Abstract
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 theQTL 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 thatmarkers located inQTL regions on chromosomes 1, 7 and 14were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone.
Highlights
There is currently a large interest in characterising variation patterns in order to identify regions of the genome that are under selection
Selected regions were chosen based on quantitative trait loci (QTL) detected in previous studies
We obtained the same picture when using only the genotypes of markers in the QTL zones but not when using the genotypes of supposedly neutral markers (Figs. 1b and 1c): for supposedly neutral markers, individuals from G11 gathered at the centre and individuals from line 3 and from the control line overlapped
Summary
There is currently a large interest in characterising variation patterns in order to identify regions of the genome that are under selection. Article published by EDP Sciences scans using microsatellites distributed over a genome [32,35] or concentrated around candidate genes under artificial or natural selection [2,28,43] are commonly performed to investigate signatures of selection. These studies highlight and compare among natural populations, differences in patterns of heterozygosity or linkage disequilibrium, but they only give a picture of variability at a certain time, with predictions of the evolution of polymorphism estimated mainly through simulations. An important aim was to determine which methods are suitable for identifying signatures of selection, and to compare those methods using a real dataset
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