Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles
Background: Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression and the genetic determinism of IMF traits in the porcine gluteus medius (GM) an...
| Autores: | , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2019 |
| País: | España |
| Institución: | Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
| Repositorio: | Recercat. Dipósit de la Recerca de Catalunya |
| OAI Identifier: | oai:recercat.cat:10459.1/66302 |
| Acceso en línea: | https://doi.org/10.1186/s12864-019-5557-9 http://hdl.handle.net/10459.1/66302 |
| Access Level: | acceso abierto |
| Palabra clave: | Intramuscular fat Fatty acid content Genome-wide association analysis Duroc pig |
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Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles |
| title |
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles |
| spellingShingle |
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles González-Prendes, Rayner Intramuscular fat Fatty acid content Genome-wide association analysis Duroc pig |
| title_short |
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles |
| title_full |
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles |
| title_fullStr |
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles |
| title_full_unstemmed |
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles |
| title_sort |
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles |
| dc.creator.none.fl_str_mv |
González-Prendes, Rayner Quintanilla Aguado, Raquel Mármol-Sánchez, Emilio Pena i Subirà, Ramona Natacha Ballester, Maria Figueiredo Cardoso, Tainã Manunza, Arianna Casellas, Joaquim Cánovas, Angela Díaz, Isabel Noguera Jiménez, José Luis Castelló, Anna Mercadé Carceller, Anna Amills i Eras, Marcel |
| author |
González-Prendes, Rayner |
| author_facet |
González-Prendes, Rayner Quintanilla Aguado, Raquel Mármol-Sánchez, Emilio Pena i Subirà, Ramona Natacha Ballester, Maria Figueiredo Cardoso, Tainã Manunza, Arianna Casellas, Joaquim Cánovas, Angela Díaz, Isabel Noguera Jiménez, José Luis Castelló, Anna Mercadé Carceller, Anna Amills i Eras, Marcel |
| author_role |
author |
| author2 |
Quintanilla Aguado, Raquel Mármol-Sánchez, Emilio Pena i Subirà, Ramona Natacha Ballester, Maria Figueiredo Cardoso, Tainã Manunza, Arianna Casellas, Joaquim Cánovas, Angela Díaz, Isabel Noguera Jiménez, José Luis Castelló, Anna Mercadé Carceller, Anna Amills i Eras, Marcel |
| author2_role |
author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Intramuscular fat Fatty acid content Genome-wide association analysis Duroc pig |
| topic |
Intramuscular fat Fatty acid content Genome-wide association analysis Duroc pig |
| description |
Background: Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression and the genetic determinism of IMF traits in the porcine gluteus medius (GM) and longissimus dorsi (LD) muscles. Results: A comparative analysis of the mRNA expression profiles of the pig GM and LD muscles in 16 Duroc pigs with available microarray mRNA expression measurements revealed the existence of 106 differentially expressed probes (fold-change > 1.5 and q-value < 0.05). Amongst the genes displaying the most significant differential expression, several loci belonging to the Hox transcription factor family were either upregulated (HOXA9, HOXA10, HOXB6, HOXB7 and TBX1) or downregulated (ARX) in the GM muscle. Differences in the expression of genes with key roles in carbohydrate and lipid metabolism (e.g. FABP3, ORMDL1 and SLC37A1) were also detected. By performing a GWAS for IMF content and composition traits recorded in the LD and GM muscles of 350 Duroc pigs, we identified the existence of one region on SSC14 (110–114 Mb) displaying significant associations with C18:0, C18:1(n-7), saturated and unsaturated fatty acid contents in both GM and LD muscles. Moreover, we detected several genome-wide significant associations that were not consistently found in both muscles. Further studies should be performed to confirm whether these associations are muscle-specific. Finally, the performance of an eQTL scan for 74 genes, located within GM QTL regions and with available microarray measurements of gene expression, made possible to identify 14 cis-eQTL regulating the expression of 14 loci, and six of them were confirmed by RNA-Seq. Conclusions: We have detected significant differences in the mRNA expression patterns of the porcine LD and GM muscles, evidencing that the transcriptomic profile of the skeletal muscle tissue is affected by anatomical, metabolic and functional factors. A highly significant association with IMF composition on SSC14 was replicated in both muscles, highlighting the existence of a common genetic determinism, but we also observed the existence of a few associations whose magnitude and significance varied between LD and GM muscles. |
| publishDate |
2019 |
| dc.date.none.fl_str_mv |
2019 2019 2019 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
https://doi.org/10.1186/s12864-019-5557-9 http://hdl.handle.net/10459.1/66302 http://hdl.handle.net/10459.1/66302 |
| url |
https://doi.org/10.1186/s12864-019-5557-9 http://hdl.handle.net/10459.1/66302 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
info:eu-repo/grantAgreement/MINECO//AGL2013-48742-C2-1-R info:eu-repo/grantAgreement/MINECO//AGL2013-48742-C2-2-R Reproducció del document publicat a https://doi.org/10.1186/s12864-019-5557-9 BMC Genomics, 2019, vol. 20, núm. 170, p. 1-18 |
