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We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL) regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in the QTL regions showed Fst values greater than 0.15. However, the non-significant difference (P> 0.05) between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm that markers located in QTL regions on chromosomes1,7 and 14 were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located onchromosome14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone

Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines (Open Access publication)