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: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10174/25995 https://doi.org/10.1038/s41598-019-49830-6 |
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 Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective 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 effective 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 differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions. |
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Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chipGenomic diversityMolecular biologyPigsLocal breedsSNP chipsGenetic 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 Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective 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 effective 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 differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.Scientific Reports2019-11-06T11:43:57Z2019-11-062019-09-19T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://hdl.handle.net/10174/25995http://hdl.handle.net/10174/25995https://doi.org/10.1038/s41598-019-49830-6engMuñoz, M.; R. Bozzi; J. García-Casco; Y. Núñez; A. Ribani; O. Franci; F. García; M. Škrlep; G. Schiavo; S. Bovo; V.J. Utzeri; R. Charneca; J.M. Martins; R. Quintanilla; J. Tibau; V. Margeta; I. Djurkin-Kušec; M.J. Mercat; J. Riquet; J. Estellé; C. Zimmer; V. Razmaite; J.P. Araujo; Č Radović; R. Savić; D. Karolyi; M. Gallo; M. Čandek-Potokar; A.I. Fernández; L. Fontanesi; C. Óvilo (2019). Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Scientific Reports, 9, 13546.Departamento de Zootecniandndndndndndndndndndndrmcc@uevora.ptjmartins@uevora.ptndndndndndndndndndndndndndndndndndnd380Muñoz, M.Bozzi, R.Garcia-Casco, J.Núñez, Y.Ribani, A.Franci, O.Garcia, F.Skrlep, M.Schiavo, G.Bovo, S.Utzeri, V.J.Charneca, R.Martins, J.M.Quintanilla, R.Tibau, J.Margeta, V.Djurkin-Kusec, I.Mercat, M.J.Riquet, J.Estellé, J.Zimmer, C.Razmaite, V.Araujo, J.P.Radovic, C.Savic, R.Karolyi, D.Gallo, M.Candek-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:RCAAP2024-01-03T19:20:13Zoai:dspace.uevora.pt:10174/25995Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T01:16:18.860182Repositório 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. Genomic diversity Molecular biology Pigs Local breeds SNP chips |
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. Garcia-Casco, J. Núñez, Y. Ribani, A. Franci, O. Garcia, F. Skrlep, M. Schiavo, G. Bovo, S. Utzeri, V.J. Charneca, R. Martins, J.M. Quintanilla, R. Tibau, J. Margeta, V. Djurkin-Kusec, I. Mercat, M.J. Riquet, J. Estellé, J. Zimmer, C. Razmaite, V. Araujo, J.P. Radovic, C. Savic, R. Karolyi, D. Gallo, M. Candek-Potokar, M. Fernández, A.I. Fontanesi, L. Óvilo, C. |
author_role |
author |
author2 |
Bozzi, R. Garcia-Casco, J. Núñez, Y. Ribani, A. Franci, O. Garcia, F. Skrlep, M. Schiavo, G. Bovo, S. Utzeri, V.J. Charneca, R. Martins, J.M. Quintanilla, R. Tibau, J. Margeta, V. Djurkin-Kusec, I. Mercat, M.J. Riquet, J. Estellé, J. Zimmer, C. Razmaite, V. Araujo, J.P. Radovic, C. Savic, R. Karolyi, D. Gallo, M. Candek-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. Garcia-Casco, J. Núñez, Y. Ribani, A. Franci, O. Garcia, F. Skrlep, M. Schiavo, G. Bovo, S. Utzeri, V.J. Charneca, R. Martins, J.M. Quintanilla, R. Tibau, J. Margeta, V. Djurkin-Kusec, I. Mercat, M.J. Riquet, J. Estellé, J. Zimmer, C. Razmaite, V. Araujo, J.P. Radovic, C. Savic, R. Karolyi, D. Gallo, M. Candek-Potokar, M. Fernández, A.I. Fontanesi, L. Óvilo, C. |
dc.subject.por.fl_str_mv |
Genomic diversity Molecular biology Pigs Local breeds SNP chips |
topic |
Genomic diversity Molecular biology Pigs Local breeds SNP chips |
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 Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective 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 effective 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 differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-11-06T11:43:57Z 2019-11-06 2019-09-19T00:00:00Z |
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/10174/25995 http://hdl.handle.net/10174/25995 https://doi.org/10.1038/s41598-019-49830-6 |
url |
http://hdl.handle.net/10174/25995 https://doi.org/10.1038/s41598-019-49830-6 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Muñoz, M.; R. Bozzi; J. García-Casco; Y. Núñez; A. Ribani; O. Franci; F. García; M. Škrlep; G. Schiavo; S. Bovo; V.J. Utzeri; R. Charneca; J.M. Martins; R. Quintanilla; J. Tibau; V. Margeta; I. Djurkin-Kušec; M.J. Mercat; J. Riquet; J. Estellé; C. Zimmer; V. Razmaite; J.P. Araujo; Č Radović; R. Savić; D. Karolyi; M. Gallo; M. Čandek-Potokar; A.I. Fernández; L. Fontanesi; C. Óvilo (2019). Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Scientific Reports, 9, 13546. Departamento de Zootecnia nd nd nd nd nd nd nd nd nd nd nd rmcc@uevora.pt jmartins@uevora.pt nd nd nd nd 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 |
Scientific Reports |
publisher.none.fl_str_mv |
Scientific Reports |
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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1799136645265489920 |