- -

Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics

Mostrar el registro sencillo del ítem

Ficheros en el ítem

[Cerrado]
Nombre: Martinez-Montes;M ...
Tamaño: 733.1Kb
Formato: PDF
Descripción: Versión editorial
Solicitar una copia al autor
dc.contributor.author Martinez-Montes, Angel M. es_ES
dc.contributor.author Muiños-Buhl, Anixa es_ES
dc.contributor.author Fernandez, Almudena es_ES
dc.contributor.author Folch, Josep M. es_ES
dc.contributor.author Ibáñez-Escriche, Noelia es_ES
dc.contributor.author Fernandez, Ana I. es_ES
dc.date.accessioned 2020-12-01T04:32:27Z
dc.date.available 2020-12-01T04:32:27Z
dc.date.issued 2017-04 es_ES
dc.identifier.issn 0938-8990 es_ES
dc.identifier.uri http://hdl.handle.net/10251/156107
dc.description.abstract [EN] Genetical genomics approaches aim at identifying quantitative trait loci for molecular traits, also known as intermediate phenotypes, such as gene expression, that could link variation in genetic information to physiological traits. In the current study, an expression GWAS has been carried out on an experimental Iberian x Landrace backcross in order to identify the genomic regions regulating the gene expression of those genes whose expression is correlated with growth, fat deposition, and premium cut yield measures in pig. The analyses were conducted exploiting Porcine 60K SNP BeadChip genotypes and Porcine Expression Microarray data hybridized on mRNA from Longissimus dorsi muscle. In order to focus the analysis on productive traits and reduce the number of analyses, only those probesets whose expression showed significant correlation with at least one of the seven phenotypes of interest were selected for the eGWAS. A total of 63 eQTL regions were identified with effects on 36 different transcripts. Those eQTLs overlapping with phenotypic QTLs on SSC4, SSC9, SSC13, and SSC17 chromosomes previously detected in the same animal material were further analyzed. Moreover, candidate genes and SNPs were analyzed. Among the most promising results, a long non-coding RNA, ALDBSSCG0000001928, was identified, whose expression is correlated with premium cut yield. Association analysis and in silico sequence domain annotation support TXNRD3 polymorphisms as candidate to regulate ALDBSSCG0000001928 expression, which can be involved in the transcriptional regulation of surrounding genes, affecting productive and meat quality traits. es_ES
dc.description.sponsorship This work was funded by Ministerio de Economia y Competitividad (MINECO) project AGL2011-29821-C02 and AGL2014-56369-C2. Angel Martinez-Montes was funded by a (FPI) PhD grant from the Spanish Ministerio de Ciencia e Innovacion. We want to thank Fabian Garcia, Anna Mercade, and Anna Castello for technical assistance. We would like to thank all the members of the INIA, IRTA, and UAB institutions who contributed to the generation and sample recollection of the animal materials used in this work. es_ES
dc.language Inglés es_ES
dc.publisher Springer-Verlag es_ES
dc.relation.ispartof Mammalian Genome es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject.classification PRODUCCION ANIMAL es_ES
dc.title Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1007/s00335-016-9674-3 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/653216/EU/Understanding how selection for body weight in mouse operates at the RNA level/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//RTA2012-00054-C02-01/ES/Utilización de información genómica masiva para mejorar la calidad de los productos de cerdo ibérico en una población de referencia mixta y el estudio de su interacción con la alimentación./ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//AGL2011-29821-C02-02/ES/APLICACION DE METODOS DE SECUENCIACION PARALELA MASIVA Y GENOMICA AL ESTUDIO DE VARIANTES GENICAS QUE REGULAN:CRECIMIENTO,CONFORMACION Y CALIDAD DE CARNE EN CERDO.SUBPROYECTO2/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//AGL2014-56369-C2-1-R/ES/VALIDACION GENETICA Y FUNCIONAL DE QTLS, GENES Y REDES GENICAS Y ESTUDIO DEL EFECTO DEL MICROBIOMA SOBRE CRECIMIENTO, DEPOSICION DE GRASA Y CALIDAD DE CARNE EN PORCINO. S1/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//AGL2014-56369-C2-2-R/ES/VALIDACION GENETICA Y FUNCIONAL DE QTLS, GENES Y REDES GENICAS Y ESTUDIO DEL EFECTO DEL MICROBIOMA EN EL CRECIMIENTO, DEPOSICION DE GRASA Y CALIDAD DE LA CARNE EN PORCINO. S2/
