Transgenerational Effects and Epigenetic Memory in the Clonal Plant Trifolium repens

Transgenerational effects (TGE) can modify phenotypes of offspring generations playing thus a potentially important role in ecology and evolution of many plant species. These effects have been studied mostly across generations of sexually reproducing species. A substantial proportion of plant species are however reproducing asexually, for instance via clonal growth. TGE are thought to be enabled by heritable epigenetic modification of DNA, although unambiguous evidence is still scarce. On the clonal herb white clover (Trifolium repens), we tested the generality of clonal TGE across five genotypes and five parental environments including soil contamination and above-ground competition. Moreover, by genome wide-methylation variation analysis we explored the role of drought, one of the parental environments that triggered the strongest TGE. We tested the induction of epigenetic changes in offspring generations using several intensities and durations of drought stress. We found that TGE of different environments were highly genotype specific and all tested environments triggered TGE at least in some genotypes. In addition, parental drought stresses triggered epigenetic change in T. repens and most of the induced epigenetic change was maintained across several clonal offspring generations. We conclude that TGE are common and genotype specific in clonal plant T. repens and potentially under epigenetic control

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

Adaptation of flowering phenology and fitness-related traits across environmental gradients in the widespread Campanula rotundifolia

Plant populations need to adjust to climate warming through phenotypic plasticity or evolution of trait means. We performed a common-garden experiment with European populations of Campanula rotundifolia to investigate current adaptation in fitness-related traits and the potential for future adaptation. The common garden was situated in Switzerland and contained plants from 18 populations from four regions: Central Europe, The Netherlands, Scandinavia and the Swiss Alps. We assessed current adaptation with trait-environment correlations, and we compared molecular marker with trait differentiation to investigate past selection. How traits may change under future climate warming was investigated via selection analysis. Trait-trait correlations were performed to reveal genetic constraints. The majority of analysed phenotypic traits showed regional differentiation and all traits showed indications of past selection. Flowering duration decreased with latitude and elevation, suggesting adaptation to growing season length. The Central European populations performed best, indicating home-site advantage. Selection analysis showed positive selection on fitness-related traits whereas phenological traits showed less clear patterns. Trait-trait correlations were mostly neutral or favourable to selection. This study suggests that flowering phenology and other fitness-related traits of C. rotundifolia are adapted to the current climatic conditions and have the potential to evolve under climate change

Adaptation to high soil trace metal element concentrations in Arabidopsis arenosa

Metalliferous soils are harsh environments for plants as a result of their low levels of macronutrients and richness in trace metal elements (TME; e.g. Cd, Pb, Zn). Plant survival under these conditions requires soil-specific adaptations. Arabidopsis arenosa, a relative of A. thaliana, is an obligate outcrosser that occurs on both metalliferous and non-metalliferous soils. We are interested in adaptive differences between populations from metalliferous (M) and non-metalliferous (NM) sites, from a genomic and a functional perspective. From natural M and NM populations, we collected leaves, soil and seeds of individual plants, determined leaf and soil TME content and performed genomic divergence scans and environmental association analyses. In a greenhouse reciprocal transplant experiment, we tested for local adaptation and differences in gene transcription (RNAseq). Further, to perform a bulked segregant analysis, we created a segregating F2 population by crossing M and NM individuals from one soil contrast. Here, we demonstrate that M populations are adapted to metalliferous soils and that metalliferous soils exert a strong selection pressure manifesting in differing survival rates of M and NM plants on metalliferous soil. We present how we identify candidate loci underlying adaptive differences between M and NM populations, by integrating population genomics (genome scans, association analyses), quantitative genetics (bulked segregant analysis, RNAseq) and in the near future molecular biology (cloning of alleles, characterisation of knock-out mutants). To date, our approach identified well characterised metal-adaptation genes (e.g. HMA4, MTP1) next to a majority of undescribed and (so far) non-metal related candidate loci

Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils

It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.ISSN:1471-2970ISSN:0962-843

Convergent evolution in<i>Arabidopsis halleri</i>and<i>Arabidopsis arenosa</i>on calamine metalliferous soils

It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species,Arabidopsis halleriandArabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in severalA. hallerigenes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.</jats:p

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

Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress-adapted<i>Arabidopsis halleri</i>

AbstractHeavy metal-rich toxic soils and ordinary soils are both natural habitats ofArabidopsis halleri. The molecular divergence underlying survival in sharply contrasting environments is unknown. Here we comparatively address metal physiology and transcriptomes ofA. hallerioriginating from the most highly heavy metal-contaminated soil in Europe, Ponte Nossa (Noss/IT), and from non-metalliferous (NM) soil. Noss exhibits enhanced hypertolerance and attenuated accumulation of cadmium (Cd), and transcriptomic Cd responsiveness is decreased, compared to plants of NM soil origin. Among the condition-independent transcriptome characteristics of Noss, the most highly overrepresented functional class of “meiotic cell cycle” comprises 21 transcripts with elevated abundance in vegetative tissues, in particularArgonaute 9(AGO9) and the synaptonemal complex transverse filament protein-encodingZYP1a/b. IncreasedAGO9transcript levels in Noss are accompanied by decreased long terminal repeat retrotransposon expression, and are shared by plants from milder metalliferous sites in Poland and Germany. Expression ofIron-regulated Transporter(IRT1) is very low and ofHeavy Metal ATPase 2(HMA2) strongly elevated in Noss, which can account for its specific Cd handling. In plants adapted to the most extreme abiotic stress, broadly enhanced functions comprise genes with likely roles in somatic genome integrity maintenance, accompanied by few alterations in stress-specific functional networks.</jats:p