Detection of signatures of selection in commercial chicken lines
Stainton, John Joseph
Within the last 100 years, commercial chickens have been split into two main groups. Broiler chickens are produced for meat production while layers are produced for egg production. This has caused large phenotypic changes and the genomic signatures of selection may be detectable using statistical techniques. Genomic regions identified by these techniques may include genes associated with production traits, and is therefore of interest to animal breeders. This thesis investigates signatures of selection in a number of commercial chicken lines using several statistical techniques based on population differentiation and levels of genetic diversity. First, signatures of selection were investigated using population differentiation in nine lines of broiler chickens. Weir and Cockerham's pairwise FST was calculated for genome-wide markers between the broiler lines and averaged into overlapping sliding windows to remove stochastic effects. A chromosome bound, circular permutation method was used to generate a null distribution and determine the significance of each window. A total of 51 putative selection signatures were found shared between lines and 87 putative selection signatures were found to be unique to one line. The majority of these regions contain peak positions for broiler QTL found in previous studies and eight regions were significantly enriched for broiler QTL. One region located on chromosome 27 contained 39 broiler QTL and 114 genes, several of which were functional candidates for association with broiler traits. Secondly, areas of low diversity were investigated in three different SNP datasets. All three datasets were taken from the same broiler line at different time points and consisted of different SNP densities, including 12k, 42k and 600k. A number of zero diversity regions were found in each dataset and several were shared between the datasets. The 600k dataset was also analysed using a regression test, which investigates the patterns of diversity as the distance from the selected site increases. This method searches for signatures of selections by fitting a regression to the diversity data to test the fit of the data to the theoretical model. A total of 15 regions were found displaying significant asymptotic regression and diversity values less than 0.005. One of these regions located on chromosome 1 was also found as a fixed region in the 12k and 42k datasets and contained the gene IGF1, which encodes an important protein for growth. Finally, signatures of selection were investigated between broiler and layer datasets by investigating population differentiation and diversity based analysis. Weir and Cockerham's pairwise FST was calculated between the two lines and outliers extracted. A total of 32 regions were found displaying high differentiation. Seven regions of low diversity in the layer dataset were also investigated. Several broiler and layer QTL had been previously identified in these regions. Two genes related to hedgehog proteins were identified within selected regions, which are known to be involved in embryogenesis. Finally seven regions were found to be highly differentiated between the broiler and layer lines, and the nine broiler lines in the first chapter. This may indicate selection which occurred during breed separation. Signatures of selection were identified in four broiler and layer datasets using several statistical techniques. A number of regions were identified in multiple datasets by a number of techniques and are therefore good candidate regions for selection. Other statistical techniques could be used in future studies to further confirm these regions and identify causative genes and variants.