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Genome-wide association study for intramuscular fatty acid composition in an Iberian x Landrace cross

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Genome-wide association study for intramuscular fatty acid composition in an Iberian x Landrace cross

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Nombre: Ramayo-Caldas;Mer ...
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dc.contributor.author Ramayo-Caldas, Y. es_ES
dc.contributor.author Mercadé, A. es_ES
dc.contributor.author Castelló, A. es_ES
dc.contributor.author Yang, B. es_ES
dc.contributor.author Rodríguez, C. es_ES
dc.contributor.author Alves, E. es_ES
dc.contributor.author Díaz, I. es_ES
dc.contributor.author Ibáñez-Escriche, Noelia es_ES
dc.contributor.author Noguera, J. L. es_ES
dc.contributor.author Pérez-Enciso, M. es_ES
dc.contributor.author Fernández, A. I. es_ES
dc.contributor.author Folch, J. M. es_ES
dc.date.accessioned 2020-03-16T14:46:52Z
dc.date.available 2020-03-16T14:46:52Z
dc.date.issued 2012-09 es_ES
dc.identifier.issn 0021-8812 es_ES
dc.identifier.uri http://hdl.handle.net/10251/138963
dc.description.abstract [EN] The lipid content and fatty acid (FA) profile have an important impact in human health as well as in the technological transformation and nutritional and organoleptic quality of meat. A genome-wide association study (GWAS) on 144 backcross pigs (25% Iberian x 75% Landrace) was performed for 32 traits associated with intramuscular FA composition and indices of FA metabolism. The GWAS was carried out using Qxpak 5.0 and the genotyping information obtained from the Porcine SNP60K BeadChip (Illumina Inc., San Diego, CA). Signals of significant association considering a false-discovery rate (q-value < 0.05) were observed in 15 of the 32 analyzed traits, and a total of 813 trait-associated SNP (TAS), distributed in 43 chromosomal intervals on almost all autosomes, were annotated. According to the clustering analysis based on functional classification, several of the annotated genes are related to FA composition and lipid metabolism. Some interesting positional concordances among TAS and previously reported QTL for FA compositions and/or other lipid traits were also found. These common genomic regions for different traits suggest pleiotropic effects for FA composition and were found primarily on SSC4, SSC8, and SSC16. These results contribute to our understanding of the complex genetic basis of FA composition and FA metabolism. es_ES
dc.description.sponsorship This work was funded by MICINN Project AGL2008-04818-C03/GAN (Spanish Ministry of Science) and by the Innovation Consolider-Ingenio 2010 Program (CSD2007-00036, Centre for Research in Agrigenomics). We are indebted to Nova Genetica (Lleida, Spain) and its staff for their technical support. Y. Ramayo-Caldas was funded by a FPU Ph.D. grant from the Spanish Ministerio de Educacion (AP2008-01450). We thank Joaquin Casellas (UAB) and Jordi Estelle (INRA Jouy-en-Josas) for their comments, and also Martien Groenen (Wageningen, NL) for providing information about SNP positioning in Assembly 10. This manuscript has been proofread by Chuck Simons, a native English-speaking university instructor of English. es_ES
dc.language Inglés es_ES
dc.publisher American Society of Animal Science es_ES
dc.relation.ispartof Journal of Animal Science es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject Candidate gene es_ES
dc.subject Fatty acid es_ES
dc.subject Genome-wide association study es_ES
dc.subject Intramuscular fat es_ES
dc.subject Meat quality es_ES
dc.subject.classification PRODUCCION ANIMAL es_ES
