Awad et al. Genetics Selection Evolution 2011, 43:8 http://www.gsejournal.org/content/43/1/8 R E S E A R C H G e n e t i c s Se l e c t i o n Ev o l u t i o n Open Access Mapping of a milk production quantitative trait locus to a 1.056 Mb region on bovine chromosome 5 in the Fleckvieh dual purpose cattle breed Ashraf Awad1, Ingolf Russ2, Martin Förster1,2, Ivica Medugorac1* Abstract Background: In a previous study in the Fleckvieh dual purpose cattle breed, we mapped a quantitative trait locus (QTL) affecting milk yield (MY1), milk protein yield (PY1) and milk fat yield (FY1) during first lactation to the distal part of bovine chromosome 5 (BTA5), but the confidence interval was too large for positional cloning of the causal gene. Our objective here was to refine the position of this QTL and to define the candidate region for high- throughput sequencing. Methods: In addition to those previously studied, new Fleckvieh families were genotyped, in order to increase the number of recombination events. Twelve new microsatellites and 240 SNP markers covering the most likely QTL region on BTA5 were analysed. Based on haplotype analysis performed in this complex pedigree, families segregating for the low frequency allele of this QTL (minor allele) were selected. Single- and multiple-QTL analyses using combined linkage and linkage disequilibrium methods were performed. Results: Single nucleotide polymorphism haplotype analyses on representative family sires and their ancestors revealed that the haplotype carrying the minor QTL allele is rare and most probably originates from a unique ancestor in the mapping population. Analyses of different subsets of families, created according to the results of haplotype analysis and availability of SNP and microsatellite data, refined the previously detected QTL affecting MY1 and PY1 to a region ranging from 117.962 Mb to 119.018 Mb (1.056 Mb) on BTA5. However, the possibility of a second QTL affecting only PY1 at 122.115 Mb was not ruled out. Conclusion: This study demonstrates that targeting families segregating for a less frequent QTL allele is a useful method. It improves the mapping resolution of the QTL, which is due to the division of the mapping population based on the results of the haplotype analysis and to the increased frequency of the minor allele in the families. Consequently, we succeeded in refining the region containing the previously detected QTL to 1 Mb on BTA5. This candidate region contains 27 genes with unknown or partially known function(s) and is small enough for high- throughput sequencing, which will allow future detailed analyses of candidate genes. Background Recent developments in molecular biology and statistical methodologies for quantitative trait loci (QTL) mapping have made it possible to identify genetic factors affecting economically important traits. Such developments have the potential to significantly increase the rate of genetic improvement of livestock species, through marker- * Correspondence: ivica.medjugorac@gen.vetmed.uni-muenchen.de 1Chair of Animal Genetics and Husbandry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr .13, 80539 Munich, Germany Full list of author information is available at the end of the article assisted selection of specific loci, genome-wide selection, gene introgression and positional cloning [1]. However, after an initial exaggerated enthusiasm animal geneti- cists, like their colleagues in human genetics e.g. [2] have faced somewhat unexpected challenges. The first step in QTL mapping usually involves a com- plete or partial genome scan, where the mapping popula- tion is genotyped for markers covering the entire genome or only selected chromosomes, respectively. The QTL are then mapped using linkage analysis (LA) methods. The resolution of this mapping approach is low because rela- tively few new recombination events are generated in the © 2011 Awad et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.