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Open Access Highly Accessed Research article

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

Yuri Tani Utsunomiya1, Lorenzo Bomba2, Giordana Lucente2, Licia Colli23, Riccardo Negrini2, Johannes Arjen Lenstra4, Georg Erhardt5, José Fernando Garcia16, Paolo Ajmone-Marsan23* and European Cattle Genetic Diversity Consortium

Author Affiliations

1 Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo 14884-900, Brazil

2 Institute of Zootechnics, Università Cattolica del Sacro Cuore, Piacenza, Italy

3 BioDNA Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy

4 Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands

5 Institute of Animal Breeding and Genetics, Justus-Liebig University, Giessen 21b, 35390, Ludwigstrasse, Germany

6 Faculdade de Medicina Veterinária de Araçatuba, UNESP – Univ Estadual Paulista, Araçatuba, São Paulo 16050-680, Brazil

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BMC Genetics 2014, 15:47  doi:10.1186/1471-2156-15-47

Published: 17 April 2014

Abstract

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.

Keywords:
Cattle; AFLP; Genetic differentiation; Ascertainment bias