Awad et al. Genetics Selection Evolution 2011, 43:8 http://www.gsejournal.org/content/43/1/8 candidate region on BTA5. And finally, despite the over- all presence of haplotypes with a high IBD to ancestor haplotypes around position 122.115 Mb, the complete absence of this peak in SNPPED308 pedigree can be explained by either a novel mutation in ancestor A0 or by the incapacity of the method and design used here to map it in a relatively small pedigree like SNPPED308. More reasonable explanations may be the lower statisti- cal power of the pedigree SNPPED308, possible local inconsistencies in the map order (which was based on map release Btau_4.0), the presence of a strong QTL at position 118.000 Mb with carryover effects to other regions, or a combination of all these explanations. The LDL analysis using SNPs and pedigree SNPP ED723 indicate several peaks affecting MY1 and PY1 in the region investigated here. In principle, these results (Figure 4) are comparable to the fine-mapping results reported on BTA3 by Druet et al. [38]. In this study, the authors have also first carried out mapping by linkage analysis and finally ended up with LDL analyses and multiple LRT peaks. We used larger overlapping marker windows (80 SNP) than Druet et al. [38]. By dividing the data set according to the results of linkage and hap- lotype analyses, most of the multiple peaks were explained as genetic background noise in a larger family set. The multiple peak profile could be explained by the heterogeneous LD structure within the QTL region or by the use of LD in the model when there is no LD information at all [38]. This might be increased by pos- sible local inconsistencies in the map order, which was based on the draft assembly, or on comparative map information. Moreover, the method and the data struc- ture may not make it possible to discard some regions even though they do not harbour the QTL [38]. To check for possible effects of the data structure on the reported mapping results, we tested regression of EBV on genetic distance from ancestor A0 for all car- riers of haplotype 1 (A0H1). The apparent lack of this regression suggests that we are looking at a real QTL effect, and not an artifact of pedigree-tracking. Searching the region between 117.900 and 119.100 Mb for candidate genes revealed 27 genes, 13 of which had no known function. Based on current biological infor- mation, the genes with partly known function could only be indirectly related to milk yield traits. Conclusions In the present study, we have performed a haplotype- assisted extension of the mapping design and thus increased the allele frequency of the minor QTL allele in mapping families. Alternative analyses with family subsets resulted in a substantial reduction of the genetic background noise and an increased frequency of the minor QTL allele. Using these subsets, we succeeded in Page 10 of 11 refining the map position of the previously detected QTL for milk production traits on BTA5 to a 1 Mb interval. In spite of implementing a two-QTL analysis, the possibility of a second QTL affecting only PY1 could not be ruled out. All in all, the results of both this study and the previous study by Awad et al. [24] support the presence of a QTL affecting both MY1 and PY1 that is close to the centromeric part of the long homozygous region (~5 Mb) in ancestor A0. Therefore, positional cloning and high-throughput sequencing of the candi- date region located between 117.900 Mb and 119.100 Mb should now be considered, but should also not neglect the second possible QTL around position 122.115 Mb. Acknowledgements Ashraf Awad was supported by the Ministry of Higher Education, Egypt. We thank Stela Masle and Matt North for useful editorial comments. We thank Tierzuchtforschung e.V. München for providing genome-wide SNP genotypes of animals related to ancestor A0 and for providing a part of the DNA samples analysed here. One hundred and seventy-three Fleckvieh animals not connected with A0 were genome-wide genotyped within the project ME3404/1-1, gratefully funded by German Research Foundation (DFG). We thank all breeders and breeding associations who sent us remaining samples free of charge to support this study. In particular, we thank Arbeitsgemeinschaft Süddeutscher Rinderzucht-und Besamungsorganisationen e. V. (ASR) and the Bavarian Gene Reserves at LfL, Grub, Germany. We also thank the associate editor in charge and the two reviewers whose comments resulted in substantial improvement of the final manuscript version. Author details 1Chair of Animal Genetics and Husbandry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr .13, 80539 Munich, Germany. 2Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, D- 85586 Grub, Germany. Authors’ contributions AA carried out DNA extraction, microsatellite genotyping; AA and IM performed all data analysis and wrote the paper; IM and MF designed the study; IR performed SNP genotyping and partly performed sampling. All authors read and approved the final manuscript. Competing interests The authors declare that they have no competing interests. Received: 14 July 2010 Accepted: 24 February 2011 Published: 24 February 2011 References 1. Andersson L: Genetic dissection of phenotypic diversity in farm animals. Nat Rev Genet 2001, 2:130-138. 2. Weiss KM, Terwilliger JD: How many diseases does it take to map a gene with SNPs? Nat Genet 2000, 26:151-157. 3. Meuwissen THE, Karlsen A, Lien S, Olsaker I, Goddard ME: Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping. Genetics 2002, 161:373-379. 4. Olsen HG, Lien S, Gautier M, Nilsen H, Roseth A, Berg PR, Sundsaasen KK, Svendsen M, Meuwissen TH: Mapping of a milk production quantitative trait locus to a 420-kb region on bovine chromosome 6. Genetics 2005, 169:275-283. 5. Gautier M, Barcelona RR, Fritz S, Grohs C, Druet T, Boichard D, Eggen A, Meuwissen TH: Fine mapping and physical characterization of two linked quantitative trait loci affecting milk fat yield in dairy cattle on BTA26. Genetics 2006, 172:425-436.