A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.

ABSTRACT: In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gap

SUBMITTER: Qanbari S 

PROVIDER: S-EPMC3510216 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature