Small RNAs Reflect Grandparental Environments in Apomictic Dandelion

Plants can show long-term effects of environmental stresses and in some cases a stress “memory” has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here, we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21 and 24 nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up- or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This suggests that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent changes in epigenetic gene regulation

Pest categorisation of potato virus Y (non-EU isolates)

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus Y (PVY). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways and potential additional impact of non-EU isolates of PVY, has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVY are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVY can be subdivided into several strains and groups of isolates: strain C (PVY-C), strain N (PVY-N), strain O (PVY-O) and a wide range of recombinant isolates (PVYrecombinants) which have a worldwide distribution (including the EU). Two groups of isolates, i.e. the Brazilian (PVY-Br) and Chilean (PVY-Ch) isolates, are considered absent from the EU. Non-EU isolates of PVY-C, PVY-N, PVY-O and PVY-recombinants identified so far are not expected to have an additional impact in the EU compared to the PVY isolates already present and, therefore, do not meet the corresponding criterion to qualify as a potential Union quarantine pest. The Panel is unable to conclude on the potential additional impact of isolates of PVY-Br and PVY-Ch in the EU territory, but these isolates meet all the other criteria to qualify as potential Union quarantine pests

Data from: Range expansion in asexual dandelions: selection for general-purpose genotypes?

Phenotypic plasticity and broad ecological tolerance are hypothesized as important traits in the range expansion of asexual species, because individual asexual lineages have to face spatial and temporal environmental variation with limited opportunity for genetic adaptation. The hypothesis that asexual lineages are general-purpose genotypes (GPG) has been previously tested, with mixed results, in species that have both sexual and asexual variants. Such comparisons can be confounded with intra-specific ploidy level differences that are often observed between the two reproductive types. Avoiding the confounding effects of ploidy differences, we test whether northward range expansion selects for a GPG strategy in asexual lineages of the common dandelion (Taraxacum officinale), a species that shows geographic parthenogenesis. We compared the biomass of asexual lineages that were collected along a geographic transect from close to the asexuals’ area of origin (central Europe, where asexuals descend from sexual ancestors in mixed populations) towards their northern distribution edge (Northern Europe, where only asexual lineages occur) in three different experimental environments: optimal, drought and shaded conditions. The geometric mean performance across test environments did not differ significantly between plants from different regions along the transect. However, southern lineages typically showed larger differences in biomass between different test environments, mainly caused by a relatively high performance in the optimal environment. Northern and mid-latitude lineages showed more even performance across the different environments. Synthesis. Our results suggest that phenotypic plasticity is important in the asexual range expansion of Taraxacum officinale and that range shifting in this species is accompanied by a change in phenotypic plasticity strategy from lineages with high ability to increase biomass in optimal growing conditions (master-of-some strategy) to lineages that maintain more constant performance in different environments (GPG or jack-of-all-trades strategy) from core to range edge

Oplaat_JECOL_GPGpaper_data

Trait scores of dandelion genotypes that were collected along a transect of historic range expansion in north-western Europe, when grown in a common greenhouse environment under control, drought and shade experimental treatments

Data from: Heritable gene expression differences between apomictic clone members in Taraxacum officinale: insights into early stages of evolutionary divergence in asexual plants

Illumina sequencing Trinity assembl

Data from: Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage

Epigenetic variation has been proposed to contribute to the success of asexual plants, either as a contributor to phenotypic plasticity or by enabling transient adaptation via selection on transgenerationally stable, but reversible, epialleles. While recent studies in experimental plant populations have shown the potential for epigenetic mechanisms to contribute to adaptive phenotypes, it remains unknown whether heritable variation in ecologically relevant traits is at least partially epigenetically determined in natural populations. Here, we tested the hypothesis that DNA methylation variation contributes to heritable differences in flowering time within a single widespread apomictic clonal lineage of the common dandelion (Taraxacum officinale s. lat.). Apomictic clone members of the same apomictic lineage collected from different field sites showed heritable differences in flowering time, which was correlated with inherited differences in methylation-sensitive AFLP marker profiles. Differences in flowering between apomictic clone members were significantly reduced after in vivo demethylation using the DNA methyltransferase inhibitor zebularine. This synchronization of flowering times suggests that flowering time divergence within an apomictic lineage was mediated by differences in DNA methylation. While the underlying basis of the methylation polymorphism at functional flowering time-affecting loci remains to be demonstrated, our study shows that epigenetic variation contributes to heritable phenotypic divergence in ecologically relevant traits in natural plant populations. This result also suggests that epigenetic mechanisms can facilitate adaptive divergence within genetically uniform asexual lineages

Data from: Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages

DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci

Flowering time, microsatellite and MS-AFLP data from apomictic dandelion

Apomictic clone members from common dandelion microspecies Taraxacum officinale 'Alatum' screened under common greenhouse environments for variation in microsatellites, methylation-sensitive AFLPs and flowering time

Identification of oligoclonal agamospermous microspecies : Taxonomic specialists versus microsatellites

There has been a decrease in the ability of biologists to identify their material correctly, particularly plants of complicated genera with common agamospermy, where old clonal entities are accorded the rank of species (microspecies). Agamospermous microspecies are taxonomic entities recognizable from one another by a set of minute morphological features. The knowledge of microspecies is confined to a few specialists. Specialists use microspecies names but there could be inconsistencies in the taxonomic concepts used by different, geographically remote experts. A selection of nine widespread, generally recognized agamospermous microspecies of Taraxacum sect. Taraxacum, which are characterized by means of eight microsatellite loci, were used to evaluate the ability of four European Taraxacum specialists to identify these microspecies consistently. With two exceptions (and one unclear result) for 125 plants coming from an area extending from Finland to central Europe, the experts identified the microspecies consistently, exclusively on the basis of morphological differences. Another problem studied was within-species variation. The within-species microsatellite variation corresponded to the mutational clone cluster hypothesis, with a single unclear result. Each microspecies consisted of one, more or less dominant, clone and several minority clones, each usually confined to a single plant. A combination of the traditional microspecies identification by experts and the characterization of microspecies by a set of molecular markers opens the field of microtaxonomy to a wider group of researchers