602 Prasad et al. frequencies at neighbouring loci as a result of selection. It is also important to note that the reported QTL peaks are generally quite broad and were reported from different re- source populations, which may not have direct relevance to the populations studied here. To address these issues, we utilized an EHH approach, which detects selection by detecting the presence of long-range haplotypes that puta- tively harbour selected alleles within a population. The chromosome-wide scan detected three regions (44.417– 44.514, 61.308–61.355 and 62.017–62.184 Mb) in Hol- stein and one region (40.444–40.889 Mb) in Angus on BTA19 that showed evidence of selection. On BTA29, we found four regions (11.655–11.739, 29.840–31.096, 31.807–32.078 and 33.693–34.136 Mb) in Holstein and one region (7.767–8.006 Mb) in Angus. In all these regions identiﬁed using the EHH approach, we found a core hap- lotype with the highest frequency and the highest EHH among other core haplotypes at those loci, indicating posi- tive selection (Figs S1–S9). By comparing these regions with the regions identiﬁed using the sliding-window approach, we found two regions (11.655–11.739 and 33.693– 34.136 Mb) in Holstein and one region (7.767–8.006 Mb) in Angus on BTA29 that were common in both approaches and showed evidence of selection (Table S4). Graphical representation of the patterns of LD shows regions of high and low LD across the chromosomes in both breeds. A clear difference in the pattern of LD is observed in Angus and Holstein (Figs S10–S13). For instance, on BTA19 from 0 to 2.1 Mb, Holstein shows higher LD than Angus. On BTA29, we see moderate- Holstein Angus 0.7 0.6 0.5 0.4 e r a u q s r- 0.3 0.2 0.1 0 to-high regions of LD in Holstein at regions 0.54–2.93 and at 37.73–40.82 Mb, which are clearly absent in Angus. However, these regions of higher LD do not align with the regions that possess higher allele frequency differences (results not shown). Although these regions may be expected to show some correlation, the disparity may have arisen because of the use of different sets of SNPs. The LD in these regions could have been generated by complex interactions between biological factors, such as recombi- nation and mutation, and the population s evolutionary history (Mueller 2004). We observed long-range LD with LD dissipating to background levels at a locus separation of about 20 Mb on both chromosomes (Fig. 4). We cannot make direct comparisons between our study and some of the previous LD studies in cattle (Farnir et al. 2000; Tenesa et al. 2003; Vallejo et al. 2003; Khatkar et al. 2006a; Odani et al. 2006) that used D¢ as a measure of LD because we used r2. We compared our study with that of McKay et al. (2007), where LD was also estimated using r2 and found similar results for Angus and Holstein data. For example, at intermarker distances of 5, 100 and 500 kb in Holstein, the r2-values in our study were 0.6, 0.26 and 0.1 compared to 0.53, 0.23 and 0.1 in McKay et al. (2007). It is important to mention here that the SNPs used in our study and in the McKay et al. (2007) study were not the same. McKay et al. (2007) used approximately 2670 markers genome-wide, with 54 and 55 markers, respectively for BTA19 and BTA29. However, the animals used by McKay et al. (2007) were included in our study. The average r2-values for BTA19 in McKay et al. (2007) 5 Kb 50 Kb 100 Kb 250 Kb 500 Kb 1 Mb 2 Mb 5 Mb 7 Mb 10 Mb 20 Mb 40 Mb 65 Mb Intermarker distances Figure 4 Decay of LD shown by the distribution of r2 as a function of bins of intermarker distances averaged across both chromosomes. 2008 The Authors, Journal compilation 2008 International Society for Animal Genetics, Animal Genetics, 39, 597–605