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 Martinez-Montes, AM.; Muiños-Buhl, A.; Fernandez, A.; Folch, JM.; Ibáñez-Escriche, N.; Fernandez, AI. (2017). Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics. Mammalian Genome. 28(3-4):130-142. https://doi.org/10.1007/s00335-016-9674-3 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1007/s00335-016-9674-3 es_ES
dc.description.upvformatpinicio 130 es_ES
dc.description.upvformatpfin 142 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 28 es_ES
dc.description.issue 3-4 es_ES
dc.identifier.pmid 27942838 es_ES
dc.relation.pasarela S\343529 es_ES
dc.contributor.funder Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.contributor.funder Ministerio de Ciencia e Innovación
dc.description.references Angrand PO, Vennin C, Le Bourhis X, Adriaenssens E (2015) The role of long non-coding RNAs in genome formatting and expression. Front Genet 6:165 es_ES
dc.description.references Ayuso M, Fernández A, Núñez Y, Benítez R, Isabel B, Barragán C, Fernández AI, Rey AI, Medrano JF, Cánovas Á, González-Bulnes A, López-Bote C, Ovilo C (2015) Comparative analysis of muscle transcriptome between pig genotypes identifies genes and regulatory mechanisms associated to growth, fatness and metabolism. PLoS One 10:e0145162 es_ES
dc.description.references Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36 es_ES
dc.description.references Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:202–208 es_ES
dc.description.references Bass JD, Swcf AJ, Dabney A, Robinson D (2015). qvalue: Q-value estimation for false discovery rate control. R package version 2.2.2 es_ES
dc.description.references Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI, Jansen RC (2008) Genetical genomics: spotlight on QTL hotspots. PLoS Genet 4:e1000232 es_ES
dc.description.references Buske FA, Bodén M, Bauer DC, Bailey TL (2010) Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics 26:860–866 es_ES
dc.description.references Chang TH, Huang HY, Hsu JB, Weng SL, Horng JT, Huang HD (2013) An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinform 14(Suppl 2):S4 es_ES
dc.description.references Corominas J, Ramayo-Caldas Y, Puig-Oliveras A, Pérez-Montarelo D, Noguera JL, Folch JM, Ballester M (2013) Polymorphism in the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs. PLoS One 8:e53687 es_ES
dc.description.references Corominas J, Marchesi JA, Puig-Oliveras A, Revilla M, Estellé J, Alves E, Folch JM, Ballester M (2015) Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs. Genet Sel Evol 47:20 es_ES
dc.description.references Deng HW, Chen WM, Recker RR (2000) QTL fine mapping by measuring and testing for Hardy–Weinberg and linkage disequilibrium at a series of linked marker loci in extreme samples of populations. Am J Hum Genet 66:1027–1045 es_ES
dc.description.references Espigolan R, Baldi F, Boligon AA, Souza FR, Fernandes Júnior GA, Gordo DG, Venturini GC, de Camargo GM, Feitosa FL, Garcia DA, Tonhati H, Chardulo LA, Oliveira HN, Albuquerque LG (2015) Associations between single nucleotide polymorphisms and carcass traits in Nellore cattle using high-density panels. Genet Mol Res 14:11133–11144 es_ES
dc.description.references Estellé J, Pérez-Enciso M, Mercadé A, Varona L, Alves E, Sánchez A, Folch JM (2006) Characterization of the porcine FABP5 gene and its association with the FAT1 QTL in an Iberian by Landrace cross. Anim Genet 37:589–591 es_ES
