- -

Genomic differentiation among varieties of Iberian pig

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Genomic differentiation among varieties of Iberian pig

Mostrar el registro completo del ítem

Alonso, I.; Ibáñez-Escriche, N.; Noguera, JL.; Casellas, J.; Martin De Hijas-Villalba, M.; Gracia-Santana, MJ.; Varona, L. (2020). Genomic differentiation among varieties of Iberian pig. Spanish Journal of Agricultural Research (Online). 18(1):1-20. https://doi.org/10.5424/sjar/2020181-15411

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/176401

Ficheros en el ítem

Thumbnail
Nombre: AlonsoIbanez-Escr ...
Tamaño: 1.289Mb
Formato: PDF
Descripción: Versión editorial
Abrir/Preview

Metadatos del ítem

Título: Genomic differentiation among varieties of Iberian pig
Autor: Alonso, Ines Ibáñez-Escriche, Noelia Noguera, Jose L. Casellas, Joaquim Martin de Hijas-Villalba, Melani Gracia-Santana, Maria J. Varona, Luis
Entidad UPV: Universitat Politècnica de València. Departamento de Ciencia Animal - Departament de Ciència Animal
Fecha difusión:
Resumen:
[EN] Aim of study: The objective of this study was to identify the autosomal genomic regions associated with genetic differentiation between three commercial strains of Iberian pig. Area of study: Extremadura (Spain). Material ...[+]
Palabras clave: Sus scrofa , Single nucleotide polymorphism , Founder haplotypes , Candidate genes , Gene ontology
Derechos de uso: Reconocimiento (by)
Fuente:
Spanish Journal of Agricultural Research (Online). (eissn: 2171-9292 )
DOI: 10.5424/sjar/2020181-15411
Editorial:
Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria
Versión del editor: https://doi.org/10.5424/sjar/2020181-15411
Código del Proyecto:
info:eu-repo/grantAgreement/INIA//RTA2012-00054-C02-01//IBERCAL: 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/
info:eu-repo/grantAgreement/MCIU//CGL2016-80155-R/
info:eu-repo/grantAgreement/MCIU//IDI-20170304/
Agradecimientos:
Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Spain RTA2012-00054-C02-01 Ministry of Science, Innovation and Universities, Spain CGL2016-80155-R; IDI-20170304 (CDTI)
Tipo: Artículo

References

Alexander DH, Novembre J, Lange K, 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19: 1655-1664.

Audetat KA, Galbraith MD, Odell AT, Lee T, Pandey A, Espinosa JM, Dowell RD, Taatjes D J, 2017. A kinase-independent role for cyclin-dependent kinase 19 in p53 response. Mol Cell Biol 37: e00626-16.

Cepica S, Ovilo, C, Masopust M, Knoll A, Fernández A, López A, Rohrer GA, Nonneman D, 2012. Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace x Chinese-European crossbred population. Anim Genet 43: 333-336. [+]
Alexander DH, Novembre J, Lange K, 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19: 1655-1664.

Audetat KA, Galbraith MD, Odell AT, Lee T, Pandey A, Espinosa JM, Dowell RD, Taatjes D J, 2017. A kinase-independent role for cyclin-dependent kinase 19 in p53 response. Mol Cell Biol 37: e00626-16.

Cepica S, Ovilo, C, Masopust M, Knoll A, Fernández A, López A, Rohrer GA, Nonneman D, 2012. Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace x Chinese-European crossbred population. Anim Genet 43: 333-336.

Conaway RC, Conaway JW, 2009. The INO80 chromatin remodeling complex in transcription, replication and repair. Trends Biochem Sci 34: 71-77.

Correa RG, Krajewska M, Ware CF, Gerlic M, Reed JC, 2014. The NLR-related protein NWD1 is associated with prostate cancer and modulates androgen receptor signaling. Oncotarget 30: 1666-1682.

Fabuel EC, Barragán C, Silio L, Rodríguez MC, Toro MA, 2004. Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity 93: 104-113.

