doi:10.1111/j.1365-2052.2008.01772.x Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle A. Prasad*, R. D. Schnabel†, S. D. McKay*,†, B. Murdoch*, P. Stothard*, D. Kolbehdari*, Z. Wang*, J. F. Taylor† and S. S. Moore* *Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5. †Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA OnlineOpen: This article is available free online at www.blackwell-synergy.com Summary The objective of this study was to quantify the extent of linkage disequilibrium (LD) on bovine chromosomes 19 and 29 and to study the pattern of selection signatures in beef and dairy breeds (Angus and Holstein) of Bos taurus. The extent of LD was estimated for 370 and 186 single nucleotide polymorphism markers on BTA19 and 29 respectively using the square of the correlation coefﬁcient (r2) among alleles at pairs of loci. A comparison of the extent of LD found that the decline of LD followed a similar pattern in both breeds. We observed long-range LD and found that LD dissipates to background levels at a locus separation of about 20 Mb on both chromosomes. Along each chromosome, patterns of LD were variable in both breeds. We ﬁnd that a minimum of 30 000 informative and evenly spaced markers would be required for whole-genome association studies in cattle. In addition, we have identiﬁed chromosomal regions that show some evidence of selection for economically important traits in Angus and Holstein cattle. The results of this study are of importance for the design and application of association studies. Keywords bovine, linkage disequilibrium, selection, single nucleotide polymorphism. Introduction Linkage disequilibrium (LD) is the non-random association of alleles at different loci. If two alleles at two different loci are in LD, combinations of alleles within haplotypes occur at frequencies that differ from that expected under the hypothesis of independence. An association between the genetic variation at a locus and a phenotype indicates that either the genetic variation at that locus directly affects the phenotype of interest or the locus is in LD with the causal mutation (Mueller 2004). The feasibility of association studies depend strongly on the extent of LD, which deter- Address for correspondence S. S. Moore, Department of Agricultural, Food and Nutritional Science, University of Alberta, 410-Agriculture/Forestry Centre, Edmonton, Alberta, Canada T6G 2P5. E-mail: stephen.moore@afhe.ualberta.ca Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. Accepted for publication 20 May 2008 mines how many markers should be typed in a genome scan to detect a quantitative trait locus (QTL) using LD. The ﬁrst whole-genome LD study in cattle, to quantify the extent and pattern of LD, was performed using 284 micro- satellite markers sampled from 581 maternally inherited gametes in Dutch black and white dairy cattle, where high levels of LD extended over several tens of centimorgans (Farnir et al. 2000). Several subsequent studies have con- ﬁrmed extensive LD in cattle (Tenesa et al. 2003; Vallejo et al. 2003; Khatkar et al. 2006a; Odani et al. 2006). Only recently, a study performed in a large mildly selected cattle population from Western Africa under an extensive breed- ing system has shown that LD extends over shorter dis- tances than the previous studies from developed countries, which was explained by increasing selective pressure and/or by an admixture process (Thevenon et al. 2007). All these LD studies were performed using very informative micro- satellite loci, but at a relatively low locus density. However, with the completion of the bovine genome sequencing project, it has become possible to estimate the extent of LD using dense single nucleotide polymorphism (SNP) marker maps, thereby dramatically increasing resolution. In 2008 The Authors, Journal compilation 2008 International Society for Animal Genetics, Animal Genetics, 39, 597–605 597