dc.title Genome-wide association study for intramuscular fatty acid composition in an Iberian x Landrace cross es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.2527/jas.2011-4900 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//AGL2008-04818-C03-03/ES/GENES CANDIDATOS E IDENTIFICACION GENOMICA DE LOCI Y RUTAS GENICAS QUE AFECTAN A LA CALIDAD DE LA CARNE EN CERDOS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//AGL2008-04818-C03-02/ES/GENES CANDIDATOS E IDENTIFICACION GENOMICA DE LOCI Y RUTAS GENETICAS QUE AFECTAN A LA CALIDAD DE LA CARNE EN CERDOS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MECD//AP2008-01450/ES/AP2008-01450/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//AGL2008-04818-C03-01/ES/GENES CANDIDATOS E IDENTIFICACION GENOMICA DE LOCI Y RUTAS GENETICAS QUE AFECTAN A LA CALIDAD DE LA CARNE EN CERDOS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MEC//CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/ es_ES
dc.rights.accessRights Cerrado es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ciencia Animal - Departament de Ciència Animal es_ES
dc.description.bibliographicCitation Ramayo-Caldas, Y.; Mercadé, A.; Castelló, A.; Yang, B.; Rodríguez, C.; Alves, E.; Díaz, I.... (2012). Genome-wide association study for intramuscular fatty acid composition in an Iberian x Landrace cross. Journal of Animal Science. 90(9):2883-2893. https://doi.org/10.2527/jas.2011-4900 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.2527/jas.2011-4900 es_ES
dc.description.upvformatpinicio 2883 es_ES
dc.description.upvformatpfin 2893 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 90 es_ES
dc.description.issue 9 es_ES
dc.relation.pasarela S\395262 es_ES
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
dc.contributor.funder Ministerio de Educación y Ciencia es_ES
dc.description.references Amills, M., Vidal, O., Varona, L., Tomàs, A., Gil, M., Sànchez, A., & Noguera, J. L. (2005). Polymorphism of the pig 2,4-dienoyl CoA reductase 1 gene (DECR1) and its association with carcass and meat quality traits1. Journal of Animal Science, 83(3), 493-498. doi:10.2527/2005.833493x es_ES
dc.description.references Casellas, J., Noguera, J. L., Reixach, J., Díaz, I., Amills, M., & Quintanilla, R. (2010). Bayes factor analyses of heritability for serum and muscle lipid traits in Duroc pigs1. Journal of Animal Science, 88(7), 2246-2254. doi:10.2527/jas.2009-2205 es_ES
dc.description.references Chuang, S. S., Helvig, C., Taimi, M., Ramshaw, H. A., Collop, A. H., Amad, M., … Korczak, B. (2003). CYP2U1, a Novel Human Thymus- and Brain-specific Cytochrome P450, Catalyzes ω- and (ω-1)-Hydroxylation of Fatty Acids. Journal of Biological Chemistry, 279(8), 6305-6314. doi:10.1074/jbc.m311830200 es_ES
dc.description.references Clop, A., Ovilo, C., Perez-Enciso, M., Cercos, A., Tomas, A., Fernandez, A., … Noguera, J. L. (2003). Detection of QTL affecting fatty acid composition in the pig. Mammalian Genome, 14(9), 650-656. doi:10.1007/s00335-002-2210-7 es_ES
dc.description.references Corella, D. (2009). APOA2, Dietary Fat, and Body Mass Index. Archives of Internal Medicine, 169(20), 1897. doi:10.1001/archinternmed.2009.343 es_ES
dc.description.references Estellé, J., Fernández, A. I., Pérez-Enciso, M., Fernández, A., Rodríguez, C., Sánchez, A., … Folch, J. M. (2009). A non-synonymous mutation in a conserved site of theMTTPgene is strongly associated with protein activity and fatty acid profile in pigs. Animal Genetics, 40(6), 813-820. doi:10.1111/j.1365-2052.2009.01922.x es_ES
dc.description.references Estellé, J., Pérez-Enciso, M., Mercadé, A., Varona, L., Alves, E., Sánchez, A., & Folch, J. M. (2006). Characterization of the porcine FABP5 gene and its association with the FAT1 QTL in an Iberian by Landrace cross. Animal Genetics, 37(6), 589-591. doi:10.1111/j.1365-2052.2006.01535.x es_ES
dc.description.references Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Chen, Y., … Fitzgerald, S. (2010). Ensembl 2011. Nucleic Acids Research, 39(Database), D800-D806. doi:10.1093/nar/gkq1064 es_ES
dc.description.references Gallardo, D., Pena, R. N., Amills, M., Varona, L., Ramírez, O., Reixach, J., … Quintanilla, R. (2008). Mapping of quantitative trait loci for cholesterol, LDL, HDL, and triglyceride serum concentrations in pigs. Physiological Genomics, 35(3), 199-209. doi:10.1152/physiolgenomics.90249.2008 es_ES
