Selective sweeps using hapFLK combined with genome re-sequencing data reveals strong candidate mutations in QTL regions in divergent chicken lines

Session 1: Genomics and contemporary resources and methodologies; In the context of genome wide re-sequencing using NGS technologies, we analyzed selective sweeps in two divergent chicken lines selected for abdominal fat weight (AF). We applied a new statistic, hapFLK, to analyze the 9.4 M of SNP observed for the whole genome of 20 chickens. This genome scan revealed 129 significant selective sweeps with a size of 86 kb that contained 839 SNP and 2.2 genes, on average. These selective sweeps colocalize with different QTL responsible for abdominal fat and muscle weight, and drastically reduce their size. We then performed three complementary analyses for positional genes in these regions: 1) analysis of their biological functions to select functional candidate genes; 2) analysis in different tissues of their differential expression between both lines to argue in favor of a candidate mutation in regulatory or coding regions; 3) analysis of their polymorphism from DNA-seq and RNA-seq data to identify candidate mutations. The combination of these approaches reveals several strong candidate genes and mutations associated with the traits of interest.