dc.description.references Fernández AI, Pérez-Montarelo D, Barragán C, Ramayo-Caldas Y, Ibáñez-Escriche N, Castelló A, Noguera JL, Silió L, Folch JM, Rodríguez MC (2012) Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip. BMC Genet 13:41 es_ES
dc.description.references Fernández AI, Muñoz M, Alves E, Folch JM, Noguera JL, Enciso MP, del Rodríguez MC, Silió L (2014) Recombination of the porcine X chromosome: a high density linkage map. BMC Genet 15:148 es_ES
dc.description.references Fontanesi L, Colombo M, Scotti E, Buttazzoni L, Bertolini F, Dall’Olio S, Davoli R, Russo V (2010) The porcine tribbles homolog 3 (TRIB3) gene: identification of a missense mutation and association analysis with meat quality and production traits in Italian heavy pigs. Meat Sci 86:808–813 es_ES
dc.description.references Garcia de la Serrana D, Johnston IA (2013) Expression of heat shock protein (Hsp90) paralogues is regulated by amino acids in skeletal muscle of Atlantic salmon. PLoS One 8:e74295 es_ES
dc.description.references Guntani A, Matsumoto T, Kyuragi R, Iwasa K, Onohara T, Itoh H, Katusic ZS, Maehara Y (2011) Reduced proliferation of aged human vascular smooth muscle cells–role of oxygen-derived free radicals and BubR1 expression. J Surg Res 170:143–149 es_ES
dc.description.references Guo K, Wang J, Andrés V, Smith RC, Walsh K (1995) MyoD-induced expression of p21 inhibits cyclin-dependent kinase activity upon myocyte terminal differentiation. Mol Cell Biol 15:3823–3829 es_ES
dc.description.references Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS (2007) Quantifying similarity between motifs. Genome Biol 8:R24 es_ES
dc.description.references Hill WG (2012) Quantitative genetics in the genomics era. Curr Genom 13:196–206 es_ES
dc.description.references Hong J, Kim D, Cho K, Sa S, Choi S, Kim Y, Park J, Schmidt GS, Davis ME, Chung H (2015) Effects of genetic variants for the swine FABP3, HMGA1, MC4R, IGF2, and FABP4 genes on fatty acid composition. Meat Sci 110:46–51 es_ES
dc.description.references Hu ZL, Dracheva S, Jang W, Maglott D, Bastiaansen J, Rothschild MF, Reecy JM (2005) A QTL resource and comparison tool for pigs: PigQTLDB. Mamm Genome 16:792–800 es_ES
dc.description.references Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends Genet 17:388–391 es_ES
dc.description.references Karisa BK, Thomson J, Wang Z, Stothard P, Moore SS, Plastow GS (2013) Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle. J Anim Sci 91:3502–3513 es_ES
dc.description.references Karssen LC, van Duijn CM, Aulchenko YS (2016) The GenABEL Project for statistical genomics. F1000Res 5:914 es_ES
dc.description.references Kipp AP, Müller MF, Göken EM, Deubel S, Brigelius-Flohé R (2012) The selenoproteins GPx2, TrxR2 and TrxR3 are regulated by Wnt signalling in the intestinal epithelium. Biochim Biophys Acta 1820:1588–1596 es_ES
dc.description.references Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ (2012) Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci USA 109:7049–7054 es_ES
dc.description.references Lahaye LL, Wouda RR, de Jong AW, Fradkin LG, Noordermeer JN (2012) WNT5 interacts with the Ryk receptors doughnut and derailed to mediate muscle attachment site selection in Drosophila melanogaster. PLoS One 7:e32297 es_ES
dc.description.references Li A, Zhang J, Zhou Z, Wang L, Liu Y, Liu Y (2015) ALDB: a domestic-animal long noncoding RNA database. PLoS One 10:e0124003 es_ES
dc.description.references Martínez-Montes AM, Fernández A, Pérez-Montarelo D, Alves E, Benítez RM, Nuñez Y, Óvilo C, Ibañez-Escriche N, Folch JM, Fernández AI (2016) Using RNA-Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing. Anim Genet. doi: 10.1111/age.12507 es_ES