dc.description.references Grindflek, E., Szyda, J., Liu, Z., & Lien, S. (2001). Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross. Mammalian Genome, 12(4), 299-304. doi:10.1007/s003350010278 es_ES
dc.description.references Guo, T., Ren, J., Yang, K., Ma, J., Zhang, Z., & Huang, L. (2009). Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2population. Animal Genetics, 40(2), 185-191. doi:10.1111/j.1365-2052.2008.01819.x es_ES
dc.description.references Henderson, C. R. (1975). Best Linear Unbiased Estimation and Prediction under a Selection Model. Biometrics, 31(2), 423. doi:10.2307/2529430 es_ES
dc.description.references Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2008). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4(1), 44-57. doi:10.1038/nprot.2008.211 es_ES
dc.description.references Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2008). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37(1), 1-13. doi:10.1093/nar/gkn923 es_ES
dc.description.references Ledur, M. C., Navarro, N., & Pérez-Enciso, M. (2009). Large-scale SNP genotyping in crosses between outbred lines: how useful is it? Heredity, 105(2), 173-182. doi:10.1038/hdy.2009.149 es_ES
dc.description.references Mach, N., Devant, M., Díaz, I., Font-Furnols, M., Oliver, M. A., García, J. A., & Bach, A. (2006). Increasing the amount of n-3 fatty acid in meat from young Holstein bulls through nutrition1. Journal of Animal Science, 84(11), 3039-3048. doi:10.2527/jas.2005-632 es_ES
dc.description.references Malek, M., Dekkers, J. C. M., Lee, H. K., Baas, T. J., Prusa, K., Huff-Lonergan, E., & Rothschild, M. F. (2001). A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition. Mammalian Genome, 12(8), 637-645. doi:10.1007/s003350020019 es_ES
dc.description.references Murakami, M., Taketomi, Y., Miki, Y., Sato, H., Hirabayashi, T., & Yamamoto, K. (2011). Recent progress in phospholipase A2 research: From cells to animals to humans. Progress in Lipid Research, 50(2), 152-192. doi:10.1016/j.plipres.2010.12.001 es_ES
dc.description.references Nii, M., Hayashi, T., Tani, F., Niki, A., Mori, N., Fujishima-Kanaya, N., … Mikawa, S. (2006). Quantitative trait loci mapping for fatty acid composition traits in perirenal and back fat using a Japanese wild boar × Large White intercross. Animal Genetics, 37(4), 342-347. doi:10.1111/j.1365-2052.2006.01485.x es_ES
dc.description.references Ntawubizi, M., Colman, E., Janssens, S., Raes, K., Buys, N., & De Smet, S. (2010). Genetic parameters for intramuscular fatty acid composition and metabolism in pigs1. Journal of Animal Science, 88(4), 1286-1294. doi:10.2527/jas.2009-2355 es_ES
dc.description.references Ojeda, A., Estellé, J., Folch, J. M., & Pérez-Enciso, M. (2008). Nucleotide variability and linkage disequilibrium patterns at the porcineFABP5gene. Animal Genetics, 39(5), 468-473. doi:10.1111/j.1365-2052.2008.01752.x es_ES
dc.description.references Pérez-Enciso, M., Clop, A., Noguera, J. L., Ovilo, C., Coll, A., Folch, J. M., … Sánchez, A. (2000). A QTL on pig chromosome 4 affects fatty acid metabolism: evidence from an Iberian by Landrace intercross. Journal of Animal Science, 78(10), 2525. doi:10.2527/2000.78102525x es_ES
dc.description.references Pérez-Enciso, M., & Misztal, I. (2011). Qxpak.5: Old mixed model solutions for new genomics problems. BMC Bioinformatics, 12(1). doi:10.1186/1471-2105-12-202 es_ES
dc.description.references Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., … Sham, P. C. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics, 81(3), 559-575. doi:10.1086/519795 es_ES
dc.description.references Quintanilla, R., Pena, R. N., Gallardo, D., Cánovas, A., Ramírez, O., Díaz, I., … Amills, M. (2011). Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects1. Journal of Animal Science, 89(10), 2963-2971. doi:10.2527/jas.2011-3974 es_ES
