1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 X 157 169 208 110 276 59 217 94 133 160 177 89 128 222 147 121 115 200 156 58 62 111 129 68 136 75 65 65 149 110 90 123 172 63 230 34 166 59 70 123 136 53 90 189 55 89 80 164 111 35 27 79 85 21 102 40 34 36 113 66 8 11 10 10 9 6 13 7 8 17 14 16 14 1 12 9 15 9 7 9 9 5 8 6 6 6 3 5 4 5 2 3 3 94 10 2 3 1 169 2 1 5 53 5 1 5 1 11 4 1 69 98 134 64 105 33 141 35 58 91 102 34 64 16 77 72 68 141 58 26 18 69 80 19 89 36 18 25 103 56 70 46 35 36 40 20 45 38 64 40 48 36 36 33 38 33 27 25 35 23 33 31 20 35 31 30 29 22 34 39 8 11 26 28 18 4 3 10 10 2 14 3 18 6 5 20 3 2 1 20 3 9 3 4 9 8 9 cR 3695.8 3487.7 4405.4 2605.2 4210.3 1699.4 4408.8 2458.6 3004.1 2760.5 3658.9 1553.3 2275.4 2667.1 2434.1 2957.2 2654.1 3182.1 2136.7 1712.2 1449 2031.9 2345.7 1588.7 2256.2 1715.1 1191.2 1141.3 1895.7 2390.7 154.67 128.88 128.9 119.93 135.6 134.42 135.56 128.62 116.17 118.83 130.97 109.95 105.38 103.95 109.75 94.46 95.86 84.38 109.61 82.94 83.79 88.1 80.05 78.13 68.42 79.39 67.37 61.66 69.73 146.5 102.83 86.54 85.36 69.56 76.43 69.62 69.14 62.12 64.65 70 87.17 48.61 62.72 50.71 53.82 56.99 45.92 56.51 56.39 42.95 49.72 48.33 41.6 45.25 41.41 35.72 31.57 34.89 45.82 47.9 23.39 20.64 21.39 23.05 15.31 28.8 20.32 26.44 22.59 17.04 20.56 17.45 17.78 11.96 16.56 24.64 23.08 15.91 13.7 29.52 23.37 18.31 18.04 23.36 16.96 22.87 18.33 17.56 12.64 22.14 0.65 0.51 0.41 0.62 0.28 1.18 0.32 0.67 0.49 0.43 0.49 0.55 0.49 0.23 0.37 0.47 0.4 0.28 0.36 0.74 0.8 0.44 0.32 0.67 0.31 0.48 0.49 0.54 0.31 0.44 BMC Genomics 2006, 7:283 http://www.biomedcentral.com/1471-2164/7/283 Table 1: Statistics of the BovGen RH map by chromosome BTA marker numbers no of markers new mapped AFLP [26] BESa genes micro-satellites unknown ESTsb cM Mbp cR/marker Mbp/marker Total 3966 2473 262 376 1999 1072 257 75972.4 3151.97 1740.25 19.16c 0.44c a BAC end sequences b ESTs which could not be assigned to an annotated sequence c average over whole genome over the whole genome, is 19 cR ranging between 12 cR (BTA 29) to 29 cR (BTA 20). Distance comparisons between common markers on the RH map, MARC 2004 linkage map and the bovine sequence suggests, on aver- age, 1 cR on the BovGen RH map is equivalent to 0.04 cM and 23 Kbp, respectively, although this varies considera- bly across the genome. Comparison with the ILTX 2005 RH map There are 160 marker loci in common between the Bov- Gen RH map described here and the Illinois-Texas (ILTX 2005) RH map [15]. All of these common loci were assigned to the same chromosomes on both maps (see Additional File 1). Three chromosomes (BTA 19, 28 and 29) cannot be assessed for consistency of their order between the ILTX 2005 and BovGen RH map because they have no markers in common. For the remaining 27 chromosomes, 19 are consistent with the BovGen RH map. For example, the BovGen RH map of chromosome 14 has 9 markers in common with the ILTX 2005 map and the order agrees between maps (Figure 1). Out of the 27 chromosomes another 7 have one marker out of 3 to 9 corresponding loci inconsistently positioned. On BTA 8 there are marker order discrepancies between the maps involving 2 out of the 11 corresponding markers. Comparison with MARC 2004 linkage map There are 885 marker loci in common between the Bov- Gen RH and the MARC 2004 linkage map [3] which allows a detailed comparison of map order and chromo- some assignment. Inconsistencies in chromosomal assignment are found for 5 of these 885 loci (see Addi- tional File 2). In all these cases only individual markers are involved. Page 3 of 15 (page number not for citation purposes)