Genomic structure of a crossbred Landrace pig population
Autor(a) principal: | |
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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.0212266 http://hdl.handle.net/11449/190159 |
Resumo: | Single nucleotide polymorphism (SNP) markers are used to study population structure and conservation genetics, which permits assessing similarities regarding the linkage disequilibrium and information about the relationship among individuals. To investigate the population genomic structure of 300 females and 25 males from a commercial maternal pig line we analyzed linkage disequilibrium extent, inbreeding coefficients using genomic and conventional pedigree data, and population stratification. The average linkage disequilibrium (r2) was 0.291 ± 0.312 for all adjacent SNPs, distancing less than 100 Kb (kilobase) between markers. The average inbreeding coefficients obtained from runs of homozygosity (ROH) and pedigree analyses were 0.119 and 0.0001, respectively. Low correlation was observed between the inbreeding coefficients possibly as a result of genetic recombination effect accounted for the ROH estimates or caused by pedigree identification errors. A large number of long ROHs might indicate recent inbreeding events in the studied population. A total of 36 homozygous segments were found in more than 30% of the population and these ROH harbor genes associated with reproductive traits. The population stratification analysis indicated that this population was possibly originated from two distinct populations, which is a result from crossings between the eastern and western breeds used in the formation of the line. Our findings provide support to understand the genetic structure of swine populations and may assist breeding companies to avoid a high level of inbreeding coefficients to maintain genetic diversity, showing the effectiveness of using genomewide SNP information for quantifying inbreeding when the pedigree was incomplete or incorrect. |
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Genomic structure of a crossbred Landrace pig populationSingle nucleotide polymorphism (SNP) markers are used to study population structure and conservation genetics, which permits assessing similarities regarding the linkage disequilibrium and information about the relationship among individuals. To investigate the population genomic structure of 300 females and 25 males from a commercial maternal pig line we analyzed linkage disequilibrium extent, inbreeding coefficients using genomic and conventional pedigree data, and population stratification. The average linkage disequilibrium (r2) was 0.291 ± 0.312 for all adjacent SNPs, distancing less than 100 Kb (kilobase) between markers. The average inbreeding coefficients obtained from runs of homozygosity (ROH) and pedigree analyses were 0.119 and 0.0001, respectively. Low correlation was observed between the inbreeding coefficients possibly as a result of genetic recombination effect accounted for the ROH estimates or caused by pedigree identification errors. A large number of long ROHs might indicate recent inbreeding events in the studied population. A total of 36 homozygous segments were found in more than 30% of the population and these ROH harbor genes associated with reproductive traits. The population stratification analysis indicated that this population was possibly originated from two distinct populations, which is a result from crossings between the eastern and western breeds used in the formation of the line. Our findings provide support to understand the genetic structure of swine populations and may assist breeding companies to avoid a high level of inbreeding coefficients to maintain genetic diversity, showing the effectiveness of using genomewide SNP information for quantifying inbreeding when the pedigree was incomplete or incorrect.Departamento de Ciências Exatas Faculdade de Ciências Agrá Rias E Veteriná Rias Universidade Estadual Paulista (Unesp)Departamento de Zootecnia Universidade Federal da Paraíba (UFPB)Universidade de Passo Fundo (UPF)Embrapa Suínos e AvesDepartamento de Zootecnia E Desenvolvimento Rural Centro de Ciências Agrá Rias Universidade Federal de Santa Catarina (UFSC)Departamento de Ciências Exatas Faculdade de Ciências Agrá Rias E Veteriná Rias Universidade Estadual Paulista (Unesp)Universidade Estadual Paulista (Unesp)Universidade Federal da Paraíba (UFPB)Universidade de Passo Fundo (UPF)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Universidade Federal de Santa Catarina (UFSC)Joaquim, Letícia Borges [UNESP]Chud, Tatiane Cristina Seleguim [UNESP]Marchesi, Jorge Augusto Petroli [UNESP]Savegnago, Rodrigo Pelicioni [UNESP]Buzanskas, Marcos EliZanella, RicardoCantão, Mauricio EgidioPeixoto, Jane OliveiraLedur, Mônica CorreaIrgang, RenatoMunari, Danísio Prado [UNESP]2019-10-06T17:04:17Z2019-10-06T17:04:17Z2019-02-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1371/journal.pone.0212266PLoS ONE, v. 14, n. 2, 2019.1932-6203http://hdl.handle.net/11449/19015910.1371/journal.pone.02122662-s2.0-85062341138Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPLoS ONEinfo:eu-repo/semantics/openAccess2024-06-06T13:43:43Zoai:repositorio.unesp.br:11449/190159Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T21:25:56.257618Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genomic structure of a crossbred Landrace pig population |
