0.45 0.42 0.39 0.36 0.33 0.3 0.27 0.24 0.21 y 0.18 n c 0.15 e qu 0.12 fre 0.09 llee 0.06 l_a 0.03 e–3E–17 g rea –0.03 va –0.06 g_n –0.09 i llo –0.12 R –0.15 –0.18 –0.21 –0.24 –0.27 –0.3 –0.33 –0.36 –0.39 –0.42 –0.45 0.27 0.26 0.25 0.24 0.23 0.22 0.21 0.2 0.19 0.18 0.17 0.16 0.15 0.14 0.13 0.12 0.11 0.1 cyn 00..0089 e 0.07 u 0.06 q 0.05 e r 0.04 f_ 0.03 e 0.02 rag 0.001 ve –0.01 a –0.02 _ –0.03 ng –0.04 lli –0.05 o –0.06 R–0.07 –0.08 –0.09 –0.1 –0.11 –0.12 –0.13 –0.14 –0.15 –0.16 –0.17 –0.18 –0.19 –0.2 –0.21 –0.22 –0.23 –0.24 –0.25 LD and signatures of selection 601 Stature (0–4.45 Mb) SCS (22.29 Mb) Milk fat (31.80 Mb) Milk fat (52.26–55.88 Mb), fat % (54.52 Mb) 7 9 7 0 0 8 537 .889 .31 51 01 51 82 72 82 42 33 23 83 03 43 36 04 14 54 04 04 55 25 25 75 55 85 86 0416 .4236 .01 .62 .53 .04 .45 .16 . 91 .74 .17 .69 .80 .83 .57 .68 .80 .83 .05 .26 .67 .98 .21 .54 .25 .96 .38 .11 .03 .45 .16 .71 .69 .60 . Backfat and pre–weaning Backfat (23.46– average daily gain (4.45– 28.56 cM), ribeye 8.97 Mb), Yield grade (4.45– area (24.76– 22.25 Mb), Retail product 31.11 Mb) yield (5.49–8.97 Mb) Position (Mb) Backfat (57.80– 59.04 cM) Figure 2 Rolling average allele frequency distribution of 355 SNP markers along BTA19 for beef and dairy cattle. The deviations above and below the axis show evidence of selection in dairy and beef cattle respectively with signiﬁcant thresholds of 0.27 and )0.25 respectively shown by red lines. PTA type, Structural soundness, teat Protein and Protein % (13.16 Mb) placement, udder attachment and udder composite index (20.04–32.04 Mb) Foot angle & structural soundness (32.04– 38.89 Mb), Milk & protein yield (13.16– 38.89 Mb) 6 9 6 5 6 957 .328 .01 71 91 51 01 61 61 41 42 12 82 62 72 22 02 72 52 82 62 13 13 23 33 33 83 34 1214 .1914 .90 .23 .15 .85 .56 . 11 .71 .62 .15 .18 .28 .88 .49 .50 .91 .72 .94 .95 .46 .86 .47 .87 .68 .92 .81 .82 .63 .74 .96 .49 .60 . Marbling score (6.16–18.29 Mb), hot carcass weight (6.79–28.77) Position (Mb) Marbling score (6.16–18.29 Marbling score (28.22–38.89 Mb), meat tenderness Mb), hot carcass weight (6.79– (26.28–41.21; 34.22–38.89 Mb), retail product yield 28.77) & body weight at castration (34.22–38.22 Mb), hot carcass weight (34.22–38.89 Mb) Figure 3 Rolling average allele frequency distribution of 175 SNP markers along BTA29 for beef and dairy cattle. The deviations above and below the axis show evidence of selection in dairy and beef cattle with signiﬁcant thresholds of 0.19 and )0.21 respectively shown by red lines. chromosomal regions having large allele frequency differ- ences with QTL regions provides independent evidence for selection over drift, which is a random process. Our ap- proach does suffer from the fact that when markers are not equally spaced on the chromosome, the ﬁve-locus sliding window will not cover the same physical distance, which may affect the correlation between allele frequencies ex- pected within each window and thus the range of breed differences. In addition, permutation tests may disrupt the correlation that is expected to exist between allelic 2008 The Authors, Journal compilation 2008 International Society for Animal Genetics, Animal Genetics, 39, 597–605