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Journal of Animal Science Abstract - Animal Genetics

Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip1


This article in JAS

  1. Vol. 93 No. 11, p. 5164-5174
    Received: May 05, 2015
    Accepted: Sept 09, 2015
    Published: October 16, 2015

    4 Corresponding author(s): jesus.piedrafita@uab.es

  1. J. J. Cañas-Álvarez*22,
  2. A. González-Rodríguez33,
  3. S. Munilla†‡,
  4. L. Varona†§,
  5. C. Díaz#,
  6. J. A. Baro,
  7. J. Altarriba†§,
  8. A. Molina and
  9. J. Piedrafita 4*
  1. * Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
     Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013-Zaragoza, Spain
     Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, 1417, CABA, Argentina
    § Instituto Agroalimentario de Aragón (IA2), 50013-Zaragoza, Spain
    # Departamento de Mejora Genética Animal, INIA, 28040-Madrid, Spain
     Departamento de Ciencias Agroforestales, Universidad de Valladolid, 34004-Palencia, Spain
     MERAGEM, Universidad de Córdoba, 14071-Córdoba, Spain


The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD BeadChip genotyping array was used to describe the genetic variability and divergence among 7 important autochthonous Spanish beef cattle breeds. The within-breed genetic diversity, measured as the marker expected heterozygosity, was around 0.30, similar to other European cattle breeds. The analysis of molecular variance revealed that 94.22% of the total variance was explained by differences within individuals whereas only 4.46% was the result of differences among populations. The degree of genetic differentiation was small to moderate as the pairwise fixation index of genetic differentiation among breeds (FST) estimates ranged from 0.026 to 0.068 and the Nei’s D genetic distances ranged from 0.009 to 0.016. A neighbor joining (N-J) phylogenetic tree showed 2 main groups of breeds: Pirenaica, Bruna dels Pirineus, and Rubia Gallega on the one hand and Avileña-Negra Ibérica, Morucha, and Retinta on the other. In turn, Asturiana de los Valles occupied an independent and intermediate position. A principal component analysis (PCA) applied to a distance matrix based on marker identity by state, in which the first 2 axes explained up to 17.3% of the variance, showed a grouping of animals that was similar to the one observed in the N-J tree. Finally, a cluster analysis for ancestries allowed assigning all the individuals to the breed they belong to, although it revealed some degree of admixture among breeds. Our results indicate large within-breed diversity and a low degree of divergence among the autochthonous Spanish beef cattle breeds studied. Both N-J and PCA groupings fit quite well to the ancestral trunks from which the Spanish beef cattle breeds were supposed to derive.

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