Genetic and epigenetic differentiation between natural Betula ermanii (Betulaceae) populations inhabiting contrasting habitats

Wu, Weiqing; Yi, Ma Re; Wang, Xinfeng; Ma, Lili; Jiang, Lijin; Li, Xiwen; Xiao, Hongxing; Sun, Mingzhou; Li, Linfeng; B, Liu

doi:10.1007/s11295-013-0641-9

Cited by 20 publications

(20 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast to our results, other studies in diverse plant species have shown that global methylation levels tend to be higher in more stressful environments. For example, methylation was higher in alpine vs. subalpine habitats of Betula ermanii (Wu, Yi, et al, 2013) or in accessions from colder vs. warmer environments in A. thaliana (Dubin et al, 2015). Thus, we assume that environmental conditions were not particularly stressful in neither of the sites during the time since the ramets were planted.…”

Section: Discussionmentioning

confidence: 99%

Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing

Heer

Ullrich

Hiß

et al. 2018

Ecology and Evolution

View full text Add to dashboard Cite

Epigenetic mechanisms represent a possible mechanism for achieving a rapid response of long‐lived trees to changing environmental conditions. However, our knowledge on plant epigenetics is largely limited to a few model species. With increasing availability of genomic resources for many tree species, it is now possible to adopt approaches from model species that permit to obtain single‐base pair resolution data on methylation at a reasonable cost. Here, we used targeted bisulfite sequencing (TBS) to study methylation patterns in the conifer species Norway spruce (Picea abies). To circumvent the challenge of disentangling epigenetic and genetic differences, we focused on four clone pairs, where clone members were growing in different climatic conditions for 24 years. We targeted >26.000 genes using TBS and determined the performance and reproducibility of this approach. We characterized gene body methylation and compared methylation patterns between environments. We found highly comparable capture efficiency and coverage across libraries. Methylation levels were relatively constant across gene bodies, with 21.3 ± 0.3%, 11.0 ± 0.4% and 1.3 ± 0.2% in the CG, CHG, and CHH context, respectively. The variance in methylation profiles did not reveal consistent changes between environments, yet we could identify 334 differentially methylated positions (DMPs) between environments. This supports that changes in methylation patterns are a possible pathway for a plant to respond to environmental change. After this successful application of TBS in Norway spruce, we are confident that this approach can contribute to broaden our knowledge of methylation patterns in natural tree populations.

show abstract

Section: Discussionmentioning

confidence: 99%

Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing

Heer

Ullrich

Hiß

et al. 2018

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…Several studies have been conducted on model and non-model species, both in field and controlled conditions to quantify epigenetic influence on trait variation being independent of genetic variation (Abratowska et al 2012;Latzel et al 2013;Wu et al 2013). For example, in a controlled greenhouse study and reciprocal transplant experiment, genetic and epigenetic diversity were compared across 16 populations of Japanese knotweed (Fallopia japonica) from three habitat types of its invaded range in USA (Richards et al 2012).…”

Section: Epigenetic Basis Of Phenotypic Variationmentioning

confidence: 99%

Genetic and epigenetic regulation of phenotypic variation in invasive plants – linking research trends towards a unified framework

Banerjee¹,

Guo²,

Huang³

2019

View full text Add to dashboard Cite

Phenotypic variation in the introduced range of an invasive species can be modified by genetic variation, environmental conditions and their interaction, as well as stochastic events like genetic drift. Recent studies found that epigenetic modifications may also contribute to phenotypic variation being independent of genetic changes. Despite gaining profound ecological insights from empirical studies, understanding the relative contributions of these molecular mechanisms behind phenotypic variation has received little attention for invasive plant species in particular. This review therefore aimed at summarizing and synthesizing information on the genetic and epigenetic basis of phenotypic variation of alien invasive plants in the introduced range and their evolutionary consequences. Transgenerational inheritance of epigenetic modifications was highlighted focusing on its influence on microevolution of the invasive plant species. We presented a comprehensive account of epigenetic regulation of phenotypic variation and its role in plant invasion in the presence of reduced standing genetic variation, inbreeding depression and associated genomic events which have often been observed during introduction and range expansion of an invasive alien species. Finally, taking clues from the studies conducted so far, we proposed a unified framework of future experimental approaches to understand ecological and evolutionary aspects of phenotypic variation. This holistic approach, being aligned to the invasion process in particular (introduction-establishment-spread), was intended to understand the molecular mechanisms of phenotypic variation of an invasive species in its introduced range and to disentangle the effects of standing genetic variation and epigenetic regulation of phenotypic variation.

