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Genomic differentiation among varieties of Iberian pig

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Genomic differentiation among varieties of Iberian pig

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dc.contributor.author Alonso, Ines es_ES
dc.contributor.author Ibáñez-Escriche, Noelia es_ES
dc.contributor.author Noguera, Jose L. es_ES
dc.contributor.author Casellas, Joaquim es_ES
dc.contributor.author Martin de Hijas-Villalba, Melani es_ES
dc.contributor.author Gracia-Santana, Maria J. es_ES
dc.contributor.author Varona, Luis es_ES
dc.date.accessioned 2021-11-05T14:10:08Z
dc.date.available 2021-11-05T14:10:08Z
dc.date.issued 2020 es_ES
dc.identifier.uri http://hdl.handle.net/10251/176401
dc.description.abstract [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 and methods: We used the Porcine v2 BeadChip to genotype 349 individuals from three varieties of Iberian pig (EE, Entrepelado; RR, Retinto; and TT, Torbiscal) and their crosses. After standard filtering of the Single Nucleotide Polymorphism (SNP) markers, 47, 67, and 123 haplotypic phases from EE, RR, and TT origins were identified. The allelic frequencies of 31,180 SNP markers were used to calculate the fixation index (FST) that were averaged in sliding windows of 2Mb. Main results: The results confirmed the greater genetic closeness of the EE and RR varieties, and we were able to identify several genomic regions with a divergence greater than expected. The genes present in those genomic regions were used to perform an Overrepresentation Enrichment Analysis (ORA) for the Gene Ontology (GO) terms for biological process. The ORA indicated that several groups of biological processes were overrepresented: a large group involving morphogenesis and development, and others associated with neurogenesis, cellular responses, or metabolic processes. These results were reinforced by the presence of some genes within the genomic regions that had the highest genomic differentiation. Research highlights: The genomic differentiation among varieties of the Iberian pig is heterogeneous along the genome. The genomic regions with the highest differentiation contain an overrepresentation of genes related with morphogenesis and development, neurogenesis, cellular responses and metabolic processes. es_ES
dc.description.sponsorship 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) es_ES
dc.language Inglés es_ES
dc.publisher Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria es_ES
dc.relation.ispartof Spanish Journal of Agricultural Research (Online) es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Sus scrofa es_ES
dc.subject Single nucleotide polymorphism es_ES
dc.subject Founder haplotypes es_ES
dc.subject Candidate genes es_ES
dc.subject Gene ontology es_ES
dc.subject.classification PRODUCCION ANIMAL es_ES
dc.title Genomic differentiation among varieties of Iberian pig es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.5424/sjar/2020181-15411 es_ES
dc.relation.projectID 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/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MCIU//CGL2016-80155-R/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MCIU//IDI-20170304/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ciencia Animal - Departament de Ciència Animal es_ES
dc.description.bibliographicCitation 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 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.5424/sjar/2020181-15411 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 20 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 18 es_ES
dc.description.issue 1 es_ES
dc.identifier.eissn 2171-9292 es_ES
dc.relation.pasarela S\398706 es_ES
dc.contributor.funder INIA es_ES
dc.contributor.funder Ministerio de Ciencia, Innovación y Universidades es_ES
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