Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.anireprosci.2016.12.009 http://hdl.handle.net/11449/174020 |
Resumo: | The aim of this study was to determine the extent (r2) of linkage disequilibrium (LD) in the genome of Nellore cattle, and to examine associations between single nucleotide polymorphisms (SNP) and age at first calving (AFC) and early pregnancy (EP) using a panel of high-density SNPs and data from 1182 Nellore females. A total of 13 contemporary groups (CG) were used consisting of farm, season, and year of birth. For genome-wide association analysis, SNPs with a minor allele frequency (MAF) <0.05 and animals with a call rate <0.90 were excluded, totaling 431,885 SNPs. For statistical analysis, a linear model was used for AFC and a threshold model for EP. To estimate the significance of the associations for the two traits, the model included the categorical fixed effects of CG, SNPs, and sire. In addition, the polygenic effect was included in the analysis. The additive effects and dominance deviations of Bonferroni-adjusted significant SNPs for AFC and EP were estimated using orthogonal contrasts. The average estimate of r2 for all autosomes was 0.18 at a distance of 4.8 kb and the mean MAF was 0.25 ± 0.13. The LD decreased as the distance between markers increased: 0.35 (1 kb) to 0.12 (100 kb). Eleven significant associations were detected in seven different chromosomes. Seven SNPs were associated with AFC and four were associated with EP. Three SNPs were significant for both traits. The identification of SNPs associated with AFC and EP may contribute for selecting sexually precocious animals. |
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Association between single nucleotide polymorphisms and sexual precocity in Nellore heifersAge at first calvingBeef cattleGenome-wide associationHeifer pregnancyLinkage disequilibriumThe aim of this study was to determine the extent (r2) of linkage disequilibrium (LD) in the genome of Nellore cattle, and to examine associations between single nucleotide polymorphisms (SNP) and age at first calving (AFC) and early pregnancy (EP) using a panel of high-density SNPs and data from 1182 Nellore females. A total of 13 contemporary groups (CG) were used consisting of farm, season, and year of birth. For genome-wide association analysis, SNPs with a minor allele frequency (MAF) <0.05 and animals with a call rate <0.90 were excluded, totaling 431,885 SNPs. For statistical analysis, a linear model was used for AFC and a threshold model for EP. To estimate the significance of the associations for the two traits, the model included the categorical fixed effects of CG, SNPs, and sire. In addition, the polygenic effect was included in the analysis. The additive effects and dominance deviations of Bonferroni-adjusted significant SNPs for AFC and EP were estimated using orthogonal contrasts. The average estimate of r2 for all autosomes was 0.18 at a distance of 4.8 kb and the mean MAF was 0.25 ± 0.13. The LD decreased as the distance between markers increased: 0.35 (1 kb) to 0.12 (100 kb). Eleven significant associations were detected in seven different chromosomes. Seven SNPs were associated with AFC and four were associated with EP. Three SNPs were significant for both traits. The identification of SNPs associated with AFC and EP may contribute for selecting sexually precocious animals.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Department of Animal Science Faculdade de Ciências Agrárias e Veterinárias UNESP – Univ Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane, s/n, JaboticabalDepartment of Ecology Zoology and Genetics Capão do Leão Campus Institute of Biology – IB Federal University of PelotasVeterinary Medicine and Animal Science School Federal University of Bahia UFBADepartment of Animal Science Faculdade de Ciências Agrárias e Veterinárias UNESP – Univ Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane, s/n, JaboticabalUniversidade Estadual Paulista (Unesp)Federal University of PelotasUniversidade Federal da Bahia (UFBA)Regatieri, Inaê Cristina [UNESP]Boligon, Arione Augusti [UNESP]Costa, Raphael Bermal [UNESP]de Souza, Fábio Ricardo Pablos [UNESP]Baldi, Fernando [UNESP]Takada, Luciana [UNESP]Venturini, Guilherme Costa [UNESP]de Camargo, Gregório Miguel Ferreira [UNESP]Fernandes, Gerardo Alves [UNESP]Tonhati, Humberto [UNESP]de Oliveira, Henrique Nunes [UNESP]de Albuquerque, Lucia Galvão [UNESP]2018-12-11T17:08:46Z2018-12-11T17:08:46Z2017-02-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article88-96application/pdfhttp://dx.doi.org/10.1016/j.anireprosci.2016.12.009Animal Reproduction Science, v. 177, p. 88-96.0378-4320http://hdl.handle.net/11449/17402010.1016/j.anireprosci.2016.12.0092-s2.0-850081528262-s2.0-85008152826.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengAnimal Reproduction Science0,704info:eu-repo/semantics/openAccess2023-12-31T06:19:11Zoai:repositorio.unesp.br:11449/174020Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-12-31T06:19:11Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers |
title |
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers |
spellingShingle |
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers Regatieri, Inaê Cristina [UNESP] Age at first calving Beef cattle Genome-wide association Heifer pregnancy Linkage disequilibrium |
title_short |
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers |
title_full |
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers |
title_fullStr |
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers |
title_full_unstemmed |
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers |
title_sort |
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers |
author |
Regatieri, Inaê Cristina [UNESP] |
author_facet |
Regatieri, Inaê Cristina [UNESP] Boligon, Arione Augusti [UNESP] Costa, Raphael Bermal [UNESP] de Souza, Fábio Ricardo Pablos [UNESP] Baldi, Fernando [UNESP] Takada, Luciana [UNESP] Venturini, Guilherme Costa [UNESP] de Camargo, Gregório Miguel Ferreira [UNESP] Fernandes, Gerardo Alves [UNESP] Tonhati, Humberto [UNESP] de Oliveira, Henrique Nunes [UNESP] de Albuquerque, Lucia Galvão [UNESP] |
author_role |
author |
author2 |
Boligon, Arione Augusti [UNESP] Costa, Raphael Bermal [UNESP] de Souza, Fábio Ricardo Pablos [UNESP] Baldi, Fernando [UNESP] Takada, Luciana [UNESP] Venturini, Guilherme Costa [UNESP] de Camargo, Gregório Miguel Ferreira [UNESP] Fernandes, Gerardo Alves [UNESP] Tonhati, Humberto [UNESP] de Oliveira, Henrique Nunes [UNESP] de Albuquerque, Lucia Galvão [UNESP] |
author2_role |
author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Federal University of Pelotas Universidade Federal da Bahia (UFBA) |
dc.contributor.author.fl_str_mv |
Regatieri, Inaê Cristina [UNESP] Boligon, Arione Augusti [UNESP] Costa, Raphael Bermal [UNESP] de Souza, Fábio Ricardo Pablos [UNESP] Baldi, Fernando [UNESP] Takada, Luciana [UNESP] Venturini, Guilherme Costa [UNESP] de Camargo, Gregório Miguel Ferreira [UNESP] Fernandes, Gerardo Alves [UNESP] Tonhati, Humberto [UNESP] de Oliveira, Henrique Nunes [UNESP] de Albuquerque, Lucia Galvão [UNESP] |
dc.subject.por.fl_str_mv |
Age at first calving Beef cattle Genome-wide association Heifer pregnancy Linkage disequilibrium |
topic |
Age at first calving Beef cattle Genome-wide association Heifer pregnancy Linkage disequilibrium |
description |
The aim of this study was to determine the extent (r2) of linkage disequilibrium (LD) in the genome of Nellore cattle, and to examine associations between single nucleotide polymorphisms (SNP) and age at first calving (AFC) and early pregnancy (EP) using a panel of high-density SNPs and data from 1182 Nellore females. A total of 13 contemporary groups (CG) were used consisting of farm, season, and year of birth. For genome-wide association analysis, SNPs with a minor allele frequency (MAF) <0.05 and animals with a call rate <0.90 were excluded, totaling 431,885 SNPs. For statistical analysis, a linear model was used for AFC and a threshold model for EP. To estimate the significance of the associations for the two traits, the model included the categorical fixed effects of CG, SNPs, and sire. In addition, the polygenic effect was included in the analysis. The additive effects and dominance deviations of Bonferroni-adjusted significant SNPs for AFC and EP were estimated using orthogonal contrasts. The average estimate of r2 for all autosomes was 0.18 at a distance of 4.8 kb and the mean MAF was 0.25 ± 0.13. The LD decreased as the distance between markers increased: 0.35 (1 kb) to 0.12 (100 kb). Eleven significant associations were detected in seven different chromosomes. Seven SNPs were associated with AFC and four were associated with EP. Three SNPs were significant for both traits. The identification of SNPs associated with AFC and EP may contribute for selecting sexually precocious animals. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-02-01 2018-12-11T17:08:46Z 2018-12-11T17:08:46Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.anireprosci.2016.12.009 Animal Reproduction Science, v. 177, p. 88-96. 0378-4320 http://hdl.handle.net/11449/174020 10.1016/j.anireprosci.2016.12.009 2-s2.0-85008152826 2-s2.0-85008152826.pdf |
url |
http://dx.doi.org/10.1016/j.anireprosci.2016.12.009 http://hdl.handle.net/11449/174020 |
identifier_str_mv |
Animal Reproduction Science, v. 177, p. 88-96. 0378-4320 10.1016/j.anireprosci.2016.12.009 2-s2.0-85008152826 2-s2.0-85008152826.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Animal Reproduction Science 0,704 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
88-96 application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1799965468695461888 |