Fontanesi L, Schiavo G, Galimberti G, Bovo S, Russo V, Gallo M, Buttazzoni L, 2017. A genome-wide association study for a proxy of intermuscular fat level in the Italian Large White breed identifies genomic regions affecting an important quality parameter for dry-cured hams. Anim Genet 48: 459-465.

Hérault Y, Hraba-Renevey S, van der Hoeven F, Duboule D, 1997. Function of the Evx-2 gene in the morphogenesis of vertebrate limbs. EMBO J 15: 6727-6738.

Herrero-Medrano JM, Megens HJ, Groenen MAM, Ramis G, Bosse M, Pérez-Enciso M, Crooijmans RPMA, 2013. Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula. BMC Genet 14: 106.

Izu Y, Sun M, Zwolanek D, Veit G, Williams V, Cha B, Jepsen KJ, Koch M, Birk DE, 2011. Type XII collagen regulates osteoblast polarity and communication during bone formation. J Cell Biol 193: 1115-1130.

Jeyabal PVS, Rubio V, Chen H, Zhang J, Shi ZZ, 2014. Regulation of cell-matrix adhesion by OLA1, the Obg-like ATPase 1. Biochem Biophys Res Commun 444: 568-574.

Kawakami Y, Rodríguez-Esteban C, Matsui T, Rodríguez-León J, Kato S, Izpisúa-Belmonte JC, 2004. Sp8 and Sp9, two closely related buttonhead-like transcription factors, regulate Fgf8 expression and limb outgrowth in vertebrate embryos. Development 131: 4763-4774.

Laval G, Iannucelli N, Legault C, Milan D, Groenen MAM, Giuffra E, Andersson L, Nissen PH, Jorgensen CB, Beeckmann P et al., 2000. Genetic diversity of eleven European pig breeds. Genet Sel Evol 32: 187-203.

Lim HH, Michael GJ, Smith P, Lim L, Hall C, 1992. Developmental regulation and neuronal expression of the mRNA of rat n-chimaerin, a p21rac GAP:cDNA sequence. Biochem J 287: 415-422.

Marchand M, Schroeder IS, Markossian S, Skoudy A, Nègre D, Cosset FL, Real P, Kaiser C, Wobus AM, Savarier P, 2009. Mouse ES cells over-expressing the transcription factor NeuroD1 show increased differentiation towards endocrine lineages and insulin-expressing cells. Int J Dev Biol 53: 569-578.

Martínez AM, Delgado JV, Rodero A, Vega-Pla JL, 2000. Genetic structure of the Iberian pig breed using microsatellites. Anim Genet 31: 295-301.

Myers P, 2008. Hox genes in development: the HOX code. Nature Education 1: 2.

Onteru SK, Fan B, Nikkilä MT, Garrick DJ, Stalder KJ, Rothschild MF, 2011. Whole-genome association analyses for lifetime reproductive traits in pig. J Anim Sci 89: 988-995.

Onteru SK, Fan B, Du ZQ, Garrick DJ. Stalder KJ, Rothschild MF, 2012. A whole-genome association study for pig reproductive traits. Anim Genet 43: 18-26.

Pallares LF, Carbonetto P, Gopalakrishnan S, Parker CC, Ackert-Bicknell CL, Palmer AA, Tautz D, 2015. Mapping of craniofacial traits in outbred mice identifies major developmental genes involved in shape determination. Plos Genet 11: e1005607.

Ponsuksili S, Zebunke M, Murani E, Trakooljul N, Krieter J, Puppe B, Schwerin M, Wimmers K, 2015. Integrated genome-wide association and hypothalamus eQTL studies indicate a link between the circadian rhythm-related gene PER1 and coping behavior. Sci Rep 5: 16264.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC, 2007. PLINK: a tool set for whole-genome association and population-based linkage analysis. Am J Human Genet 81: 559-575.

