Opportunities and challenges of next‐generation sequencing applications in ecological epigenetics

Robertson, Marta; Richards, Christina L.

doi:10.1111/mec.13277

Cited by 23 publications

(17 citation statements)

References 11 publications

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“…It is necessary to conduct transplantation or common garden experiments with offspring from populations in different habitats to distinguish the contribution of induced and inherited epigenetic variation to adaptive phenotypes. As the MSAP marker only provides limited anonymous loci that are difficult to link to functional genomic elements or phenotype, a reduced representation bisulfite sequencing approach based on next‐generation sequencing methods is the next level of epigenetic study in natural populations (Gugger et al., ; Platt et al., ; Robertson & Richards, ; Trucchi et al., ).…”

Section: Discussionmentioning

confidence: 99%

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

Liu

Cuiping

et al. 2018

Ecology and Evolution

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Environmentally induced phenotypic plasticity is thought to play an important role in the adaption of plant populations to heterogeneous habitat conditions, and yet the importance of epigenetic variation as a mechanism of adaptive plasticity in natural plant populations still merits further research. In this study, we investigated populations of Vitex negundo var. heterophylla (Chinese chastetree) from adjacent habitat types at seven sampling sites. Using several functional traits, we detected a significant differentiation between habitat types. With amplified fragment length polymorphisms (AFLP) and methylation‐sensitive AFLP (MSAP), we found relatively high levels of genetic and epigenetic diversity but very low genetic and epigenetic differences between habitats within sites. Bayesian clustering showed a remarkable habitat‐related differentiation and more genetic loci associated with the habitat type than epigenetic, suggesting that the adaptation to the habitat is genetically based. However, we did not find any significant correlation between genetic or epigenetic variation and habitat using simple and partial Mantel tests. Moreover, we found no correlation between genetic and ecologically relevant phenotypic variation and a significant correlation between epigenetic and phenotypic variation. Although we did not find any direct relationship between epigenetic variation and habitat environment, our findings suggest that epigenetic variation may complement genetic variation as a source of functional phenotypic diversity associated with adaptation to the heterogeneous habitat in natural plant populations.

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Section: Discussionmentioning

confidence: 99%

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

Liu

Cuiping

et al. 2018

Ecology and Evolution

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“…In future studies, a reduced‐representation bisulfite sequencing approach would allow the direct comparison of genetic and epigenetic data sets, and at a much finer scale, with substantially increased statistical power to detect epigenetic differences between populations (van Gurp et al., 2016; Robertson & Richards, 2015; Schrey et al., 2013; Trucchi et al., 2016). In addition, sequencing‐based methods provide an increased ability to disentangle the relationship of methylation variation and gene function when fragments overlap with the promoters or coding regions of genes.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, sequencing‐based methods provide an increased ability to disentangle the relationship of methylation variation and gene function when fragments overlap with the promoters or coding regions of genes. By increasing the number of loci surveyed, future studies may better identify the environmental conditions under which genetic or epigenetic variation is associated with environmental cues (Robertson & Richards, 2015). …”

Section: Discussionmentioning

confidence: 99%

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

Robertson

Schrey

Shayter

et al. 2017

Evolutionary Applications

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Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation sensitive fragment length polymorphism (MS‐AFLP) to test the hypothesis that response to oil exposure in S. alterniflora resulted in genetically and epigenetically based population differentiation. We found high genetic and epigenetic variation within and among sites and found significant genetic differentiation between contaminated and uncontaminated sites, which may reflect nonrandom mortality in response to oil exposure. Additionally, despite a lack of genomewide patterns in DNA methylation between contaminated and uncontaminated sites, we found five MS‐AFLP loci (12% of polymorphic MS‐AFLP loci) that were correlated with oil exposure. Overall, our findings support genetically based differentiation correlated with exposure to the oil spill in this system, but also suggest a potential role for epigenetic mechanisms in population differentiation.

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“…This would, however, contrast results of an earlier study on the same species in which a strong relation between DNA methylation and phenotypic variation was revealed (Vergeer et al., ). Moreover, it is widely accepted that epigenetic variation may significantly affect phenotypic variation (Bossdorf et al., ; Cortijo et al., ; Cubas et al., ; Johannes et al., ; Zhang, Fischer, Colot, & Bossdorf, ), although how exactly gene expression and phenotype are influenced by DNA methylation, it is not entirely understood and often no obvious connection between phenotype, gene expression and DNA methylation is observed (Robertson & Richards, ; Schrey et al., ). In this study, AFLP and MS‐AFLP methods were used to analyze genetic and epigenetic variation.…”

Section: Discussionmentioning

confidence: 99%

“…In this study, AFLP and MS-AFLP methods were used to analyze genetic and epigenetic variation. Although these methods have proven to be useful methods to analyze overall correlations between genetic, epigenetic and phenotypic relatedness, they are not suitable to uncover functionality or direct links between phenotypic and genetic or epigenetic variation (Robertson & Richards, 2015b;Schrey et al, 2013). In order to pinpoint the mechanic link between methylation and phenotype, other in-depth methods such as next-generation sequencing are necessary (van Gurp et al, 2016;Robertson & Richards, 2015b;Schrey et al, 2013).…”

Section: Correlation Between Phenotype Genetic and Epigenetic Varmentioning

confidence: 99%

Epigenetic population differentiation in field‐ and common garden‐grown Scabiosa columbaria plants

Groot

Wagemaker

Ouborg

et al. 2018

Ecology and Evolution

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Populations often differ in phenotype and these differences can be caused by adaptation by natural selection, random neutral processes, and environmental responses. The most straightforward way to divide mechanisms that influence phenotypic variation is heritable variation and environmental‐induced variation (e.g., plasticity). While genetic variation is responsible for most heritable phenotypic variation, part of this is also caused by nongenetic inheritance. Epigenetic processes may be one of the underlying mechanisms of plasticity and nongenetic inheritance and can therefore possibly contribute to heritable differences through drift and selection. Epigenetic variation may be influenced directly by the environment, and part of this variation can be transmitted to next generations. Field screenings combined with common garden experiments will add valuable insights into epigenetic differentiation, epigenetic memory and can help to reveal part of the relative importance of epigenetics in explaining trait variation. We explored both genetic and epigenetic diversity, structure and differentiation in the field and a common garden for five British and five French Scabiosa columbaria populations. Genetic and epigenetic variation was subsequently correlated with trait variation. Populations showed significant epigenetic differentiation between populations and countries in the field, but also when grown in a common garden. By comparing the epigenetic variation between field and common garden‐grown plants, we showed that a considerable part of the epigenetic memory differed from the field‐grown plants and was presumably environmentally induced. The memory component can consist of heritable variation in methylation that is not sensitive to environments and possibly genetically based, or environmentally induced variation that is heritable, or a combination of both. Additionally, random epimutations might be responsible for some differences as well. By comparing epigenetic variation in both the field and common environment, our study provides useful insight into the environmental and genetic components of epigenetic variation.

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Opportunities and challenges of next‐generation sequencing applications in ecological epigenetics

Cited by 23 publications

References 11 publications

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

Epigenetic population differentiation in field‐ and common garden‐grown Scabiosa columbaria plants

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