were not shown because of the presence of fewer than ﬁve informative locus pairs. However, with many more markers on these chromosomes and a larger sample size, our study demonstrates that LD persists over long intermarker dis- tances of up to 20 Mb. It is also important to note that the LD results from our study have come from only two chromosomes, which were not chosen at random and from only two breeds. Therefore, the results from this study may not be representative of the genome as a whole or of all Bos taurus breeds. Our study shows that at a physical distance of 100 kb, the average r2-value is 0.23–0.26. We can assume that any QTL we seek will be at most in the middle of the interval and therefore no more than 50 kb away from any marker. Hence, the average r2 between these markers and a QTL located at the mid-interval is approximately 0.3. This indicates that there should be an informative marker every 100 kb to achieve a moderate LD (r2-values ‡ 0.2) for genome-wide association studies. Because the bovine genome is approximately 3 Gb, we would need a minimum of 30 000 evenly spaced and informative markers to perform a whole-genome associa- tion study, which agrees with McKay et al. (2007) but disagrees with Khatkar et al. (2007) and Gautier et al. (2007), who have suggested that 75 000–100 000 and 300 000 SNPs, respectively capture most of the LD infor- mation within the different cattle breeds based on the identiﬁcation of haplotype blocks and tag SNPs. Consider- ing the fact that many SNPs may have low MAFs in certain breeds and with the goal of achieving an even spacing across the bovine genome, we concur with McKay et al. (2007) who suggested that a 50 000 SNP chip should be sufﬁcient for whole-genome association studies in Bos taurus cattle. The information generated from this study has important implications for the design and application of association studies in cattle populations. Acknowledgements The authors thank Jakob Mueller for intellectual contribu- tions and Graham Plastow for his critical review of the manuscript. The authors gratefully acknowledge the early pre-publication access under the Fort Lauderdale conven- tions to the draft bovine genome sequence provided by the Baylor College of Medicine Human Genome Sequencing Center and the Bovine Genome Sequencing Project Consortium. The authors also acknowledge the ﬁnancial contributions of Semex Alliance and Alberta Livestock Industry Development Fund (ALIDF). This work was supported by Alberta Agriculture Research Institute (2002L030R), CDN-DairyGen/CRD 313675-04 and NSERC-CRD PJ313675-04. 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