Genetic and genomic analyses of testicular hypoplasia in Nellore cattle

Detalhes bibliográficos
Autor(a) principal: Neves, Haroldo H.R.
Data de Publicação: 2019
Outros Autores: Vargas, Giovana [UNESP], Brito, Luiz F., Schenkel, Flavio S., Albuquerque, Lucia G. [UNESP], Carvalheiro, Roberto
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1371/journal.pone.0211159
http://hdl.handle.net/11449/190069
Resumo: Reproductive performance is a key indicator of the long-term sustainability of any livestock production system. Testicular hypoplasia (TH) is a morphological and functional reproductive disorder that affects bulls around the world and consequently causes major economic losses due to reduced fertility rates. Despite the improvements in management practices to enhance performance of affected animals, the use of hypoplastic animals for reproduction might contribute to expand the prevalence of this disorder. The aim of this study was to identify genomic regions that are associated with TH in Nellore cattle by performing a genome-wide association study (GWAS) and functional analyses. Phenotypic and pedigree data from 47,563 animals and genotypes (500,689 Single Nucleotide Polymorphism, SNPs) from 265 sires were used in this study. TH was evaluated as a binary trait measured at 18 months of age. The estimated breeding values (EBVs) were calculated by fitting a single-trait threshold animal model using a Bayesian approach. The SNP effects were estimated using the Bayes C method and de-regressed EBVs for TH as the response variable (pseudo-phenotype). The top-15 ranking windows (5-adjacent SNPs) that explained the highest proportion of variance were identified for further functional and biological network analyses. The posterior mean (95% highest posterior density) of the heritability for TH was 0.16 (0.08; 0.23). The most important genomic windows were located on BTA1, BTA3, BTA4, BTA5, BTA9, BTA22, BTA23, and BTA25. These windows explained together 22.69% of the total additive genetic variance for TH. Strong candidate genes associated with metabolism and synthesis of steroids, cell survival, spermatogenesis process and sperm motility were identified, which might play an important role in the expression of TH. Our findings contribute to a better biological understanding of TH and future characterization of causal variants might enable improved genomic prediction of this trait in beef cattle.
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spelling Genetic and genomic analyses of testicular hypoplasia in Nellore cattleReproductive performance is a key indicator of the long-term sustainability of any livestock production system. Testicular hypoplasia (TH) is a morphological and functional reproductive disorder that affects bulls around the world and consequently causes major economic losses due to reduced fertility rates. Despite the improvements in management practices to enhance performance of affected animals, the use of hypoplastic animals for reproduction might contribute to expand the prevalence of this disorder. The aim of this study was to identify genomic regions that are associated with TH in Nellore cattle by performing a genome-wide association study (GWAS) and functional analyses. Phenotypic and pedigree data from 47,563 animals and genotypes (500,689 Single Nucleotide Polymorphism, SNPs) from 265 sires were used in this study. TH was evaluated as a binary trait measured at 18 months of age. The estimated breeding values (EBVs) were calculated by fitting a single-trait threshold animal model using a Bayesian approach. The SNP effects were estimated using the Bayes C method and de-regressed EBVs for TH as the response variable (pseudo-phenotype). The top-15 ranking windows (5-adjacent SNPs) that explained the highest proportion of variance were identified for further functional and biological network analyses. The posterior mean (95% highest posterior density) of the heritability for TH was 0.16 (0.08; 0.23). The most important genomic windows were located on BTA1, BTA3, BTA4, BTA5, BTA9, BTA22, BTA23, and BTA25. These windows explained together 22.69% of the total additive genetic variance for TH. Strong candidate genes associated with metabolism and synthesis of steroids, cell survival, spermatogenesis process and sperm motility were identified, which might play an important role in the expression of TH. Our findings contribute to a better biological understanding of TH and future characterization of causal variants might enable improved genomic prediction of this trait in beef cattle.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)GenSys Associated ConsultantsDepartment of Animal Sciences School of Agricultural and Veterinary Sciences São Paulo State University (UNESP)Department of Animal Sciences Purdue UniversityCentre for Genetic Improvement of Livestock (CGIL) Department of Animal Biosciences University of GuelphNational Council for Science and Technological Development (Cnpq)Department of Animal Sciences School of Agricultural and Veterinary Sciences São Paulo State University (UNESP)GenSys Associated ConsultantsUniversidade Estadual Paulista (Unesp)Purdue UniversityUniversity of GuelphNational Council for Science and Technological Development (Cnpq)Neves, Haroldo H.R.Vargas, Giovana [UNESP]Brito, Luiz F.Schenkel, Flavio S.Albuquerque, Lucia G. [UNESP]Carvalheiro, Roberto2019-10-06T17:01:14Z2019-10-06T17:01:14Z2019-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1371/journal.pone.0211159PLoS ONE, v. 14, n. 1, 2019.1932-6203http://hdl.handle.net/11449/19006910.1371/journal.pone.02111592-s2.0-85060463156Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPLoS ONEinfo:eu-repo/semantics/openAccess2024-06-07T18:40:51Zoai:repositorio.unesp.br:11449/190069Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T16:14:05.990158Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
title Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
spellingShingle Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
Neves, Haroldo H.R.