dc.description.references Mercadé A, Estellé J, Noguera JL, Folch JM, Varona L, Silió L, Sánchez A, Pérez-Enciso M (2005) On growth, fatness, and form: a further look at porcine chromosome 4 in an Iberian × Landrace cross. Mamm Genome 16:374–382 es_ES
dc.description.references Muñoz M, Fernández AI, Ovilo C, Muñoz G, Rodriguez C, Fernández A, Alves E, Silió L (2010) Non-additive effects of RBP4, ESR1 and IGF2 polymorphisms on litter size at different parities in a Chinese-European porcine line. Genet Sel Evol 42:23 es_ES
dc.description.references Nguyen DT, Lee K, Choi H, Choi MK, Le MT, Song N, Kim JH, Seo HG, Oh JW, Lee K, Kim TH, Park C (2012) The complete swine olfactory subgenome: expansion of the olfactory gene repertoire in the pig genome. BMC Genom 13:584 es_ES
dc.description.references Ovilo C, Pérez-Enciso M, Barragán C, Clop A, Rodríquez C, Oliver MA, Toro MA, Noruera JL (2000) A QTL for intramuscular fat and backfat thickness is located on porcine chromosome 6. Mamm Genome 11:344–346 es_ES
dc.description.references Óvilo C, Fernández A, Noguera JL, Barragán C, Letón R, Rodríguez C, Mercadé A, Alves E, Folch JM, Varona L, Toro MA (2005) Fine mapping of porcine chromosome 6 QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross. Genet Res 85:57–67 es_ES
dc.description.references Pang W, Wang Y, Wei N, Xu R, Xiong Y, Wang P, Shen Q, Yang G (2013) Sirt1 inhibits akt2-mediated porcine adipogenesis potentially by direct protein–protein interaction. PLoS One 8:e71576 es_ES
dc.description.references Hong EP1, Park JW (2012) Sample size and statistical power calculation in genetic association studies. Genom Inform 10:117–122 es_ES
dc.description.references Pena RN, Noguera JL, Casellas J, Díaz I, Fernández AI, Folch JM, Ibáñez-Escriche N (2013) Transcriptional analysis of intramuscular fatty acid composition in the longissimus thoracis muscle of Iberian × Landrace back-crossed pigs. Anim Genet 44:648–660 es_ES
dc.description.references Pérez-Enciso M, Misztal I (2011) Qxpak.5: old mixed model solutions for new genomics problems. BMC Bioinforma 12:202 es_ES
dc.description.references Pérez-Montarelo D, Fernández A, Folch JM, Pena RN, Ovilo C, Rodríguez C, Silió L, Fernández AI (2012) Joint effects of porcine leptin and leptin receptor polymorphisms on productivity and quality traits. Anim Genet 43:805–809 es_ES
dc.description.references Priori D, Colombo M, Clavenzani P, Jansman AJ, Lallès JP, Trevisi P, Bosi P (2015) The olfactory receptor OR51E1 is present along the gastrointestinal tract of pigs, co-localizes with enteroendocrine cells and is modulated by intestinal microbiota. PLoS One 10:e0129501 es_ES
dc.description.references Puig-Oliveras A, Revilla M, Castelló A, Fernández AI, Folch JM, Ballester M (2016) Expression-based GWAS identifies variants, gene interactions and key regulators affecting intramuscular fatty acid content and composition in porcine meat. Sci Rep 6:31803 es_ES
dc.description.references Qin LL, Li XK, Xu J, Mo DL, Tong X, Pan ZC, Li JQ, Chen YS, Zhang Z, Wang C, Long (2012) QM Mechano growth factor (MGF) promotes proliferation and inhibits differentiation of porcine satellite cells (PSCs) by down-regulation of key myogenic transcriptional factors. Mol Cell Biochem 370:221–230 es_ES
dc.description.references Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, Churcher C, Clark R, Dehais P, Hansen MS, Hedegaard J, Hu ZL, Kerstens HH, Law AS, Megens HJ, Milan D, Nonneman DJ, Rohrer GA, Rothschild MF, Smith TP, Schnabel RD, Van Tassell CP, Taylor JF, Wiedmann RT, Schook LB, Groenen MA (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:e6524 es_ES
dc.description.references Ren X, Zhou L, Terwilliger R, Newton SS, de Araujo IE (2009) Sweet taste signaling functions as a hypothalamic glucose sensor. Front Integr Neurosci 3:12 es_ES
