_short | Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle |
| title_sort | weighted single step genome wide association analyses for milk traits in holstein and holstein x jersey crossbred dairy cattle |
| topic | Crossbreds Dairy Cattle Milk Fat Milk Protein Milk Yield Genomes Genetic Variance Productos del Cruzamiento Ganado de Leche Grasa de la Leche Proteínas de la Leche Rendimiento Lechero Genomas Varianza Genética Raza Holstein Raza Holstein x Jersey |
| url | http://hdl.handle.net/20.500.12123/8109 https://www.sciencedirect.com/science/article/abs/pii/S187114132030281X https://doi.org/10.1016/j.livsci.2020.104294 |
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