Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle

Autores
Raschia, Maria Agustina; Nani, Juan Pablo; Carignano, Hugo Adrian; Amadio, Ariel; Maizon, Daniel Omar; Poli, Mario Andres
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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
Fuente
Livestock Science 242 : 104294 (Diciembre 2020)
Materia
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
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/8109
Acceder
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oai_identifier_str oai:localhost:20.500.12123/8109
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network_name_str INTA Digital (INTA)
spelling Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattleRaschia, Maria AgustinaNani, Juan PabloCarignano, Hugo AdrianAmadio, ArielMaizon, Daniel OmarPoli, Mario AndresCrossbredsDairy CattleMilk FatMilk ProteinMilk YieldGenomesGenetic VarianceProductos del CruzamientoGanado de LecheGrasa de la LecheProteínas de la LecheRendimiento LecheroGenomasVarianza GenéticaRaza HolsteinRaza Holstein x JerseyThe 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 GenéticaFil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; ArgentinaFil: Carignano, Hugo Adrian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Amadio, Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Maizon, Daniel Omar. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil; ArgentinaFil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaElsevier2020-10-22T16:32:30Z2020-10-22T16:32:30Z2020-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/8109https://www.sciencedirect.com/science/article/abs/pii/S187114132030281X1871-1413https://doi.org/10.1016/j.livsci.2020.104294Livestock Science 242 : 104294 (Diciembre 2020)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo: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/restrictedAccess2025-09-04T09:48:39Zoai:localhost:20.500.12123/8109instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:48:40.121INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv 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
spellingShingle Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle
Raschia, Maria Agustina
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
title_short 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_sort Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle
dc.creator.none.fl_str_mv Raschia, Maria Agustina
Nani, Juan Pablo
Carignano, Hugo Adrian
Amadio, Ariel
Maizon, Daniel Omar
Poli, Mario Andres
author Raschia, Maria Agustina
author_facet Raschia, Maria Agustina
Nani, Juan Pablo
Carignano, Hugo Adrian
Amadio, Ariel
Maizon, Daniel Omar
Poli, Mario Andres
author_role author
author2 Nani, Juan Pablo
Carignano, Hugo Adrian
Amadio, Ariel
Maizon, Daniel Omar
Poli, Mario Andres
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv 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
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
dc.description.none.fl_txt_mv 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
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.
publishDate 2020
dc.date.none.fl_str_mv 2020-10-22T16:32:30Z
2020-10-22T16:32:30Z
2020-12
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/20.500.12123/8109
https://www.sciencedirect.com/science/article/abs/pii/S187114132030281X
1871-1413
https://doi.org/10.1016/j.livsci.2020.104294
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
identifier_str_mv 1871-1413
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 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.
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.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv Livestock Science 242 : 104294 (Diciembre 2020)
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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