Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10174/28201 https://doi.org/10.1186/s12711-020-00553-7 |
Resumo: | Background: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining wholegenome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources. |
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Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systemsPigsAlentejano pigEuropean local breedsSNPsBísaro pigBackground: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining wholegenome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.Springer Nature2020-10-23T11:16:16Z2020-10-232020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://hdl.handle.net/10174/28201http://hdl.handle.net/10174/28201https://doi.org/10.1186/s12711-020-00553-7engBovo, S.; A. Ribani; M. Muñoz; E. Alves; J.P. Araujo; R. Bozzi; M. Čandek-Potokar; R. Charneca; F.D. Palma; G. Etherington; A.I. Fernandez; F. García; J. García-Casco; D. Karolyi; M. Gallo; V. Margeta; J.M. Martins; M.J. Mercat; G. Moscatelli; Y. Núñez; R. Quintanilla; C. Radović; V. Razmaite; J. Riquet; R. Savić; G. Schiavo; G. Usai; V.J. Utzeri; C. Zimmer; C. Ovilo; L. Fontanesi (2020). Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems. Genetics Selection Evolution, 52(1), 33.Departamento de Zootecniandndndndndndndrmcc@uevora.ptndndndndndndndndjmartins@uevora.ptndndndndndndndndndndndndndnd552Bovo, S.Ribani, A.Muñoz, M.Alves, E.Araujo, J.P.Bozzi, R.Čandek-Potokar, M.Charneca, RPalma, F.D.Etherington, G.Fernandez, A.I.García, F.García-Casco, J.Karolyi, D.Gallo, M.Margeta, V.Martins, J.M.Mercat, M.J.Moscatelli, G.Núñez, Y.Quitanilla, R.Radović, C.Razmaite, V.Riquet, J.Savić, R.Schiavo, G.Usai, G.Utzeri, V.J.Zimmer, C.Ovilo, C.Fontanesi, L.info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-01-03T19:23:50Zoai:dspace.uevora.pt:10174/28201Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T01:17:55.555219Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems |
title |
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems |
spellingShingle |
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems Bovo, S. Pigs Alentejano pig European local breeds SNPs Bísaro pig |
title_short |
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems |
title_full |
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems |
title_fullStr |
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems |
title_full_unstemmed |
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems |
title_sort |
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems |
author |
Bovo, S. |
author_facet |
Bovo, S. Ribani, A. Muñoz, M. Alves, E. Araujo, J.P. Bozzi, R. Čandek-Potokar, M. Charneca, R Palma, F.D. Etherington, G. Fernandez, A.I. García, F. García-Casco, J. Karolyi, D. Gallo, M. Margeta, V. Martins, J.M. Mercat, M.J. Moscatelli, G. Núñez, Y. Quitanilla, R. Radović, C. Razmaite, V. Riquet, J. Savić, R. Schiavo, G. Usai, G. Utzeri, V.J. Zimmer, C. Ovilo, C. Fontanesi, L. |
author_role |
author |
author2 |
Ribani, A. Muñoz, M. Alves, E. Araujo, J.P. Bozzi, R. Čandek-Potokar, M. Charneca, R Palma, F.D. Etherington, G. Fernandez, A.I. García, F. García-Casco, J. Karolyi, D. Gallo, M. Margeta, V. Martins, J.M. Mercat, M.J. Moscatelli, G. Núñez, Y. Quitanilla, R. Radović, C. Razmaite, V. Riquet, J. Savić, R. Schiavo, G. Usai, G. Utzeri, V.J. Zimmer, C. Ovilo, C. Fontanesi, L. |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Bovo, S. Ribani, A. Muñoz, M. Alves, E. Araujo, J.P. Bozzi, R. Čandek-Potokar, M. Charneca, R Palma, F.D. Etherington, G. Fernandez, A.I. García, F. García-Casco, J. Karolyi, D. Gallo, M. Margeta, V. Martins, J.M. Mercat, M.J. Moscatelli, G. Núñez, Y. Quitanilla, R. Radović, C. Razmaite, V. Riquet, J. Savić, R. Schiavo, G. Usai, G. Utzeri, V.J. Zimmer, C. Ovilo, C. Fontanesi, L. |
dc.subject.por.fl_str_mv |
Pigs Alentejano pig European local breeds SNPs Bísaro pig |
topic |
Pigs Alentejano pig European local breeds SNPs Bísaro pig |
description |
Background: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining wholegenome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-10-23T11:16:16Z 2020-10-23 2020-01-01T00:00:00Z |
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://hdl.handle.net/10174/28201 http://hdl.handle.net/10174/28201 https://doi.org/10.1186/s12711-020-00553-7 |
url |
http://hdl.handle.net/10174/28201 https://doi.org/10.1186/s12711-020-00553-7 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Bovo, S.; A. Ribani; M. Muñoz; E. Alves; J.P. Araujo; R. Bozzi; M. Čandek-Potokar; R. Charneca; F.D. Palma; G. Etherington; A.I. Fernandez; F. García; J. García-Casco; D. Karolyi; M. Gallo; V. Margeta; J.M. Martins; M.J. Mercat; G. Moscatelli; Y. Núñez; R. Quintanilla; C. Radović; V. Razmaite; J. Riquet; R. Savić; G. Schiavo; G. Usai; V.J. Utzeri; C. Zimmer; C. Ovilo; L. Fontanesi (2020). Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems. Genetics Selection Evolution, 52(1), 33. Departamento de Zootecnia nd nd nd nd nd nd nd rmcc@uevora.pt nd nd nd nd nd nd nd nd jmartins@uevora.pt nd nd nd nd nd nd nd nd nd nd nd nd nd nd 552 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Springer Nature |
publisher.none.fl_str_mv |
Springer Nature |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799136661017198592 |