dc.description.references Rutenberg-Schoenberg M, Sexton AN, Simon MD (2016) The properties of long noncoding RNAs that regulate chromatin. Annu Rev Genom Hum Genet 17:69–94 es_ES
dc.description.references Saura M, Tenesa A, Woolliams JA, Fernández A, Villanueva B (2015) Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case. BMC Genom 16:922 es_ES
dc.description.references Schön CC, Utz HF, Groh S, Truberg B, Openshaw S, Melchinger AE (2004) Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167:485–498 es_ES
dc.description.references Scimè A, Grenier G, Huh MS, Gillespie MA, Bevilacqua L, Harper ME, Rudnicki MA (2005) Rb and p107 regulate preadipocyte differentiation into white versus brown fat through repression of PGC-1alpha. Cell Metab 2:283–295 es_ES
dc.description.references Stephens M, Smith N, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978–989 es_ES
dc.description.references Sun R, Chang Y, Yang F, Wang Y, Li H, Zhao Y, Chen D, Wu T, Zhang X, Han Z (2015) A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality. BMC Genom 16:747 es_ES
dc.description.references Szczerbal I, Chmurzynska A (2008) Chromosomal localization of nine porcine genes encoding transcription factors involved in adipogenesis. Cytogenet Genome Res 121:150–154 es_ES
dc.description.references Tabangin ME, Woo JG, Martin LJ (2009) The effect of minor allele frequency on the likelihood of obtaining false positives. BMC Proc 3(Suppl 7):S41 es_ES
dc.description.references Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Haley CS, Buys N, Tally M, Andersson G, Georges M, Andersson L (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425:832–836 es_ES
dc.description.references Varona L, Ovilo C, Clop A, Noguera JL, Pérez-Enciso M, Coll A, Folch JM, Barragán C, Toro MA, Babot D, Sánchez A (2002) QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects. Genet Res 80:145–154 es_ES
dc.description.references Wang D, Lemon WJ, You M (2002) Linkage disequilibrium mapping of novel lung tumor susceptibility quantitative trait loci in mice. Oncogene 21:6858–6865 es_ES
dc.description.references Wewer UM, Thornell LE, Loechel F, Zhang X, Durkin ME, Amano S, Burgeson RE, Engvall E, Albrechtsen R, Virtanen I (1997) Extrasynaptic location of laminin beta 2 chain in developing and adult human skeletal muscle. Am J Pathol 151:621–631 es_ES
dc.description.references Williams RB, Chan EK, Cowley MJ, Little PF (2007) The influence of genetic variation on gene expression. Genome Res 17:1707–1716 es_ES
dc.description.references Würschum T, Kraft T (2014) Cross-validation in association mapping and its relevance for the estimation of QTL parameters of complex traits. Heredity (Edinb) 112:463–468 es_ES
dc.description.references Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M (2014) PredictProtein—an open resource for online prediction of protein structural and functional features. Nucleic Acids Res 42(Web Server issue):W337–W343 es_ES
dc.description.references Yan X, Weijun P, Ning W, Yu W, Wenkai R, Gongshe Y (2013) Knockdown of both FoxO1 and C/EBPβ promotes adipogenesis in porcine preadipocytes through feedback regulation. Cell Biol Int 37:905–916 es_ES
dc.description.references Zizola CF, Frey SK, Jitngarmkusol S, Kadereit B, Yan N, Vogel S (2010) Cellular retinol-binding protein type I (CRBP-I) regulates adipogenesis. Mol Cell Biol 30:3412–3420 es_ES
dc.description.references Zou F, Chai HS, Younkin CS, Allen M, Crook J, Pankratz VS, Carrasquillo MM, Rowley CN, Nair AA, Middha S, Maharjan S, Nguyen T, Ma L, Malphrus KG, Palusak R, Lincoln S, Bisceglio G, Georgescu C, Kouri N, Kolbert CP, Jen J, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD; Alzheimer’s Disease Genetics Consortium, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N (2012) Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants. PLoS Genet 8:e1002707 es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem