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An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

Stephanie D McKay12, Robert D Schnabel2, Brenda M Murdoch1, Lakshmi K Matukumalli34, Jan Aerts5, Wouter Coppieters6, Denny Crews17, Emmanuel Dias Neto89, Clare A Gill10, Chuan Gao10, Hideyuki Mannen11, Zhiquan Wang1, Curt P Van Tassell3, John L Williams12, Jeremy F Taylor2 and Stephen S Moore1*

Author Affiliations

1 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada

2 Division of Animal Sciences, University of Missouri, Columbia, MO, USA

3 Bovine Functional Genomics Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA

4 Bioinformatics and Computational Biology, George Mason University, Manassas, VA, USA

5 Division of Genetics and Genomics, Roslin Institute (Edinburgh), Midlothian, Scotland, UK

6 Department of Genetics, Faculty of Veterinary Medicine, University of Liege, 4000-Liege, Belgium

7 Agriculture and Agri-Food Canada Research Centre, Lethbridge, Alberta, Canada

8 Instituto de Psiquiatria, Faculdade de Medicina – Universidade de São Paulo, São Paulo, SP, Brazil

9 Genoa Biotecnologia S/A, São Paulo, SP, Brazil

10 Department of Animal Science, Texas A&M University, College Station, Texas, USA

11 Laboratory of Animal Breeding and Genetics, Graduate School of Science and Technology, Kobe University, Japan

12 Parco Tecnologico Padano, Via Einstein, Polo Universitario, Lodi, Italy

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BMC Genetics 2008, 9:37  doi:10.1186/1471-2156-9-37

Published: 20 May 2008



Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus.


Two thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds.


The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.