Awad et al. Genetics Selection Evolution 2011, 43:8 http://www.gsejournal.org/content/43/1/8 reconstructed haplotypes were used to identify families segregating for the QTL detected in the initial study [24]. As already shown by the microsatellite analysis, the grandsires of families G01 and G02 which are het- erozygous at the QTL, inherited the same haplotype in the distal region of BTA5 from their ancestor A0 (Figure 1). This was confirmed by the haplotype recon- struction using the 1 976 SNP. This A0 ancestral hap- lotype is named “haplotype 1” or (A0H1) and its A0 alternative haplotype “haplotype 2” or (A0H2). Family G03, previously declared as heterozygous for the target QTL [24] but not identified here, has inherited haplo- types not related to A0H1 (Figure 1). All animals with haplotype A0H1 (surrounding the putative QTL posi- tion) can be traced back to A0. Two of these, grand- sires G10 and G11 are paternal and maternal grandsons of A0, and are very important Fleckvieh bull sires. We have collected samples of all the available progeny-tested sons of these two grandsires and all available progeny-tested maternal grandsons of grand- sires G01, G02, G10 and G11, to add more recombi- nant A0 haplotypes into the mapping population. In total, 485 animals were genotyped by the SNP chip and haplotyped for BTA5. By calculating the indepen- dent haplotypes in the complex pedigrees, and consid- ering the traceability of all A0H1 haplotypes to A0, we estimated a very low frequency (<0.005) of A0H1 in the Fleckvieh population. Consequently, throughout the rest of this paper, the less frequent putative QTL allele embedded in this less frequent haplotype is referred to as the minor QTL allele. Combined linkage disequilibrium and linkage analysis Thirty-seven microsatellite markers (three markers BM6026, BMS610 and MNB71 showed extensive recom- binations and were excluded) and the complex pedigree MSPED2089 were used for initial LDL mapping ana- lyses. As shown in Figure 2, we observed a highly signif- icant QTL effect (LRT = 20 to 22, i.e. P = 0.0000077 to 0.0000027), but were unable to improve the mapping accuracy because of the presence of two or three peaks. According to previous results [24], and to the results obtained in the first part of this study, we have assumed that haplotype A0H1 has only introduced one QTL into the mapping population. Therefore, we performed a sec- ond LDL analysis using the 21 most distal markers, and limited to GD and MGS families descending from A0 and known to carry A0H1, i.e. pedigree MSPED1038 (Figure 3). Unlike the analysis of pedigree MSPED2089, Figure 3 illustrates a single rather broad peak between positions 119.005 cM and 120.166 cM. However, this highly significant QTL (P = 0.000062 to 0.000021) is still mapped with a low accuracy, i.e. 1-LOD drop-off Page 7 of 11 0 1 2 3 4 5 6 7 8 9 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 2 3 0 0 0 0 Position (cM) Figure 2 LDL analysis by variance component approach using microsatellites in a complex pedigree of 2089 animals. Joint linkage disequilibrium and linkage (LDL) analysis for three milk yield traits; Milk Yield (MY1), Milk Protein Yield (PY1) and Milk Fat Yield (FY1) during first lactation using 37 microsatellites, a complex pedigree of 2 089 animals, EBV as phenotype and AIREML as implemented in LDLRAMS and LDL program. Chromosome length in centiMorgan (cM) on the X-axis, log-likelihood ratio test (LRT) values on the Y-axis. Solid triangles on the X-axis represent positions of markers included in the analysis. 0 1 2 3 4 5 6 7 8 9 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 2 3 0 0 0 0 Position (cM) Figure 3 LDL analysis by variance component approach using microsatellites in a complex pedigree of 1 038 animals. Joint linkage disequilibrium and linkage (LDL) analysis for three milk yield traits; Milk Yield (MY1), Milk Protein Yield (PY1) and Milk Fat Yield (FY1) during first lactation using 21 microsatellites covered the most likely region containing the QTL in the distal part of bovine chromosome 5 (BTA5), a complex pedigree of 1 038 animals, EBV as phenotype and AIREML as implemented in LDLRAMS and LDL program. Chromosome length in centiMorgan (cM) on the X-axis, log-likelihood ratio test (LRT) values on the Y-axis. Solid triangles on the X-axis represent positions of markers included in the analysis. 24 22 20 18 16 14 TR12 L10 8 6 4 2 0 24 22 20 18 16 14 TR12 L10 8 6 4 2 0 MY1 PY1 FY1 MY1 PY1 FY1