title_short Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
title_full Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
title_fullStr Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
title_full_unstemmed Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
title_sort Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
author Neves, Haroldo H.R.
author_facet Neves, Haroldo H.R.
Vargas, Giovana [UNESP]
Brito, Luiz F.
Schenkel, Flavio S.
Albuquerque, Lucia G. [UNESP]
Carvalheiro, Roberto
author_role author
author2 Vargas, Giovana [UNESP]
Brito, Luiz F.
Schenkel, Flavio S.
Albuquerque, Lucia G. [UNESP]
Carvalheiro, Roberto
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv GenSys Associated Consultants
Universidade Estadual Paulista (Unesp)
Purdue University
University of Guelph
National Council for Science and Technological Development (Cnpq)
dc.contributor.author.fl_str_mv Neves, Haroldo H.R.
Vargas, Giovana [UNESP]
Brito, Luiz F.
Schenkel, Flavio S.
Albuquerque, Lucia G. [UNESP]
Carvalheiro, Roberto
description Reproductive performance is a key indicator of the long-term sustainability of any livestock production system. Testicular hypoplasia (TH) is a morphological and functional reproductive disorder that affects bulls around the world and consequently causes major economic losses due to reduced fertility rates. Despite the improvements in management practices to enhance performance of affected animals, the use of hypoplastic animals for reproduction might contribute to expand the prevalence of this disorder. The aim of this study was to identify genomic regions that are associated with TH in Nellore cattle by performing a genome-wide association study (GWAS) and functional analyses. Phenotypic and pedigree data from 47,563 animals and genotypes (500,689 Single Nucleotide Polymorphism, SNPs) from 265 sires were used in this study. TH was evaluated as a binary trait measured at 18 months of age. The estimated breeding values (EBVs) were calculated by fitting a single-trait threshold animal model using a Bayesian approach. The SNP effects were estimated using the Bayes C method and de-regressed EBVs for TH as the response variable (pseudo-phenotype). The top-15 ranking windows (5-adjacent SNPs) that explained the highest proportion of variance were identified for further functional and biological network analyses. The posterior mean (95% highest posterior density) of the heritability for TH was 0.16 (0.08; 0.23). The most important genomic windows were located on BTA1, BTA3, BTA4, BTA5, BTA9, BTA22, BTA23, and BTA25. These windows explained together 22.69% of the total additive genetic variance for TH. Strong candidate genes associated with metabolism and synthesis of steroids, cell survival, spermatogenesis process and sperm motility were identified, which might play an important role in the expression of TH. Our findings contribute to a better biological understanding of TH and future characterization of causal variants might enable improved genomic prediction of this trait in beef cattle.
publishDate 2019
dc.date.none.fl_str_mv 2019-10-06T17:01:14Z
2019-10-06T17:01:14Z
2019-01-01
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/10.1371/journal.pone.0211159
PLoS ONE, v. 14, n. 1, 2019.
1932-6203
http://hdl.handle.net/11449/190069
10.1371/journal.pone.0211159
2-s2.0-85060463156
url http://dx.doi.org/10.1371/journal.pone.0211159
http://hdl.handle.net/11449/190069
identifier_str_mv PLoS ONE, v. 14, n. 1, 2019.
1932-6203
10.1371/journal.pone.0211159
2-s2.0-85060463156
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv PLoS ONE
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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)
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