title |
Genomic structure of a crossbred Landrace pig population |
spellingShingle |
Genomic structure of a crossbred Landrace pig population Joaquim, Letícia Borges [UNESP] |
title_short |
Genomic structure of a crossbred Landrace pig population |
title_full |
Genomic structure of a crossbred Landrace pig population |
title_fullStr |
Genomic structure of a crossbred Landrace pig population |
title_full_unstemmed |
Genomic structure of a crossbred Landrace pig population |
title_sort |
Genomic structure of a crossbred Landrace pig population |
author |
Joaquim, Letícia Borges [UNESP] |
author_facet |
Joaquim, Letícia Borges [UNESP] Chud, Tatiane Cristina Seleguim [UNESP] Marchesi, Jorge Augusto Petroli [UNESP] Savegnago, Rodrigo Pelicioni [UNESP] Buzanskas, Marcos Eli Zanella, Ricardo Cantão, Mauricio Egidio Peixoto, Jane Oliveira Ledur, Mônica Correa Irgang, Renato Munari, Danísio Prado [UNESP] |
author_role |
author |
author2 |
Chud, Tatiane Cristina Seleguim [UNESP] Marchesi, Jorge Augusto Petroli [UNESP] Savegnago, Rodrigo Pelicioni [UNESP] Buzanskas, Marcos Eli Zanella, Ricardo Cantão, Mauricio Egidio Peixoto, Jane Oliveira Ledur, Mônica Correa Irgang, Renato Munari, Danísio Prado [UNESP] |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidade Federal da Paraíba (UFPB) Universidade de Passo Fundo (UPF) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Universidade Federal de Santa Catarina (UFSC) |
dc.contributor.author.fl_str_mv |
Joaquim, Letícia Borges [UNESP] Chud, Tatiane Cristina Seleguim [UNESP] Marchesi, Jorge Augusto Petroli [UNESP] Savegnago, Rodrigo Pelicioni [UNESP] Buzanskas, Marcos Eli Zanella, Ricardo Cantão, Mauricio Egidio Peixoto, Jane Oliveira Ledur, Mônica Correa Irgang, Renato Munari, Danísio Prado [UNESP] |
description |
Single nucleotide polymorphism (SNP) markers are used to study population structure and conservation genetics, which permits assessing similarities regarding the linkage disequilibrium and information about the relationship among individuals. To investigate the population genomic structure of 300 females and 25 males from a commercial maternal pig line we analyzed linkage disequilibrium extent, inbreeding coefficients using genomic and conventional pedigree data, and population stratification. The average linkage disequilibrium (r2) was 0.291 ± 0.312 for all adjacent SNPs, distancing less than 100 Kb (kilobase) between markers. The average inbreeding coefficients obtained from runs of homozygosity (ROH) and pedigree analyses were 0.119 and 0.0001, respectively. Low correlation was observed between the inbreeding coefficients possibly as a result of genetic recombination effect accounted for the ROH estimates or caused by pedigree identification errors. A large number of long ROHs might indicate recent inbreeding events in the studied population. A total of 36 homozygous segments were found in more than 30% of the population and these ROH harbor genes associated with reproductive traits. The population stratification analysis indicated that this population was possibly originated from two distinct populations, which is a result from crossings between the eastern and western breeds used in the formation of the line. Our findings provide support to understand the genetic structure of swine populations and may assist breeding companies to avoid a high level of inbreeding coefficients to maintain genetic diversity, showing the effectiveness of using genomewide SNP information for quantifying inbreeding when the pedigree was incomplete or incorrect. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-06T17:04:17Z 2019-10-06T17:04:17Z 2019-02-01 |
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.0212266 PLoS ONE, v. 14, n. 2, 2019. 1932-6203 http://hdl.handle.net/11449/190159 10.1371/journal.pone.0212266 2-s2.0-85062341138 |
url |
http://dx.doi.org/10.1371/journal.pone.0212266 http://hdl.handle.net/11449/190159 |
identifier_str_mv |
PLoS ONE, v. 14, n. 2, 2019. 1932-6203 10.1371/journal.pone.0212266 2-s2.0-85062341138 |
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 |
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1808129319091830784 |