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Title: Genomic Landscape of Selection in Domestic Cat Breeds
Authors: Mona Mahmoud Abdi 
Supervisor: Dr. Hasan Alhaddad
Keywords: Genomic : Cat Breeds
Issue Date: 2018
Publisher:  Kuwait university - college of graduate studies
Abstract: Domestic cat breeds exhibit remarkable phenotypic diversity and unique population histories that revolved around the selection of desirable aesthetic traits. In this thesis, two different approaches, population differentiation index (Fst) and integrated haplotype homozygosity score (iHS), were applied to study the landscape of selection within the genomes of cat breeds. The analytical approaches were performed using a comprehensive dataset of 41 cat populations/breeds that were genotyped for ~58K genome-wide autosomal SNP markers. Population structure and breed ancestries were explored using PCA and Admixture analysis. Both PCA and Admixture initially showed three major clusters of cat breeds; (1) Western breeds, (2) Eastern breeds and (3) In-between breeds that were closer to Western breeds. Across breeds, 273 candidate selective sweeps were identified using the Fst-based approach whereas 317 candidate sweeps were localized using the haplotype-based approach. Runs of homozygosity (ROH) were determined within each breed where only 25 breeds exhibited segments of ROH >500kb. Comparative analysis of signals of selection in light of the population structure of cat breeds suggested that signatures of selection were more intense and confined to a smaller region when the breed under investigation is compared to closely related breeds or large number of breeds, which might be due to the minimization the effect of population structure. Annotating the regions harboring candidate selective sweeps revealed a panel of previously identified genes associated with phenotypic traits in cat breeds such as LPAR6, KRT71, KIT, FGF5 and TYR. In addition, other genes (n=5090) were found to reside within the regions under selection and most of which were strongly enriched for nervous system development and regulation. Four genomic regions were highlighted as unique signatures for single breed or multiple related breeds. The four regions were found in ChrB2, ChrB3, ChrB4 and ChrD2 each of which contains 120, 5, 80 and 1 genes, respectively. Overall, 590 genomic regions were identified to be putatively under positive selection in the cat genome across all breeds. Further investigation of genes within the identified regions and the associated biological functions need to be addressed in future studies.
Appears in Programs:2050 Molecular Biology

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