Soft selective sweep near a gene that increases plant height in wheat

Abstract

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 (N(eg) = 18) compared to the whole genome estimation (N(eg) = 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.

Signatures of selection in mammalian clock genes with coding trinucleotide repeats: Implications for studying the genomics of high‐pace adaptation

“…Such approaches generally have lower power than approaches based on environmental associations (De Mita et al., 2013) as they mainly aim to detect hard selective sweeps where only one or few beneficial alleles are selected to high frequency, producing more significant patterns of differentiation between populations (Hohenlohe, Philips, & Cresko, 2010; Raquin et al., 2008). Most genes, on the other hand, act in pleiotropy (Harrisson et al., 2014), which produces more modest increases in allele frequencies over multiple loci (Hermisson & Pennings, 2005) and is less likely to affect the patterns of divergence between populations.…”

Inbreeding depression and low between-population heterosis in recently diverged experimental populations of a selfing species

“…This result shows that neutral diversity is not as informative as desired for assessing potentially adaptive diversity in the DM system, although linkage disequilibrium is expected to be high in a selfing species (Golding and Strobeck, 1979). However, low linkage disequilibrium in DM has been shown around genes submitted to high selective pressure (Raquin et al, 2008).…”

The Angiosperm Gibberellin-GID1-DELLA Growth Regulatory Mechanism: How an “Inhibitor of an Inhibitor” Enables Flexible Response to Fluctuating Environments

“…Recent studies monitored the effects of artificial selection on an experimental wheat population segregating for Rht-B1a and Rht-B1b (wheat DELLA-encoding alleles conferring tall and dwarf plant phenotypes, respectively; Peng et al, 1999a;Raquin et al, 2008). Mean plant height increased steadily with number of generations post the founder population generation, as did the relative frequency of the RhtB1a allele, indicating that Rht-B1a was under strong positive selection throughout the 17 generations of the experiment (Raquin et al, 2008). At first sight this may seem paradoxical given the welldocumented increases in grain yield conferred by Rht-B1b (see above), the very increases that were responsible for the use of the Rht-B1b allele in green revolution wheat varieties.…”