Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/s12864-018-5060-8 http://hdl.handle.net/11449/176858 |
Resumo: | Background: The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results: The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (- 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (- 0.01 to - 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (- 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions: Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. |
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Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 GeneticsBos indicusGene ontologyGenomic inbreedingIndicineBackground: The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results: The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (- 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (- 0.01 to - 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (- 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions: Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle.Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita FilhoInstitute for Animal Breeding and Genetics University of Veterinary Medicine HannoverDepartamento de Ciências Exatas Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita FilhoAssociação Nacional de Criadores e Pesquisadores (ANCP)Embrapa CerradosZoetisUniversidade de São Paulo Departamento de Nutrição e Produção AnimalDepartamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita FilhoDepartamento de Ciências Exatas Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita FilhoUniversidade Estadual Paulista (Unesp)University of Veterinary Medicine HannoverAssociação Nacional de Criadores e Pesquisadores (ANCP)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)ZoetisUniversidade de São Paulo (USP)Peripolli, Elisa [UNESP]Metzger, JuliaDe Lemos, Marcos Vinícius Antunes [UNESP]Stafuzza, Nedenia Bonvino [UNESP]Kluska, Sabrina [UNESP]Olivieri, Bianca Ferreira [UNESP]Feitosa, Fabieli Louise Braga [UNESP]Berton, Mariana Piatto [UNESP]Lopes, Fernando Brito [UNESP]Munari, Danísio Prado [UNESP]Lôbo, Raysildo BarbosaMagnabosco, Cláudio De UlhoaDi Croce, FernandoOsterstock, JasonDenise, SuePereira, Angélica Simone CravoBaldi, Fernando [UNESP]2018-12-11T17:22:48Z2018-12-11T17:22:48Z2018-09-17info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.1186/s12864-018-5060-8BMC Genomics, v. 19, n. 1, 2018.1471-2164http://hdl.handle.net/11449/17685810.1186/s12864-018-5060-82-s2.0-850535619552-s2.0-85053561955.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Genomics2,110info:eu-repo/semantics/openAccess2024-06-07T18:41:04Zoai:repositorio.unesp.br:11449/176858Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T16:53:48.982618Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics |
title |
Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics |
spellingShingle |
Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics Peripolli, Elisa [UNESP] Bos indicus Gene ontology Genomic inbreeding Indicine |
title_short |
Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics |
title_full |
Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics |
title_fullStr |
Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics |
title_full_unstemmed |
Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics |
title_sort |
Autozygosity islands and ROH patterns in Nellore lineages: Evidence of selection for functionally important traits 06 Biological Sciences 0604 Genetics |
author |
Peripolli, Elisa [UNESP] |
author_facet |
Peripolli, Elisa [UNESP] Metzger, Julia De Lemos, Marcos Vinícius Antunes [UNESP] Stafuzza, Nedenia Bonvino [UNESP] Kluska, Sabrina [UNESP] Olivieri, Bianca Ferreira [UNESP] Feitosa, Fabieli Louise Braga [UNESP] Berton, Mariana Piatto [UNESP] Lopes, Fernando Brito [UNESP] Munari, Danísio Prado [UNESP] Lôbo, Raysildo Barbosa Magnabosco, Cláudio De Ulhoa Di Croce, Fernando Osterstock, Jason Denise, Sue Pereira, Angélica Simone Cravo Baldi, Fernando [UNESP] |
author_role |
author |
author2 |
Metzger, Julia De Lemos, Marcos Vinícius Antunes [UNESP] Stafuzza, Nedenia Bonvino [UNESP] Kluska, Sabrina [UNESP] Olivieri, Bianca Ferreira [UNESP] Feitosa, Fabieli Louise Braga [UNESP] Berton, Mariana Piatto [UNESP] Lopes, Fernando Brito [UNESP] Munari, Danísio Prado [UNESP] Lôbo, Raysildo Barbosa Magnabosco, Cláudio De Ulhoa Di Croce, Fernando Osterstock, Jason Denise, Sue Pereira, Angélica Simone Cravo Baldi, Fernando [UNESP] |
author2_role |
author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) University of Veterinary Medicine Hannover Associação Nacional de Criadores e Pesquisadores (ANCP) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Zoetis Universidade de São Paulo (USP) |
dc.contributor.author.fl_str_mv |
Peripolli, Elisa [UNESP] Metzger, Julia De Lemos, Marcos Vinícius Antunes [UNESP] Stafuzza, Nedenia Bonvino [UNESP] Kluska, Sabrina [UNESP] Olivieri, Bianca Ferreira [UNESP] Feitosa, Fabieli Louise Braga [UNESP] Berton, Mariana Piatto [UNESP] Lopes, Fernando Brito [UNESP] Munari, Danísio Prado [UNESP] Lôbo, Raysildo Barbosa Magnabosco, Cláudio De Ulhoa Di Croce, Fernando Osterstock, Jason Denise, Sue Pereira, Angélica Simone Cravo Baldi, Fernando [UNESP] |
dc.subject.por.fl_str_mv |
Bos indicus Gene ontology Genomic inbreeding Indicine |
topic |
Bos indicus Gene ontology Genomic inbreeding Indicine |
description |
Background: The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results: The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (- 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (- 0.01 to - 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (- 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions: Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-12-11T17:22:48Z 2018-12-11T17:22:48Z 2018-09-17 |
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/10.1186/s12864-018-5060-8 BMC Genomics, v. 19, n. 1, 2018. 1471-2164 http://hdl.handle.net/11449/176858 10.1186/s12864-018-5060-8 2-s2.0-85053561955 2-s2.0-85053561955.pdf |
url |
http://dx.doi.org/10.1186/s12864-018-5060-8 http://hdl.handle.net/11449/176858 |
identifier_str_mv |
BMC Genomics, v. 19, n. 1, 2018. 1471-2164 10.1186/s12864-018-5060-8 2-s2.0-85053561955 2-s2.0-85053561955.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
BMC Genomics 2,110 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
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 |
|
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1808128717767049216 |