Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs

The selection in commercial swine breeds for meat-production efficiency has been increasing among the past decades, reducing the intramuscular fat content, which has changed the sensorial and technological properties of pork. Through processes of natural adaptation and selective breeding, the accumu...

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Detalhes bibliográficos
Autores: Crespo-Piazuelo, Daniel, Criado-Mesas, Lourdes, Revilla, Manuel, Castelló, Anna, Fernández, Ana I., Folch, Josep M., Ballester, Maria
Formato: artículo
Fecha de publicación:2019
País:España
Recursos:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
Repositorio:IRTA Pubpro. Open Digital Archive
OAI Identifier:oai:repositori.irta.cat:20.500.12327/564
Acesso em linha:http://hdl.handle.net/20.500.12327/564
https://doi.org/10.1371/journal.pone.0218862
Access Level:acceso abierto
Palavra-chave:619
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spelling Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigsCrespo-Piazuelo, DanielCriado-Mesas, LourdesRevilla, ManuelCastelló, AnnaFernández, Ana I.Folch, Josep M.Ballester, Maria619The selection in commercial swine breeds for meat-production efficiency has been increasing among the past decades, reducing the intramuscular fat content, which has changed the sensorial and technological properties of pork. Through processes of natural adaptation and selective breeding, the accumulation of mutations has driven the genetic divergence between pig breeds. The most common and well-studied mutations are single-nucleotide polymorphisms (SNPs). However, insertions and deletions (indels) usually represents a fifth part of the detected mutations and should also be considered for animal breeding. In the present study, three different programs (Dindel, SAMtools mpileup, and GATK) were used to detect indels from Whole Genome Sequencing data of Iberian boars and Landrace sows. A total of 1,928,746 indels were found in common with the three programs. The VEP tool predicted that 1,289 indels may have a high impact on protein sequence and function. Ten indels inside genes related with lipid metabolism were genotyped in pigs from three different backcrosses with Iberian origin, obtaining different allelic frequencies on each backcross. Genome-Wide Association Studies performed in the Longissimus dorsi muscle found an association between an indel located in the C1q and TNF related 12 (C1QTNF12) gene and the amount of eicosadienoic acid (C20:2(n-6)).info:eu-repo/semantics/publishedVersionPublic Library of ScienceProducció AnimalGenètica i Millora Animal201920192019info:eu-repo/semantics/article17application/pdfhttp://hdl.handle.net/20.500.12327/564https://doi.org/10.1371/journal.pone.0218862reponame:IRTA Pubpro. Open Digital Archiveinstname:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)InglésPLoS ONEAttribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.irta.cat:20.500.12327/5642026-06-16T08:51:17Z
dc.title.none.fl_str_mv Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
title Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
spellingShingle Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
Crespo-Piazuelo, Daniel
619
title_short Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
title_full Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
title_fullStr Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
title_full_unstemmed Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
title_sort Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
dc.creator.none.fl_str_mv Crespo-Piazuelo, Daniel
Criado-Mesas, Lourdes
Revilla, Manuel
Castelló, Anna
Fernández, Ana I.
Folch, Josep M.
Ballester, Maria
author Crespo-Piazuelo, Daniel
author_facet Crespo-Piazuelo, Daniel
Criado-Mesas, Lourdes
Revilla, Manuel
Castelló, Anna
Fernández, Ana I.
Folch, Josep M.
Ballester, Maria
author_role author
author2 Criado-Mesas, Lourdes
Revilla, Manuel
Castelló, Anna
Fernández, Ana I.
Folch, Josep M.
Ballester, Maria
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Producció Animal
Genètica i Millora Animal
dc.subject.none.fl_str_mv 619
topic 619
description The selection in commercial swine breeds for meat-production efficiency has been increasing among the past decades, reducing the intramuscular fat content, which has changed the sensorial and technological properties of pork. Through processes of natural adaptation and selective breeding, the accumulation of mutations has driven the genetic divergence between pig breeds. The most common and well-studied mutations are single-nucleotide polymorphisms (SNPs). However, insertions and deletions (indels) usually represents a fifth part of the detected mutations and should also be considered for animal breeding. In the present study, three different programs (Dindel, SAMtools mpileup, and GATK) were used to detect indels from Whole Genome Sequencing data of Iberian boars and Landrace sows. A total of 1,928,746 indels were found in common with the three programs. The VEP tool predicted that 1,289 indels may have a high impact on protein sequence and function. Ten indels inside genes related with lipid metabolism were genotyped in pigs from three different backcrosses with Iberian origin, obtaining different allelic frequencies on each backcross. Genome-Wide Association Studies performed in the Longissimus dorsi muscle found an association between an indel located in the C1q and TNF related 12 (C1QTNF12) gene and the amount of eicosadienoic acid (C20:2(n-6)).
publishDate 2019
dc.date.none.fl_str_mv 2019
2019
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12327/564
https://doi.org/10.1371/journal.pone.0218862
url http://hdl.handle.net/20.500.12327/564
https://doi.org/10.1371/journal.pone.0218862
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv PLoS ONE
dc.rights.none.fl_str_mv Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 17
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:IRTA Pubpro. Open Digital Archive
instname:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
instname_str Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
reponame_str IRTA Pubpro. Open Digital Archive
collection IRTA Pubpro. Open Digital Archive
repository.name.fl_str_mv
repository.mail.fl_str_mv
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