Selective Sweeps Reveal Candidate Genes for Adaptation to Drought and Salt Tolerance in Common Sunflower, Helianthus annuus

Abstract

Here we report the results of an analysis of variation at 128 EST-based microsatellites in wild Helianthus annuus, using populations from the species' typical plains habitat in Kansas and Colorado, as well as two arid desert and two distinct brackish marsh areas in Utah. The test statistics lnRV and lnRH were used to find regions of the genome that were significantly less variable in one population relative to the others and thus are likely to contain genes under selection. A small but detectable percentage (1.5-6%) of genes showed evidence for selection from both statistics in any particular environment, and a total of 17 loci showed evidence of selection in at least one environment. Distance-based measures provided additional evidence of selection for 15 of the 17 loci. Global F ST -values were significantly higher for candidate loci, as expected under divergent selection. However, pairwise F ST -values were lower for populations that shared a selective sweep. Moreover, while spatially separated populations undergoing similar selective pressures showed evidence of divergence at some loci, they evolved in concert at other loci. Thus, this study illustrates how selective sweeps might contribute both to the integration of conspecific populations and to the differentiation of races or species.

New evidence for habitat-specific selection in Wadden Sea Zostera marina populations revealed by genome scanning using SNP and microsatellite markers

“…The number of markers detected as outliers in this study was slightly higher (6 (13%) out of 46) compared to other recent studies (1.4-9.5%; Campbell and Bernatchez 2004;Vasemagi et al 2005;Bonin et al 2006;Kane and Rieseberg 2007). It is to be expected that for gene-linked (EST) markers, more signals of diverging selection can be detected than for anonymous markers (e.g.…”

“…As a goal of this study, we assessed how 2 years of additional marker development would aVect the reliability of results collected with relatively few markers. Several genome scan studies have reanalysed existing data sets with diVerent outlier tests (Vitalis et al 2001;Beaumont and Balding 2004) or assessed the validity of outlier tests by using more than one test statistic (Vasemagi et al 2005;Kane and Rieseberg 2007;Tsumura et al 2007;Egan et al 2008;Mäkinen et al 2008). In contrast, extending a genome scan by doubling the number of markers has been done here for the Wrst time.…”

Detecting loci under selection in a hierarchically structured population

“…A hierarchical approach seems well suited for this purpose. For instance, one may be interested in finding loci that are particularly differentiated between two geographic regions, two species or sub-species, or between two groups of population showing distinct phenotypes or ecotypes (Campbell and Bernatchez, 2004;Kane and Rieseberg, 2007;Egan et al, 2008;Nosil et al, 2008). A nested analysis of variance under a hierarchical island model would allow one to use replicated population samples within each of the group to be contrasted, which should be more powerful than an approach based on population pairwise comparisons, and solve the problem of nonindependence in multiple pairwise tests occurring in many studies (for example, Schlotterer, 2002;Bonin et al, 2006;Kane and Rieseberg, 2007;Nosil et al, 2008;Oetjen and Reusch, 2007).…”

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

“…The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought 1 . Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives 2,3 , including numerous extremophile species 4 .…”