show abstract

“…To date, most work exploring plant epigenetic responses has been conducted on somaclonal variants produced through plant tissue culture (Neelakandan andWang 2012, Sun et al 2014) or ex situ Arabidopsis experiments (Latzel et al 2013). We are only just seeing the first reports of in situ plant ecology studies (Laguncularia racemosa, Lira-Medeiros et al 2010; Viola cazorlensis, Herrera and Bazaga 2011; Betula ermanii, Wu et al 2013) and even fewer in situ clonal plant studies (Fallopia aponica, Richards et al 2012;Helleborus foetidus, Herrera et al 2014). Some of the important attributes of clonal plants need to be re-examined in the light of recent advances in our knowledge of phenotypic plasticity and diversity of epigenomes, e.g., (1) does resource sharing among ramets permit a population to exploit environmentally heterogenous sites, such as by division of labor?…”

Section: Future Research Directionsmentioning

confidence: 99%

Epigenetics: a potential mechanism for clonal plant success

2014

View full text Add to dashboard Cite

Clonality in plants is widespread and includes species that span temporally and spatially heterogeneous environments. Yet, theory predicts that clonally reproducing plants evolve at slower rates, risk accumulating more mutations than sexuals, and potentially lack the benefits of DNA repair mechanisms afforded by meiosis. Does the apparent success of clonal plants contradict the severe costs of clonal reproduction suggested by theory? We examine how epigenetics may confer ecological advantages to clonal plants that could outweigh these evolutionary costs. Relying to various degrees on vegetative reproduction, the capacity to conserve or reverse gene regulation changes over cell divisions has clear potential for optimization of plasticity and acclimation in response to environmental variation encountered. Clonal plants may be one of the best examples of organisms taking advantage of epigenetic acclimation as an alternative to the slower mechanisms of adaptation through natural selection. If epigenetic processes are important in matching organismal response to the environment, this may prove to be a mechanism that will buffer plants against the challenges of current and future rapid environmental changes.Theory predicts that clonally reproducing plants evolve at slower rates, risk accumulating more mutations than sexuals, and potentially lack the benefits of DNA repair mechanisms afforded by meiosis mutational meltdown, Lynch et al. 1993; Muller's ratchet, Muller 1964). This suggests they are successful for evolutionarily short periods of time and under stable environments (Silvertown 2008). Yet, clonality in plants is widespread and includes species that span heterogeneous environments, are long-lived and face a range of environmental changes during their lifetime, and have survived major climatic changes such as those of the Pleistocene. Today, clonal plants make up perhaps 40 % of our planet's flora (Tiffney and Niklas 1985) dominate grasslands, deserts, wetlands, and tundras as major primary producers, comprise some of our most important crops, including almost all bioenergy crops, and feature many of the most invasive plants. Some of earth's largest, tallest, oldest, most extensive, and rarest plants are clonal. Being extremely modular organisms, clonal plants, whether large integrated clones, or fragmented into Communicated by C. Holzapfel.

show abstract

Genetic and epigenetic differentiation between natural Betula ermanii (Betulaceae) populations inhabiting contrasting habitats

Cited by 20 publications

References 57 publications

Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing

Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing

Genetic and epigenetic regulation of phenotypic variation in invasive plants – linking research trends towards a unified framework

Epigenetics: a potential mechanism for clonal plant success

Contact Info

Product

Resources

About