Genomic differentiation among varieties of Iberian pig

  • Inés Alonso Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2). 50013 Zaragoza
  • Noelia Ibáñez-Escriche Universitat Politècnica de València, Instituto Universitario de Ciencia y Tecnología Animal. 46022 Valencia http://orcid.org/0000-0002-6221-3576
  • José L. Noguera Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Genètica i Millora Animal. Av. Alcalde Rovira Roure 191, 25198 Lleida http://orcid.org/0000-0002-0492-1734
  • Joaquim Casellas Universitat Autònoma de Barcelona, Dept Ciència Animal i dels Aliments. 08193 Bellaterra (Barcelona) http://orcid.org/0000-0002-4982-3556
  • Melani Martín de Hijas-Villalba Universitat Autònoma de Barcelona, Dept Ciència Animal i dels Aliments. 08193 Bellaterra (Barcelona) http://orcid.org/0000-0002-1183-8357
  • María J. Gracia-Santana Programa de Mejora Genética “CASTUA”. INGA FOOD S.A. (Nutreco group). Av. de a Rúa, 2, 06200 Almendralejo (Badajoz)
  • Luis Varona Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2). 50013 Zaragoza http://orcid.org/0000-0001-6256-5478
DOI: https://doi.org/10.5424/sjar/2020181-15411
Keywords: Sus scrofa, single nucleotide polymorphism, founder haplotypes, candidate genes, gene ontology

Abstract

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.

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Published
2020-04-22
How to Cite
Alonso, I., Ibáñez-Escriche, N., Noguera, J. L., Casellas, J., Martín de Hijas-Villalba, M., Gracia-Santana, M. J., & Varona, L. (2020). Genomic differentiation among varieties of Iberian pig. Spanish Journal of Agricultural Research, 18(1), e0401. https://doi.org/10.5424/sjar/2020181-15411
Issue
Vol. 18 No. 1 (2020)
Section
Animal breeding, genetics and reproduction

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