dc.description.references Ramos, A. M., Crooijmans, R. P. M. A., Affara, N. A., Amaral, A. J., Archibald, A. L., Beever, J. E., … Groenen, M. A. M. (2009). Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS ONE, 4(8), e6524. doi:10.1371/journal.pone.0006524 es_ES
dc.description.references Safran, M., Dalah, I., Alexander, J., Rosen, N., Iny Stein, T., Shmoish, M., … Lancet, D. (2010). GeneCards Version 3: the human gene integrator. Database, 2010(0), baq020-baq020. doi:10.1093/database/baq020 es_ES
dc.description.references Sanchez, M.-P., Iannuccelli, N., Basso, B., Bidanel, J.-P., Billon, Y., Gandemer, G., … Le Roy, P. (2007). Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc × Large White cross. BMC Genetics, 8(1), 55. doi:10.1186/1471-2156-8-55 es_ES
dc.description.references Sellier, P., Maignel, L., & Bidanel, J. P. (2009). Genetic parameters for tissue and fatty acid composition of backfat, perirenal fat and longissimus muscle in Large White and Landrace pigs. animal, 4(4), 497-504. doi:10.1017/s1751731109991261 es_ES
dc.description.references Storey, J. D., & Tibshirani, R. (2003). Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences, 100(16), 9440-9445. doi:10.1073/pnas.1530509100 es_ES
dc.description.references Uemoto, Y., Sato, S., Ohnishi, C., Terai, S., Komatsuda, A., & Kobayashi, E. (2009). The effects of single and epistatic quantitative trait loci for fatty acid composition in a Meishan × Duroc crossbred population. Journal of Animal Science, 87(11), 3470-3476. doi:10.2527/jas.2009-1917 es_ES
dc.description.references VARONA, L., OVILO, C., CLOP, A., NOGUERA, J. L., PÉREZ-ENCISO, M., COLL, A., … SÁNCHEZ, A. (2002). QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects. Genetical Research, 80(2), 145-154. doi:10.1017/s0016672302005803 es_ES
dc.description.references Warden, C. H., Daluiski, A., Bu, X., Purcell-Huynh, D. A., De Meester, C., Shieh, B. H., … Chen, Y. D. (1993). Evidence for linkage of the apolipoprotein A-II locus to plasma apolipoprotein A-II and free fatty acid levels in mice and humans. Proceedings of the National Academy of Sciences, 90(22), 10886-10890. doi:10.1073/pnas.90.22.10886 es_ES
dc.description.references Watkins, P. A., Maiguel, D., Jia, Z., & Pevsner, J. (2007). Evidence for 26 distinct acyl-coenzyme A synthetase genes in the human genome. Journal of Lipid Research, 48(12), 2736-2750. doi:10.1194/jlr.m700378-jlr200 es_ES
dc.description.references Wigginton, J. E., & Abecasis, G. R. (2005). PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data. Bioinformatics, 21(16), 3445-3447. doi:10.1093/bioinformatics/bti529 es_ES
dc.description.references Wong, R. H., & Sul, H. S. (2010). Insulin signaling in fatty acid and fat synthesis: a transcriptional perspective. Current Opinion in Pharmacology, 10(6), 684-691. doi:10.1016/j.coph.2010.08.004 es_ES
dc.description.references Wood, J. D., Enser, M., Fisher, A. V., Nute, G. R., Sheard, P. R., Richardson, R. I., … Whittington, F. M. (2008). Fat deposition, fatty acid composition and meat quality: A review. Meat Science, 78(4), 343-358. doi:10.1016/j.meatsci.2007.07.019 es_ES
dc.description.references Yang, B., Navarro, N., Noguera, J. L., Muñoz, M., Guo, T. F., Yang, K. X., … Pérez-Enciso, M. (2011). Building phenotype networks to improve QTL detection: a comparative analysis of fatty acid and fat traits in pigs. Journal of Animal Breeding and Genetics, 128(5), 329-343. doi:10.1111/j.1439-0388.2011.00928.x es_ES
dc.description.references Yang, K. X., Ma, J. W., Guo, Y. M., Guo, T. F., Zhao, Y. G., Ding, N. S., … Huang, L. S. (2010). Correlations between fat depot traits and fatty acid composition in abdominal subcutaneous adipose tissue and longissimus muscle: Results from a White Duroc × Erhualian intercross F2 population1. Journal of Animal Science, 88(11), 3538-3545. doi:10.2527/jas.2009-2602 es_ES


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