Research article
Whole genome linkage disequilibrium maps in cattle
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* Corresponding author: Stephen S Moore Stephen.Moore@afhe.ualberta.ca
1 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
2 Division of Animal Sciences, University of Missouri, Columbia, Missouri, 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
BMC Genetics 2007, 8:74 doi:10.1186/1471-2156-8-74
Published: 25 October 2007Abstract
Background
Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle.
Results
Linkage disequilibrium was assessed using r2 among all pairs of syntenic markers within eight breeds of cattle from the Bos taurus and Bos indicus subspecies. Bos taurus breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while Bos indicus breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r2 values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle.
Conclusion
Linkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger sample of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000–50,000 loci will be needed to conduct whole genome association studies in cattle.