Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | por |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/20.500.11960/3330 |
Resumo: | Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profler (GGP) 70K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population diferentiation and structure, genetic distances, linkage disequilibrium and efective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small efective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie diferences in adaptation to specifc environments and productive systems and phenotypic traits were detected in potentially selected genomic regions. |
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spelling |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chipGenetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profler (GGP) 70K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population diferentiation and structure, genetic distances, linkage disequilibrium and efective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small efective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie diferences in adaptation to specifc environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.2023-05-29T14:36:45Z2019-09-19T00:00:00Z2019-09-192022-10-02T08:58:12Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/20.500.11960/3330por2045-232210.1038/s41598-019-49830-6Muñoz, M.Bozzi, R.García-Casco, J.Núñez, Y.Ribani, A.Franci, O.García, F.Škrlep, M.Schiavo, G.Bovo, S.Utzeri, V. J.Charneca, R.Martins, J. M.R.Quintanilla, R.Tibau, J.Margeta, V.Djurkin-Kušec, I.Mercat, M. J.Riquet, J.Estellé, J.Zimmer, C.Razmaite, V.Araújo, J. P.Radović, C.Savić, R.Karolyi, D.Gallo, M.Čandek-Potokar, M.Fernández, A. I.Fontanesi, L.Óvilo, C.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:RCAAP2023-07-27T06:46:21Zoai:repositorio.ipvc.pt:20.500.11960/3330Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T17:59:34.175007Repositório 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 |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip |
title |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip |
spellingShingle |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip Muñoz, M. |
title_short |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip |
title_full |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip |
title_fullStr |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip |
title_full_unstemmed |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip |
title_sort |
Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip |
author |
Muñoz, M. |
author_facet |
Muñoz, M. Bozzi, R. García-Casco, J. Núñez, Y. Ribani, A. Franci, O. García, F. Škrlep, M. Schiavo, G. Bovo, S. Utzeri, V. J. Charneca, R. Martins, J. M. R.Quintanilla, R. Tibau, J. Margeta, V. Djurkin-Kušec, I. Mercat, M. J. Riquet, J. Estellé, J. Zimmer, C. Razmaite, V. Araújo, J. P. Radović, C. Savić, R. Karolyi, D. Gallo, M. Čandek-Potokar, M. Fernández, A. I. Fontanesi, L. Óvilo, C. |
author_role |
author |
author2 |
Bozzi, R. García-Casco, J. Núñez, Y. Ribani, A. Franci, O. García, F. Škrlep, M. Schiavo, G. Bovo, S. Utzeri, V. J. Charneca, R. Martins, J. M. R.Quintanilla, R. Tibau, J. Margeta, V. Djurkin-Kušec, I. Mercat, M. J. Riquet, J. Estellé, J. Zimmer, C. Razmaite, V. Araújo, J. P. Radović, C. Savić, R. Karolyi, D. Gallo, M. Čandek-Potokar, M. Fernández, A. I. Fontanesi, L. Óvilo, C. |
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 |
Muñoz, M. Bozzi, R. García-Casco, J. Núñez, Y. Ribani, A. Franci, O. García, F. Škrlep, M. Schiavo, G. Bovo, S. Utzeri, V. J. Charneca, R. Martins, J. M. R.Quintanilla, R. Tibau, J. Margeta, V. Djurkin-Kušec, I. Mercat, M. J. Riquet, J. Estellé, J. Zimmer, C. Razmaite, V. Araújo, J. P. Radović, C. Savić, R. Karolyi, D. Gallo, M. Čandek-Potokar, M. Fernández, A. I. Fontanesi, L. Óvilo, C. |
description |
Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profler (GGP) 70K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population diferentiation and structure, genetic distances, linkage disequilibrium and efective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small efective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie diferences in adaptation to specifc environments and productive systems and phenotypic traits were detected in potentially selected genomic regions. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-09-19T00:00:00Z 2019-09-19 2022-10-02T08:58:12Z 2023-05-29T14:36:45Z |
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/20.500.11960/3330 |
url |
http://hdl.handle.net/20.500.11960/3330 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.relation.none.fl_str_mv |
2045-2322 10.1038/s41598-019-49830-6 |
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 |
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) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799131665155489792 |