Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
Autor(a) principal: | |
---|---|
Data de Publicação: | 2019 |
Outros Autores: | , , , , |
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. |
id |
UNSP_1f16990e4ed438fb70e86e68b1d988c6 |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/190069 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
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) |
repository.mail.fl_str_mv |
|
_version_ |
1808128223408553984 |