Awad et al. Genetics Selection Evolution 2011, 43:8 http://www.gsejournal.org/content/43/1/8 Page 3 of 11 G 17 DD DD G 2E 2D 05 G 10 M 10 G 11 M 11 G 28 G 04 G 02 M 02 A0 G 01 A1 G 14 A1 G 16 G G G DD 08 31 34 3D G 09 G 12 G 27 A1 G 23 G 22 G 29 D 3E G 06 G 13 DD 2A A1 G 21 DD 2J G 19 G 20 G 25 G 15 G 03 G 07 DD 2I DD 3F 100% RH A2 50% RH G 26 G 35 G 38 DD 3H DD G 3G 18 G 32 G 30 G 36 G 37 G 24 G 33 AAGAGGAAAGCCCGGAAGAAGGGAG G•A••••••••••••GG•••••AC• G••G•••••••AAAA••AC••AAC• G•A•••••••••••A••A•G••AC• GGA••A•G•••A•AAG•A••••AC• G•••A•G•••A••••G•A••••AC• Figure 1 Familial relationships considered in this study and segregation of most important haplotypes. A complex pedigree of 38 sires (squares) of GD families (G), ten sires of daughter design (DD) families, three maternal grandsire (M) families and 26 sampled and genotyped relevant ancestors; the pedigree has been simplified by showing only ancestors who made it possible to trace haplotypes from family-sires to the most important ancestors (A0, A1, A2); furthermore, to reduce the complexity of the figure, ancestor A1 is represented more than once; correspondingly, letters and numbers within squares of family-sires represent the internal family ID; non-genotyped individuals are represented by smaller circles (females) and squares (males) marked with a diagonal line; the estimated haplotype of 25 markers (A0H1) comprising a derived QTL allele affecting MY1 and PY1 with 97% CI between 117.962 Mb and 119.018 Mb is graphically presented by yellow bars above the individual’s symbol; five other most frequent haplotypes are represented by five different coloured bars; introgression of Red-Holstein genes into the mapping populations is represented by ancestor A2 and the corresponding haplotype presented by a red bar; to reduce the complexity of the figure, 77 low frequency haplotypes are omitted; the allelic composition of the respective haplotypes is presented within the figure; the pedigree MSPED2089 is a subset of the total material which can be constructed by keeping the families marked by a grey circle around squares and associated ancestors; pedigrees MSPED1038 and SNPPED421 are subsets of MSPED2089 which can be constructed by removing appropriate families as described in material and methods; the pedigree SNPPED308 consists of GD family G36 and animals across the entire mapping population but not descending from A0; the pedigree SNPPED723 is a sum of pedigrees SNPPED308 and SNPPED421. were obtained from the 2009 joint Austria-Germany genetic evaluation of the Fleckvieh population [26]. DNA preparation, microsatellite marker selection and genotyping Genomic DNA was prepared from semen using stan- dard methods, and from whole blood samples with QIAamp Blood-Kits (Qiagen), according to the manu- facturer’s protocol. Twelve evenly distributed microsatellite markers were added to the 28 microsatellite markers used in the pre- vious study [24]. Twenty-one of these 40 microsatellite markers covered the most likely region containing the QTL in the distal part of BTA5 (Table 1) and were used in most analyses of the present study. Previously ana- lysed animals were genotyped only for the new markers, but the five new families (G10, G11, M02, M10 and M11) were genotyped for all marker sets [24]. For 11 of