| dc.rights.none.fl_str_mv |
cc-by, (c) González-Prendes et al., 2019 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ |
| rights_invalid_str_mv |
cc-by, (c) González-Prendes et al., 2019 https://creativecommons.org/licenses/by/4.0/ |
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openAccess |
| dc.publisher.none.fl_str_mv |
BMC (part of Springer Nature) |
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BMC (part of Springer Nature) |
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reponame:Recercat. Dipósit de la Recerca de Catalunya instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
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Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
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Recercat. Dipósit de la Recerca de Catalunya |
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Recercat. Dipósit de la Recerca de Catalunya |
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1869408456356659200 |
| spelling |
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi musclesGonzález-Prendes, RaynerQuintanilla Aguado, RaquelMármol-Sánchez, EmilioPena i Subirà, Ramona NatachaBallester, MariaFigueiredo Cardoso, TainãManunza, AriannaCasellas, JoaquimCánovas, AngelaDíaz, IsabelNoguera Jiménez, José LuisCastelló, AnnaMercadé Carceller, AnnaAmills i Eras, MarcelIntramuscular fatFatty acid contentGenome-wide association analysisDuroc pigBackground: Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression and the genetic determinism of IMF traits in the porcine gluteus medius (GM) and longissimus dorsi (LD) muscles. Results: A comparative analysis of the mRNA expression profiles of the pig GM and LD muscles in 16 Duroc pigs with available microarray mRNA expression measurements revealed the existence of 106 differentially expressed probes (fold-change > 1.5 and q-value < 0.05). Amongst the genes displaying the most significant differential expression, several loci belonging to the Hox transcription factor family were either upregulated (HOXA9, HOXA10, HOXB6, HOXB7 and TBX1) or downregulated (ARX) in the GM muscle. Differences in the expression of genes with key roles in carbohydrate and lipid metabolism (e.g. FABP3, ORMDL1 and SLC37A1) were also detected. By performing a GWAS for IMF content and composition traits recorded in the LD and GM muscles of 350 Duroc pigs, we identified the existence of one region on SSC14 (110–114 Mb) displaying significant associations with C18:0, C18:1(n-7), saturated and unsaturated fatty acid contents in both GM and LD muscles. Moreover, we detected several genome-wide significant associations that were not consistently found in both muscles. Further studies should be performed to confirm whether these associations are muscle-specific. Finally, the performance of an eQTL scan for 74 genes, located within GM QTL regions and with available microarray measurements of gene expression, made possible to identify 14 cis-eQTL regulating the expression of 14 loci, and six of them were confirmed by RNA-Seq. Conclusions: We have detected significant differences in the mRNA expression patterns of the porcine LD and GM muscles, evidencing that the transcriptomic profile of the skeletal muscle tissue is affected by anatomical, metabolic and functional factors. A highly significant association with IMF composition on SSC14 was replicated in both muscles, highlighting the existence of a common genetic determinism, but we also observed the existence of a few associations whose magnitude and significance varied between LD and GM muscles.Part of the research presented in this publication was funded by grants AGL2013–48742-C2–1-R and AGL2013–48742-C2–2-R awarded by the Spanish Ministry of Economy and Competitiveness and grant 2014 SGR 1528 from the Agency for Management of University and Research Grants of the Generalitat de Catalunya. We also acknowledge the support of the Spanish Ministry of Economy and Competitiveness for the Center of Excellence Severo Ochoa 2016–2019 (SEV-2015-0533) grant awarded to the Center for Research in Agricultural Genomics. Tainã F Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education (MEC) of the Federal Government of Brazil. Rayner González-Prendes and Emilio Mármol-Sánchez were funded with FPU Ph.D. grants from the Spanish Ministry of Education (FPU12/00860 and FPU15/ 01733). Maria Ballester is financially supported by a Ramon y Cajal contract (RYC-2013-12573) from the Spanish Ministry of Economy and Competitiveness. Thanks also to the CERCA Programme of the Generalitat de Catalunya for their support. The funding bodies had no role in the design of the study, the collection, analysis, the interpretation of data or the writing of the manuscript.BMC (part of Springer Nature)201920192019info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://doi.org/10.1186/s12864-019-5557-9http://hdl.handle.net/10459.1/66302http://hdl.handle.net/10459.1/66302reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)Inglésinfo:eu-repo/grantAgreement/MINECO//AGL2013-48742-C2-1-Rinfo:eu-repo/grantAgreement/MINECO//AGL2013-48742-C2-2-RReproducció del document publicat a https://doi.org/10.1186/s12864-019-5557-9BMC Genomics, 2019, vol. 20, núm. 170, p. 1-18cc-by, (c) González-Prendes et al., 2019info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/4.0/oai:recercat.cat:10459.1/663022026-05-29T05:05:01Z |
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15,812455 |