Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states
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/10174/28179 https://doi.org/10.1111/age.12954 |
Resumo: | In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems. |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
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Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number statescopy number variantELOVL6genetic resourceKITMSRB3next-generation sequencingSus scrofaZNF622In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.Wiley2020-10-23T11:00:41Z2020-10-232020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://hdl.handle.net/10174/28179http://hdl.handle.net/10174/28179https://doi.org/10.1111/age.12954engBovo, S.; A. Ribani; M. Muñoz; E. Alves; J.P. Araujo; R. Bozzi; R. Charneca; F.D. Palma; G. Etherington; A.I. Fernandez; F. García; J. García-Casco; D. Karolyi; M. Gallo; K. Gvozdanović; J.M. Martins; M.J. Mercat; Y. Núñez; R. Quintanilla; Č. Radović; V. Razmaite; J. Riquet; R. Savić; G. Schiavo; M. Škrlep; G. Usai; V.J. Utzeri; C. Zimmer; C. Ovilo; L. Fontanesi (2020). Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states. Animal Genetics, 51(4), 541-556.Departamento de Zootecniandndndndndndrmcc@uevora.ptndndndndndndndndjmartins@uevora.ptndndndndndndndndndndndndndnd380Bovo, S.Ribani, A.Muñoz, M.Alves, E.Araujo, J.P.Bozzi, R.Charneca, R.Palma, F.D.Etherington, G.Fernandez, A.I.García, F.García-Casco, J.Karolyi, D.Gallo, M.Gvozdanović, K.Martins, J.M.Mercat, M.J.Núñez, Y.Quintanilla, R.Radović, Č.Razmaite, V.Riquet, J.Savić, R.Schiavo, G.Škrlep, M.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:RCAAP2024-01-03T19:24:00Zoai:dspace.uevora.pt:10174/28179Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T01:17:59.701182Repositório 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 |
Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states |
title |
Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states |
spellingShingle |
Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states Bovo, S. copy number variant ELOVL6 genetic resource KIT MSRB3 next-generation sequencing Sus scrofa ZNF622 |
title_short |
Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states |
title_full |
Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states |
title_fullStr |
Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states |
title_full_unstemmed |
Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states |
title_sort |
Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states |
author |
Bovo, S. |
author_facet |
Bovo, S. Ribani, A. Muñoz, M. Alves, E. Araujo, J.P. Bozzi, R. Charneca, R. Palma, F.D. Etherington, G. Fernandez, A.I. García, F. García-Casco, J. Karolyi, D. Gallo, M. Gvozdanović, K. Martins, J.M. Mercat, M.J. Núñez, Y. Quintanilla, R. Radović, Č. Razmaite, V. Riquet, J. Savić, R. Schiavo, G. Škrlep, M. 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. Charneca, R. Palma, F.D. Etherington, G. Fernandez, A.I. García, F. García-Casco, J. Karolyi, D. Gallo, M. Gvozdanović, K. Martins, J.M. Mercat, M.J. Núñez, Y. Quintanilla, R. Radović, Č. Razmaite, V. Riquet, J. Savić, R. Schiavo, G. Škrlep, M. 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 |
dc.contributor.author.fl_str_mv |
Bovo, S. Ribani, A. Muñoz, M. Alves, E. Araujo, J.P. Bozzi, R. Charneca, R. Palma, F.D. Etherington, G. Fernandez, A.I. García, F. García-Casco, J. Karolyi, D. Gallo, M. Gvozdanović, K. Martins, J.M. Mercat, M.J. Núñez, Y. Quintanilla, R. Radović, Č. Razmaite, V. Riquet, J. Savić, R. Schiavo, G. Škrlep, M. Usai, G. Utzeri, V.J. Zimmer, C. Ovilo, C. Fontanesi, L. |
dc.subject.por.fl_str_mv |
copy number variant ELOVL6 genetic resource KIT MSRB3 next-generation sequencing Sus scrofa ZNF622 |
topic |
copy number variant ELOVL6 genetic resource KIT MSRB3 next-generation sequencing Sus scrofa ZNF622 |
description |
In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-10-23T11:00:41Z 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/10174/28179 http://hdl.handle.net/10174/28179 https://doi.org/10.1111/age.12954 |
url |
http://hdl.handle.net/10174/28179 https://doi.org/10.1111/age.12954 |
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; R. Charneca; F.D. Palma; G. Etherington; A.I. Fernandez; F. García; J. García-Casco; D. Karolyi; M. Gallo; K. Gvozdanović; J.M. Martins; M.J. Mercat; Y. Núñez; R. Quintanilla; Č. Radović; V. Razmaite; J. Riquet; R. Savić; G. Schiavo; M. Škrlep; G. Usai; V.J. Utzeri; C. Zimmer; C. Ovilo; L. Fontanesi (2020). Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states. Animal Genetics, 51(4), 541-556. Departamento de Zootecnia 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 380 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Wiley |
publisher.none.fl_str_mv |
Wiley |
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 |
instname_str |
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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1799136661797339136 |