The Russian dandelion, Taraxacum kok-saghyz (TKS), is a perennial species native to Central Asia that produces high quality, natural rubber. Despite its potential to help maintain a stable worldwide rubber supply, little is known about genetic variation in this species. To facilitate future germplasm improvement efforts, we developed simple-sequence repeat (SSR) markers from available expressed-sequence tag (EST) data and used them to investigate patterns of population genetic diversity in this nascent crop species. We identified numerous SSRs (1,510 total) in 1,248 unigenes from a larger set of 6,960 unigenes (derived from 16,441 ESTs) and designed PCR primers targeting 767 of these loci. Screening of a subset of 192 of these primer pairs resulted in the identification of 48 pairs that appeared to produce single-locus polymorphisms. We then used the most reliable 17 of these primer pairs to genotype 176 individuals from 17 natural TKS populations. We observed an average of 4.8 alleles per locus with population-level expected heterozygosities ranging from 0.28 to 0.50. An average pairwise FST of 0.11 indicated moderate but statistically significant levels of genetic differentiation, though there was no clear geographic patterning to this differentiation. We also tested these 17 primer pairs in the widespread common dandelion, T. officinale, and a majority successfully produced apparently single-locus amplicons. This result demonstrates the potential utility of these markers for genetic analyses in other species in the genus.

Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D 0 ) between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005-0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species' newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system. Heredity Keywords: cyto-nuclear; linkage disequilibrium; metapopulations; spatiotemporal; Silene Keywords: cyto-nuclear; linkage disequilibrium; metapopulations; spatiotemporal; Silene INTRODUCTION Population genetic studies generally focus on either the nuclear or the cytoplasmic (mitochondria or chloroplast) genome. Additional insights can be gained by measuring joint allelic associations at loci derived from nuclear and cytoplasmic genomes, or cyto-nuclear linkage disequilibrium (LD). Analyses of cyto-nuclear LD can document evolutionary and demographic trends in population genetics. Processes like structure (Nei and Li, 1973), gene flow (Asmussen and Schnabel, 1991) and non-random mating/inbreeding (Asmussen et al., 1989;Slatkin, 2008) all influence cyto-nuclear LD. Selection-based treatments of cyto-nuclear LD focus on the importance of epistatic interactions between the nuclear and cytoplasmic genomes (Wade and Goodnight, 2006;Brandvain and Wade, 2009). Theoretical investigations of genetic drift predict an influence of population size on the variance of LD measurements (Datta et al., 1996). Additionally, demographic processes have been shown to greatly facilitate non-random associations between the nucleus and a cytoplasmic genome. For example, cyto-nuclear LD (or lack thereof) is an informative metric when considering admixture of two populations of the same species (Arnold, 2006). Thus, cytonuclear LD will be driven by the interaction of spatiotemporal selective and demographic parameters specific to a system of study, or by non-equilibrium population dynam...

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.

Mitochondrial genomes extracted from the wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is an SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study, either the sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9, and cox1 found in D. carota individuals collected from 24 populations in the eastern United States. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intragenic recombination, as opposed to the more common intergenic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other 2 genes surveyed, were nonrandomly associated with the 3 atp9 stop codon variants, though further analysis suggested that multilocus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an F(ST) of 0.34.