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Vol. 10, Issue 2, 220-227, February 2000

Extensive Genome-wide Linkage Disequilibrium in Cattle

Frédéric Farnir, Wouter Coppieters, Juan-José Arranz, Paulette Berzi, Nadine Cambisano, Bernard Grisart, Latifa Karim, Fabienne Marcq, Laurence Moreau, Myriam Mni, Carine Nezer, Patricia Simon, Pascal Vanmanshoven, Danny Wagenaar, and Michel Georges1

Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), 4000-Liège, Belgium

A genome-wide linkage disequilibrium (LD) map was generated using microsatellite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled from the dutch black-and-white dairy cattle population. LD was measured between all marker pairs, both syntenic and nonsyntenic. Analysis of syntenic pairs revealed surprisingly high levels of LD that, although more pronounced for closely linked marker pairs, extended over several tens of centimorgan. In addition, significant gametic associations were also shown to be very common between nonsyntenic loci. Simulations using the known genealogies of the studied sample indicate that random drift alone is likely to account for most of the observed disequilibrium. No clear evidence was obtained for a direct effect of selection ("Bulmer effect"). The observation of long range disequilibrium between syntenic loci using low-density marker maps indicates that LD mapping has the potential to be very effective in livestock populations. The frequent occurrence of gametic associations between nonsyntenic loci, however, encourages the combined use of linkage and linkage disequilibrium methods to avoid false positive results when mapping genes in livestock.

1 Corresponding author.

10:220-227 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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