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Supporting information Additional supporting information may be found in the online version of this article. Table S1 List of the markers used in the LD analysis and their corresponding map positions. The Btau 3.1 positions, RH map positions (Prasad et al. 2007) as well as inferred base pair positions (used in the analysis) are provided. Table S2 An example of a set of ﬁve loci on BTA29 to illustrate how linkage phase of the alleles was inferred using multigenerational pedigree in this study. Table S3 List of the frequency of the alleles of 355 and 175 SNP markers on BTA19 and 29 respectively, common in both breeds of cattle, plotted in Figs 2 & 3. Table S4 Summary of the comparison of the chromosomal regions showing evidence of selection using the ﬁve-locus sliding window and EHH approaches. The chromosomal regions, which showed evidence of selection in both approaches, are highlighted in yellow. Figure S1 Decay of EHH as a function of distance in Holstein on BTA19. The chromosomal region of 44.417– 44.514 Mb was considered as a candidate region, which was deﬁned using markers BTA-45659 and BTA-45683. The sequence and population frequency of each core hap- lotype are shown after the colons, where A, C, G and T are coded respectively as 1, 2, 3 and 4. Figure S2 Decay of EHH as a function of distance in Holstein on BTA19. The chromosomal region of 61.308– 61.355 Mb was considered as a candidate region, which was deﬁned using markers BTA-29633 and BTA-29634. The sequence and population frequency of each core hap- lotype are shown after the colons, where A, C, G and T are coded respectively as 1, 2, 3 and 4. Figure S3 Decay of EHH as a function of distance in Holstein on BTA19. The chromosomal region of 62.017– 62.184 Mb was considered as a candidate region, which was deﬁned using markers BTA-45659 and BTA-45683. The sequence and population frequency of each core hap- lotype are shown after the colons, where A, C, G and T are coded respectively as 1, 2, 3 and 4. Figure S4 Decay of EHH as a function of distance in Angus on BTA19. The chromosomal region of 40.444–40.889 Mb was considered as a candidate region, which was deﬁned using markers BTA-57053 and BTA-56081. The sequence and population frequency of each core haplotype are shown after the colons, where A, C, G and T are coded respectively as 1, 2, 3 and 4. Figure S5 Decay of EHH as a function of distance in Holstein on BTA29. The chromosomal region of 11.655– 11.739 Mb was considered as a candidate region, which was deﬁned using markers BTA-112191 and BTA-112193. The sequence and population frequency of each core hap- lotype are shown after the colons, where A, C, G and T are coded respectively as 1, 2, 3 and 4. Figure S6 Decay of EHH as a function of distance in Holstein on BTA29. The chromosomal region of 29.840– 31.096 Mb was considered as a candidate region, which was deﬁned using markers BTA-65408 and BTA-04535. The sequence and population frequency of each core hap- lotype are shown after the colons, where A, C, G and T are coded respectively as 1, 2, 3 and 4. 2008 The Authors, Journal compilation 2008 International Society for Animal Genetics, Animal Genetics, 39, 597–605