Abstract
BackgroundThe 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.ResultsIn 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 FST, was highly correlated in the two data sets. Nevertheless, 40% of the variance in FST between the two studies was attributed to the differences in breed composition. Seventy six percent of the variance in FST was attributed to differences in SNP composition and density when the same breeds were compared. The difference between FST 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 FST 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 R3HDM1 gene, which is under selection in European humans.ConclusionFirstly, 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 FST 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.
Highlights
The goal of genome wide analyses of polymorphisms is to achieve a better understanding of the link between genotype and phenotype
We found that PC1 separated out the zebu Brahman breed from the taurine breeds
The Belmont Red, which in principle does not have recent zebu ancestry but in practise may have a small percentage of Brahman ancestry, was separated along PC1 to the same extent as the Santa Gertrudis
Summary
The goal of genome wide analyses of polymorphisms is to achieve a better understanding of the link between genotype and phenotype. The study of a large number of polymorphisms spread across the genome will reveal aspects of the genetic structure of the population, including, in some cases, evidence of adaptive selection across the genome [1,2]. If the individuals in the sample are measured for a range of traits, genome wide association (GWA) studies between the polymorphisms and the trait values can lead to the genetic dissection of traits [3,4]. This applies in particular to complex traits, where genetic and environmental factors combine to produce the phenotype [5,6,7]. There are studies of a few genes that give credibility to the approach [9,10]
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