Data from: Range-wide phenotypic and genetic differentiation in wild sunflower

Background: Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of growth, plant architecture, and seed traits, along with single-nucleotide polymorphism (SNP) genotyping to characterize range-wide patterns of diversity in 15 populations of wild sunflower (Helianthus annuus L.) sampled along a latitudinal gradient in central North America. We analyzed geographic patterns of phenotypic diversity, quantified levels of within-population SNP diversity, and also determined the extent of population structure across the range of this species. We then used these data to identify significantly over-differentiated loci as indicators of genomic regions that likely contribute to local adaptation. Results: Traits including flowering time, plant height, and seed oil composition (i.e., percentage of saturated fatty acids) were significantly correlated with latitude, and thus differentiated northern vs. southern populations. Average pairwise FST was found to be 0.21, and a STRUCTURE analysis identified two significant clusters that largely separated northern and southern individuals. The significant FST outliers included a SNP in HaFT2, a flowering time gene that has been previously shown to co-localize with flowering time QTL, and which exhibits a known cline in gene expression. Conclusions: Latitudinal differentiation in both phenotypic traits and SNP allele frequencies is observed across wild sunflower populations in central North America. Such differentiation may play an important adaptive role across the range of this species, and could facilitate adaptation to a changing climate.背景：表型与基因型的分化是鉴定本地适应种群中自然选择作用靶标的关键信号。本研究结合针对多种生长性状、植株构型及种子性状的同质园表型分型技术，与单核苷酸多态性（single-nucleotide polymorphism, SNP）基因分型方法，对北美中部沿纬度梯度采样的15个野生向日葵（Helianthus annuus L.）种群的全分布区多样性分布模式进行了系统表征。我们分析了表型多样性的地理格局，量化了种群内部的SNP多样性水平，并解析了该物种全分布范围内的种群结构程度。随后利用上述实验数据，鉴定出显著过度分化的基因组位点，作为可能参与本地适应的基因组区域的指示标记。 结果：包括开花时间、株高及种子油脂组成（即饱和脂肪酸占比）在内的多个性状与纬度呈显著相关，因此可有效区分南北种群。两两群体间的平均固定指数（FST）为0.21；STRUCTURE群体结构分析鉴定出两个显著聚类，可大致区分南北个体。显著的FST离群位点包含HaFT2基因内的一个SNP，该基因是已被证实与开花时间数量性状位点（quantitative trait locus, QTL）共定位的开花调控基因，且其基因表达模式存在已知的纬度渐变群特征。 结论：北美中部的野生向日葵种群中，表型性状与SNP等位基因频率均存在显著的纬度分化现象。此类分化在该物种的全分布范围内可能发挥重要的适应功能，并可促进其应对气候变化的适应性演化。