Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

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DOI

  • Yuri T. Utsunomiya, UNESP – São Paulo State University
  • ,
  • Lorenzo Bomba, Universita Cattolica del Sacro Cuore
  • ,
  • Giordana Lucente, Universita Cattolica del Sacro Cuore
  • ,
  • Licia Colli, Universita Cattolica del Sacro Cuore
  • ,
  • Riccardo Negrini, Universita Cattolica del Sacro Cuore
  • ,
  • Johannes A. Lenstra, Utrecht University, Utrecht
  • ,
  • Georg Erhardt, Institute of Inorganic and Analytical Chemistry
  • ,
  • José F. Garcia, UNESP – São Paulo State University
  • ,
  • Paolo Ajmone-Marsan, Universita Cattolica del Sacro Cuore
  • ,
  • K. Moazami-Goudarzi, Institut national de la recherche agronomique (INRA)
  • ,
  • J. Williams
  • P. Wiener, Roslin Institute
  • ,
  • I. Olsaker, Norges Veterinærhogskole
  • ,
  • J. Kantanen, Agrifood Research Finland, MTT
  • ,
  • S. Dunner, Universidad Complutense de Madrid
  • ,
  • J. Cañón, Universidad Complutense de Madrid
  • ,
  • C. Rodellar, Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza
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  • I. Martín-Burriel, Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza
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  • A. Valentini, Università dellaTuscia
  • ,
  • M. Zanotti, Universita degli Studi di Milano
  • ,
  • L. E. Holm
  • E. Eythorsdottir, Agricultural Research Institute Reykjavik
  • ,
  • G. Mommens
  • ,
  • Van Haeringen Polygen
  • ,
  • I. J. Nijman, Utrecht University, Utrecht
  • ,
  • G. Dolf, Universitat Bern
  • ,
  • D. G. Bradley, Trinity College Dublin

Background: Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas.Results: We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy.Conclusions: The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources.

Original languageEnglish
Article number47
JournalBMC Genetics
Volume15
ISSN1471-2156
DOIs
Publication statusPublished - 17 Apr 2014

    Research areas

  • AFLP, Ascertainment bias, Cattle, Genetic differentiation

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