Abstract
BackgroundDivergent 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.ResultsTraits 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.ConclusionsLatitudinal 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0937-7) contains supplementary material, which is available to authorized users.
Highlights
Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations
The selective pressures leading to local adaptation can include a variety of abiotic and biotic factors such as: soil type [2,3,4], water availability [5], photoperiod [6], temperature [7], herbivores [8], mycorrhizal associations [9], and proximity to agricultural fields [10]
Plant materials and phenotypic analyses Seeds from 15 wild-collected populations of H. annuus were obtained from the USDA’s North Central Regional Plant Introduction Station (Ames, IA). These populations, which were sampled from a range of latitudes across central North America (Fig. 1; Table 1), were selected to represent truly wild populations that appear to be free from the effects of past introgression with cultivated sunflower
Summary
Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. We analyzed geographic patterns of phenotypic diversity, quantified levels of within-population SNP diversity, and determined the extent of population structure across the range of this species We used these data to identify significantly over-differentiated loci as indicators of genomic regions that likely contribute to local adaptation. The selective pressures leading to local adaptation can include a variety of abiotic and biotic factors such as: soil type [2,3,4], water availability [5], photoperiod [6], temperature [7], herbivores [8], mycorrhizal associations [9], and proximity to agricultural fields [10] Because these selective pressures are expected to produce characteristic patterns of genetic variation in and near genes. When combined with high-throughput genotyping approaches, such population genetic approaches have been used to identify genes thought to be involved in adaptation in a McAssey et al BMC Plant Biology (2016) 16:249 variety of species, including boreal black spruce [17], Atlantic cod [18], prairie-chickens [19], and moor frogs [20]
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