Qanbari S, Simianer H, 2014. Mapping signatures of positive selection in the genome of livestock. Livest Sci 166: 133-143.

R Core Team, 2019. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https: //www. R-project.org/.

Rohrer GA, Nonneman DJ, Wiedmann RT, Schneider JF, 2015. A study of vertebra number in pigs confirms the association of vertnin and reveals additional QTL. BMC Genet 16: 129.

Sargolzaei M, Chesnais JP, Schenkel FS, 2014. A new approach for efficient genotype imputation using information from relatives. BMC Genom 15: 478.

Schneider JF, Miles JR, Brown-Brandl TM, Nienaber JA, Rohrer GA, Vallet JL, 2015. Genomewide association analysis for average birth interval and stillbirth in swine. J Anim Sci 93: 529-540.

Sherwood NM, Krueckl SL, McRory JE, 2000. The origin and function of the pituitary adenylate cyclase-activating polypeptide (PACAP)/glucagon superfamily. Endocr Rev 21: 619-670.

Silió L, Barragan C, Fernández AI, García-Casco J, Rodríguez MC, 2016. Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed. J Anim Breed Genet 133: 145-154.

Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, et al., 2015. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucl Acids Res 43: W589-W598.

Soilleux EJ, Morris LS, Leslie G, Chehimi J, Luo Q, Levroney E, Trowsdale J, Montaner LJ, Doms RW, Weissman D, Coleman N, Lee B., 2002. Constitutive and induced expression of DC-SIGN on dendritic cell and macrophage subpopulations in situ and in vitro. J Leukoc Biol 71: 445-457.

Sterky FH, Trotter JH, Lee S, Recktenwald CV, Du X, Zhou B, Zhou P, Schwenk J, Fakler B, Südhof TC, 2017. Carbonic anhydrase-related protein CA10 is an evolutionary conserved pan-neurexin ligand. Proc Nac Acad Sci 114: E1253-E1262.

Vale-Cruz DS, Ma Q, Syme J, LuValle PA, 2008. Activating transcription factor-2 affects skeletal growth by modulating pRb gene expression. Mech Dev 125: 843-856.

Velardo LL, Silva FF, Lopes MS, Madsen O, Bastiaansen JW, Knol EF, Kelly M, Varona L, Lopes PS, Guimaräes SEF. 2016. Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways. Genet Sel Evol 48: 9.

Ventanas S, Ventanas J, Ruiz J, Estévez M, 2005. Iberian pigs for the development of high-quality cured products. In: Recent Res Devel Agricultural & Food Chem; SG Pandalai (Ed.) 6: 27-53.

Wang J, Vasaikar S, Shi Z, Greer M, Zhang B, 2017. WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit. Nucl Acids Res 45: W130-W137.

Weir WS, Cockerham CC, 1984. Estimating F-Statistics for the analysis of population structure. Evolution 38: 1358-1370.

Wright S, 1951. The genetical structure of populations. Ann Eugenics 15: 323-354.

Wu B, Gong J, Yuan S, Zhang Y, Wei T, 2013. Patterns of evolutionary selection pressure in the immune signaling protein TRAF3IP2 in mammals. Gene 531: 403-410.

Yagi T, Shigetani Y, Furuta Y, Nada S, Okado N, Ikawa Y, Aizawa S, 1994. Fyn expression during early neurogenesis in mouse embryos. Oncogene 9: 2433-2440.

Yong Y, Meng Y, Ding H, Fan Z, Tang Y, Zhou C, Luo J, Ke ZJ, 2015. PACT/RAX regulates the migration of cerebellar granule neurons in the developing cerebellum. Sci Rep 5: 7961.

Zhang F, Zhang Z, Yan X, Chen H, Zhang W, Hong Y, Huang L, 2014. Genome-wide association studies for hematological traits in Chinese Sutai pigs. BMC Genet 15:41.

[-]

recommendations

 

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

Mostrar el registro completo del ítem