| Summary: | <p>Abstract</p> <p>Background</p> <p>The goal of genome wide analyses of polymorphisms is to achieve a better understanding of the link between genotype and phenotype. Part of that goal is to understand the selective forces that have operated on a population.</p> <p>Results</p> <p>In this study we compared the signals of selection, identified through population divergence in the Bovine HapMap project, to those found in an independent sample of cattle from Australia. Evidence for population differentiation across the genome, as measured by F<sub>ST</sub>, was highly correlated in the two data sets. Nevertheless, 40% of the variance in F<sub>ST </sub>between the two studies was attributed to the differences in breed composition. Seventy six percent of the variance in F<sub>ST </sub>was attributed to differences in SNP composition and density when the same breeds were compared. The difference between F<sub>ST </sub>of adjacent loci increased rapidly with the increase in distance between SNP, reaching an asymptote after 20 kb. Using 129 SNP that have highly divergent F<sub>ST </sub>values in both data sets, we identified 12 regions that had additive effects on the traits residual feed intake, beef yield or intramuscular fatness measured in the Australian sample. Four of these regions had effects on more than one trait. One of these regions includes the <it>R3HDM1 </it>gene, which is under selection in European humans.</p> <p>Conclusion</p> <p>Firstly, many different populations will be necessary for a full description of selective signatures across the genome, not just a small set of highly divergent populations. Secondly, it is necessary to use the same SNP when comparing the signatures of selection from one study to another. Thirdly, useful signatures of selection can be obtained where many of the groups have only minor genetic differences and may not be clearly separated in a principal component analysis. Fourthly, combining analyses of genome wide selection signatures and genome wide associations to traits helps to define the trait under selection or the population group in which the QTL is likely to be segregating. Finally, the F<sub>ST </sub>difference between adjacent loci suggests that 150,000 evenly spaced SNP will be required to study selective signatures in all parts of the bovine genome.</p>
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