LD and signatures of selection 599 Table 1 Summary of the proportion of genotypes in different ranges of probabilities that a genotype is correct (pGmx) and that the order or the phase of the allele is correct (oGmx) for Angus and Holstein. Table 2 Total number of locus pairs by intermarker distances in Angus and Holstein averaged over BTA19 and 29. Intermarker distances Holstein 25 71.5 90.5 232.5 408.5 794.5 1473 3933 2463 3424 10160 12880 5590.5 Angus 29.5 80.5 91.5 244 447.5 835.5 1530 4038.5 2425.5 3482.5 10340 13171 6019 Range <0.9000 0.9000–0.9500 0.9500–0.9900 0.9900–0.9990 ‡0.999 pGmx Holstein 0.0072 0.0019 0.0239 0.3992 0.5679 Angus 0.0174 0.0027 0.0104 0.6831 0.2864 oGmx Holstein 0.0107 0.0067 0.0176 0.0334 0.8994 Angus 0.1140 0.0279 0.0567 0.1679 0.6336 sire 2672891 inherited alternate haplotypes from this sire (blue/yellow in Table S2). Sire 2672891 inherited the yel- low haplotype from his maternal granddam. This represents only a small proportion of the markers on this chromosome; there were 22 markers centromeric of the ﬁrst marker shown and an additional 150 markers telomeric of this region. The combination of all pedigree and map informa- tion available allowed the accurate reconstruction of whole- chromosome-length haplotypes via linkage. GENOPROB esti- mates the probability that a genotype is correct (pGmx) and the order (phase) of the allele is correct (oGmx) conditional on the pedigree, locus order and map distances. For the LD analysis, we excluded all genotypes with pGmx £ 0.95, but did not put any constraint on oGmx. The summary of average genotype and order probabilities for each breed is shown in Table 1. As evident from Table 1, more than 90% of the genotypes have order (phase) probabilities >0.95. Estimation of linkage disequilibrium Linkage disequilibrium was measured as the square of the correlation coefﬁcient (r2) between marker alleles using GOLD (Hill & Robertson 1968; Abecasis & Cookson 2000). Only maternally inherited haplotypes were used to estimate LD in this study to avoid the over-representation of paternal haplotypes within the essentially all-male pedigrees. The r2-values for all pairwise combinations of markers were binned according to the physical distances separating the markers. The average number of locus pairs within each intermarker distance bin for both breeds are shown in Table 2. The graphical representation of the patterns of LD along the chromosomes was generated using the GOLD package. Estimation of signatures of selection We computed allelic frequencies for those SNPs whose genotypes were scored in both breeds. There were 334 and 165 such markers on BTA19 and 29 respectively that were used for the LD study. For estimating signatures of selection, we also included markers that were ﬁxed in one breed but that were still segregating in the other breed. There were 2008 The Authors, Journal compilation 2008 International Society for Animal Genetics, Animal Genetics, 39, 597–605 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 additionally 21 and 10 such markers on BTA19 and BTA29 respectively that were included in this analysis. However, these markers had been excluded from the LD study because their MAF values were <0.03. Therefore, in total, the esti- mation of signatures of selection was carried out using 355 and 175 markers on BTA19 and BTA29 respectively. We also computed rolling average allele frequencies in both breeds (using the frequency of the allele with the lowest frequency averaged over both breeds) using a ﬁve-locus sliding window for both chromosomes and for each pair of averages; we subtracted the mean Angus allele frequency from that for Holstein. We plotted mean allele frequency differences against the location of the third locus within the ﬁve-locus window. To establish whether the allele frequency difference between the breeds differed signiﬁcantly from zero and thus was putatively indicative of a selection signature, we performed 100 000 and 1 000 000 allele-frequency- against-locus permutation tests for BTA19 and BTA29 respectively to empirically identify the 5% signiﬁcance level thresholds. To conﬁrm the chromosomal regions identiﬁed using the sliding-window approach, we performed a chro- mosome-wide scan to detect regions showing evidence of selection using a Web-based tool to compute the extended haplotype homozygosity (EHH) statistic (Mueller & Andreoli 2004). First, the haplotypes at the locus of interest (core haplotype) were identiﬁed and the decay of LD as a function of increasing distance from the core haplotype as measured by EHH was evaluated (Sabeti et al. 2002). The test for positive selection requires identiﬁcation of a core haplotype with a combination of high frequency and high EHH, as compared to other core haplotypes at the locus (Sabeti et al. 2002). Again, only maternally inherited haplotypes were used for this analysis. Results and discussion The average MAF for SNPs on BTA19 was 0.27 for both Angus and Holstein, but was 0.25 and 0.27, respectively on