title: Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle.
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.
authors.forename: Yuri Tani
authors.initials: YT
authors.lastname: Utsunomiya
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Bomba
authors.forename: Giordana
authors.initials: G
authors.lastname: Lucente
authors.forename: Licia
authors.initials: L
authors.lastname: Colli
authors.forename: Riccardo
authors.initials: R
authors.lastname: Negrini
authors.forename: Johannes Arjen
authors.initials: JA
authors.lastname: Lenstra
authors.forename: Georg
authors.initials: G
authors.lastname: Erhardt
authors.forename: José Fernando
authors.initials: JF
authors.lastname: Garcia
authors.affiliation: Institute of Zootechnics, Università Cattolica del Sacro Cuore, Piacenza, Italy. paolo.ajmone@unicatt.it.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ajmone-Marsan
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis; D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D016000:Cluster Analysis; D003247:Conservation of Natural Resources; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D008957:Models, Genetic
chemical_list: D005819:Genetic Markers
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