Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , , , |
Tipo de documento: | Artigo de conferência |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10174/33344 |
Resumo: | The Alentejano is a Mediterranean pig breed, found in southern Portugal, reared under extensive conditions and finished on grass and acorns during the fall and winter months. From these animals a variety of dry-cured meat products of great economic importance are generated. A total of 541 pigs were studied during the 2017 slaughter campaign. Phenotypic records for carcass and meat quality were collected and subsequently analyzed to identify the groups of animals that displayed the most contrasting phenotypes. Two groups comprising 13 animals each were selected, based on pH, water loss, total lipids, total protein, total collagen and pigments content. All samples were re-sequenced to a 23x coverage. The reads were aligned to the pig genome and SNPs and structural variants identified between the two groups of animals. A total of 13,418,254 SNPs were identified, of which 6,851,475 and 6,566,779 were located in the genic and intergenic genomic regions, respectively. The number of SNPs for which at least 25 samples were present comprised 88.7%. The set of genic SNPs included 43,405 exonic non-synonymous SNPs and 60,750 exonic synonymous SNPs. The remaining SNPs were located in introns and ncRNA regions. Interestingly, SNPs with markedly different allele frequencies between the groups were also identified (a total of 230 SNPs with allele frequency differences between the groups of at least 30% or 70%). This study represents the first major characterization of Alentejano pigs at the genome level, and identified a significant number of SNPs potentially associated with meat quality. |
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Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypeswhole genomeAlentejano pigmeat qualityThe Alentejano is a Mediterranean pig breed, found in southern Portugal, reared under extensive conditions and finished on grass and acorns during the fall and winter months. From these animals a variety of dry-cured meat products of great economic importance are generated. A total of 541 pigs were studied during the 2017 slaughter campaign. Phenotypic records for carcass and meat quality were collected and subsequently analyzed to identify the groups of animals that displayed the most contrasting phenotypes. Two groups comprising 13 animals each were selected, based on pH, water loss, total lipids, total protein, total collagen and pigments content. All samples were re-sequenced to a 23x coverage. The reads were aligned to the pig genome and SNPs and structural variants identified between the two groups of animals. A total of 13,418,254 SNPs were identified, of which 6,851,475 and 6,566,779 were located in the genic and intergenic genomic regions, respectively. The number of SNPs for which at least 25 samples were present comprised 88.7%. The set of genic SNPs included 43,405 exonic non-synonymous SNPs and 60,750 exonic synonymous SNPs. The remaining SNPs were located in introns and ncRNA regions. Interestingly, SNPs with markedly different allele frequencies between the groups were also identified (a total of 230 SNPs with allele frequency differences between the groups of at least 30% or 70%). This study represents the first major characterization of Alentejano pigs at the genome level, and identified a significant number of SNPs potentially associated with meat quality.2023-01-10T11:55:31Z2023-01-102020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjecthttp://hdl.handle.net/10174/33344http://hdl.handle.net/10174/33344engUsié, A.; H. Magalhães; C. Leão; D. Gaspar; B. Meireles; P. Barbosa; L. Cachucho; A. Albuquerque; R. Charneca; J. Martins; E. Jerónimo; M. Ramos (2020). Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes. In: PAGXXVIII abstracts posters, International Plant & Animal Genome Conference XXVIII, San Diego, CA, E.U.A., p. 180.naonaosimZOOndndndndndndndndndjmartins@uevora.ptndndUsié, A.Magalhães, H.Leão, C.Gaspar, D.Meireles, B.Barbosa, P.Cachucho, L.Albuquerque, A.Charneca, R.Martins, J.M.Jerónimo, E.Ramos, M.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:RCAAP2024-01-03T19:34:19Zoai:dspace.uevora.pt:10174/33344Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T01:21:55.605371Repositório 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 Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes |
title |
Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes |
spellingShingle |
Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes Usié, A. whole genome Alentejano pig meat quality |
title_short |
Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes |
title_full |
Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes |
title_fullStr |
Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes |
title_full_unstemmed |
Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes |
title_sort |
Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes |
author |
Usié, A. |
author_facet |
Usié, A. Magalhães, H. Leão, C. Gaspar, D. Meireles, B. Barbosa, P. Cachucho, L. Albuquerque, A. Charneca, R. Martins, J.M. Jerónimo, E. Ramos, M. |
author_role |
author |
author2 |
Magalhães, H. Leão, C. Gaspar, D. Meireles, B. Barbosa, P. Cachucho, L. Albuquerque, A. Charneca, R. Martins, J.M. Jerónimo, E. Ramos, M. |
author2_role |
author author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Usié, A. Magalhães, H. Leão, C. Gaspar, D. Meireles, B. Barbosa, P. Cachucho, L. Albuquerque, A. Charneca, R. Martins, J.M. Jerónimo, E. Ramos, M. |
dc.subject.por.fl_str_mv |
whole genome Alentejano pig meat quality |
topic |
whole genome Alentejano pig meat quality |
description |
The Alentejano is a Mediterranean pig breed, found in southern Portugal, reared under extensive conditions and finished on grass and acorns during the fall and winter months. From these animals a variety of dry-cured meat products of great economic importance are generated. A total of 541 pigs were studied during the 2017 slaughter campaign. Phenotypic records for carcass and meat quality were collected and subsequently analyzed to identify the groups of animals that displayed the most contrasting phenotypes. Two groups comprising 13 animals each were selected, based on pH, water loss, total lipids, total protein, total collagen and pigments content. All samples were re-sequenced to a 23x coverage. The reads were aligned to the pig genome and SNPs and structural variants identified between the two groups of animals. A total of 13,418,254 SNPs were identified, of which 6,851,475 and 6,566,779 were located in the genic and intergenic genomic regions, respectively. The number of SNPs for which at least 25 samples were present comprised 88.7%. The set of genic SNPs included 43,405 exonic non-synonymous SNPs and 60,750 exonic synonymous SNPs. The remaining SNPs were located in introns and ncRNA regions. Interestingly, SNPs with markedly different allele frequencies between the groups were also identified (a total of 230 SNPs with allele frequency differences between the groups of at least 30% or 70%). This study represents the first major characterization of Alentejano pigs at the genome level, and identified a significant number of SNPs potentially associated with meat quality. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-01-01T00:00:00Z 2023-01-10T11:55:31Z 2023-01-10 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/conferenceObject |
format |
conferenceObject |
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publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10174/33344 http://hdl.handle.net/10174/33344 |
url |
http://hdl.handle.net/10174/33344 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Usié, A.; H. Magalhães; C. Leão; D. Gaspar; B. Meireles; P. Barbosa; L. Cachucho; A. Albuquerque; R. Charneca; J. Martins; E. Jerónimo; M. Ramos (2020). Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes. In: PAGXXVIII abstracts posters, International Plant & Animal Genome Conference XXVIII, San Diego, CA, E.U.A., p. 180. nao nao sim ZOO nd nd nd nd nd nd nd nd nd jmartins@uevora.pt nd nd |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
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 |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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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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