Selection signature detection in a diverse set of chicken breeds

摘要: Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures can provide valuable insights about have under pressure, which turn leads to a better understanding genotype-phenotype relationships. The main focus this thesis is various breeds chicken. Common strategy for compare samples from several populations and search with outstanding genetic differentiation. This uses inter-populations statistics. In dissertation each chapter (chapter 2, 3 4) one two statistics signature investigate. Two sets data set were used thesis: first comprised total 96 individuals three commercial layer (White leghorn, White Rock Rhode Island Red) 14 non-commercial fancy (including, G. g. gallus spadiceus) genotyped different 600K SNP-chips. second was pool sequences (10 per pool) 43 chicken breeds. contained 40 (including gallus, spadiceus various). In our approach, as described 2nd chapter, Wright’s fixation index, FST, an index differentiation between on set. focuses groups based SNP-wise FST calculation. After removing overlapping SNPs SNP arrays 1,139,073 remained. filtering minor allele frequencies lower than 5% unknown locations, 1 million available average values calculated windows. windows then compared detect signatures. Two comparisons made study order First, we performed comparison egg layers egg-layer, white brown layers. Comparing resulted 630 signatures, while 656 detected egg-layer Annotation revealed corresponding productions traits, had selected. NCOA1, SREBF2 RALGAPA1 among genes, associated reproductive broodiness production. Several growth carcass including POMC, PRKAB2, SPP1, IGF2, CAPN1, TGFb2 IGFBP2. These good candidates further studies. Our approach 2 demonstrates specific breeding histories unique opportunity farm animal selection. In 3rd aim use haplotype considering hierarchical structure We subset 74 (G. spadiceus). To facilitate this, statistical methods FLK hapFLK. calculates variation inbreeding coefficient using population's kinship matrix incorporate structure. A similar statistic hapFLK but instead frequencies. all breeds, estimation ancestral distance. applied groups; layers, 107 41 selective studies, respectively. QTL number IGF-1R, AGRP STAT5B. also annotated interesting gene dark mutational phenotype chickens (SOX10). new analysis provided great Large overlap exists determined current meat production, well both IGF-1R STAT5B, located results showed large degree agreement discussed 2. demonstrated improve power set. The 4th extracted sequence (the set) 30 pools consisted various) study. mapping quality sequencing depth, 22 studied contrasts (i.e. skin color, shell toe number). groups, whereas heterozygosity (HE) obtained group. Both measures (FST HE) subsequently summarized kb 50% within contrast. Comparisons HE employed detection, done reliability detection. eight (in contrast) methods. (BCO2) color larger combination background In conclusion, studies identification potentially be carried out utilizing high-resolution genome scans (using dense marker data). provides (FST, hapFLK) resolution (pool high density chip). method intra-populations (heterozygosity) identified putative traits selected for. purposes biodiversity believe gives selection, particularly regard