Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens.

ABSTRACT: A whole-genome scan for identifying selection acting on pairs of linked loci is proposed and implemented. The scan is based on , one of Ohta's 1982 measures of between-population linkage disequilibrium (LD). An approximate empirical null distribution for the statistic is suggested. Although the partitioning of LD into between-population components was originally used to investigate epistatic selection, we demonstrate that values of may also be influenced by single-locus selective sweeps with linkage but no epistasis. The proposed scan is implemented in a diverse panel of chickens including 72 distinct breeds genotyped at 538 298 single-nucleotide polymorphisms. In all, 1723 locus pairs are identified as putatively corresponding to a selective sweep or epistatic selection. These pairs of lo

SUBMITTER: Beissinger TM 

PROVIDER: S-EPMC4806882 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature