ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland.
Mol Ecol. 2013 Nov;22(22):5594-607. doi: 10.1111/mec.12521. Epub 2013 Oct 28.
Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST -based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.
自然遗传变异对于生物体适应其本地环境和变化的环境条件至关重要。在这里,我们研究了异交草本植物 Arabidopsis halleri 自然种群中的全基因组核苷酸变异模式,以及与阿尔卑斯山种群中气候变异的关联。使用汇集群体测序 (Pool-Seq) 方法,我们在五个自然种群中发现了两百多万个 SNP,并使用基于 FST 的分析鉴定了高度分化的基因组区域和 SNPs。我们仅使用部分 Mantel 检验测试了与一组非冗余环境因素最强烈分化的 SNPs,以确定可能是观察到选择痕迹的地形气候因素。通过基因本体论分析,确定了显示选择特征的基因的可能功能。我们发现 175 个基因与五个测试的地形气候因素中的一个或多个高度相关。其中,23.4%的基因具有未知功能。四个候选基因的遗传变异与站点水分平衡和太阳辐射强烈相关,功能注释与这些环境因素一致。我们的研究结果从高度多样化和异质的高山环境中,为自然植物种群中适应性遗传变异的分布提供了全基因组视角。