Strong selection within a given population locally reduces genetic variability not only in the selected gene itself but also in neighbouring loci. This so-called hitch-hiking effect is related to the initial linkage disequilibrium between markers and the selected gene, and depends mainly on the number of copies of the beneficial allele at the start of the selection phase. Contrary to the classical case, in which selection acts on a single, newly arisen beneficial mutation, we considered selection from standing variation (soft selective sweeps) on a gene (Rht-B1) with a major effect on plant height, a selected trait in an experimental wheat population grown for 17 generations, and we documented the evolution of gene diversity and linkage disequilibrium near this gene. As expected, Rht-B1 was found to be under strong selection (s = 0.15) and its variation in frequency accounted for 15% of the total trait evolution. This led to a smaller genetic effective population size at Rht-B1 (Neg = 18) compared to the whole genome estimation (Neg = 167). When compared with expectations under genetic drift only, no significant decrease in gene diversity was found at the closest loci. We computed expected di-locus frequencies for any linked marker–Rht-B1 pair due to hitch-hiking effects. We found that hitch-hiking was expected to affect the two most closely linked loci, but expected reduction in gene diversity was not greater than that due to genetic drift, which was consistent with the observations. Such limited effect was attributed to the low level of linkage disequilibrium (0.16) estimated after parental intercrosses, together with a relatively high initial frequency of the gene. This situation is favourable to candidate gene approaches where small linkage disequilibrium around selected genes is expected.
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