Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids

Kakoulidou, Ioanna; Piecyk, Robert S; Meyer, Rhonda C; Kuhlmann, Markus; Gutjahr, Caroline; Altmann, Thomas; Johannes, Frank

doi:10.26508/lsa.202402599

Cited by 3 publications

(1 citation statement)

References 74 publications

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“…These lines were propagated by single‐seed descent for several generations and then used to map the epigenetic basis of complex traits, such as flowering time or root length (Cortijo et al., 2014 ). Recent efforts to re‐sequence the genome and the methylome of the epiRILs have provided further evidence that the inheritance of DNA methylation loss in these lines is truly independent from any DNA sequence changes (Kakoulidou et al., 2024 ; Quadrana et al., 2019 ; Zhang et al., 2021 ). In non‐model systems, where such genetic tricks cannot be used, the functional impact of DNA methylation loss can be nonetheless investigated using a demethylation agent, such as 5‐azacytidine or zebularine.…”

Section: Functional Consequences Of Population Epigenetic Variationmentioning

confidence: 99%

The evolutionary consequences of interactions between the epigenome, the genome and the environment

Baduel,

Sammarco,

Barrett

et al. 2024

Evolutionary Applications

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The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.

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Section: Functional Consequences Of Population Epigenetic Variationmentioning

confidence: 99%

The evolutionary consequences of interactions between the epigenome, the genome and the environment

Baduel,

Sammarco,

Barrett

et al. 2024

Evolutionary Applications

View full text Add to dashboard Cite

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Additive and partially dominant effects from genomic variation contribute to rice heterosis

Dan,

Chen,

Zhou

et al. 2024

Preprint

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The molecular mechanisms of heterosis remain debated due to discrepancies in factors such as species, phenotypes, hybrid populations, developmental stages or growth environments. Here, heterosis-associated genes and metabolites were screened from differential molecules in parents, and the main inheritance patterns of these molecules were additive and partially dominant effects, namely, at the middle parent levels and between the parental and middle parent levels. The additive and partially dominant effects contributed to heterosis of 17 rice agronomic traits, including grain yield and plant height across developmental stages, and to heterosis of F1hybrids from different populations or environments in both rice and maize. Furthermore, the two inheritance patterns were associated with parental genomic variants, particularly unique single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), which were correlated with heterosis of agronomic traits. Our study systematically integrates parental genetic variation and highlights the predominant genetic effects of additive and partially dominant in crop heterosis.

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Transposable elements are prevalent vectors of transgenerational epigenetic inheritance in nature

Baduel,

De Oliveira,

Caillieux

et al. 2024

Preprint

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Transgenerational epigenetic inheritance (TEI) mediated by transposable elements (TEs) is well established in plants. However, the molecular determinants and functional impact of this additional system of inheritance are poorly characterized. Through comprehensive analyses of severe DNA methylation loss over TEs in an experimental population and in >700 natural strains of Arabidopsis thaliana, we uncovered hundreds of TE epivariants in nature, most of which can be inherited independently of DNA sequence changes and thus are true epialleles. Furthermore, natural epivariants are enriched near genes and we uncovered a novel role for the Paf1 complex as a major facilitator of their prevalence. Conversely, related TE copies limit epiallelic variation, by producing the small RNAs that guide DNA methylation in trans. Crucially, natural epivariants mainly affect stress-responsive genes, making them unique targets for selection. Our findings therefore demonstrate that TEs are important mediators of transgenerational epigenetic variation in nature, with singular properties for plant adaptation.

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Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids

Cited by 3 publications

References 74 publications

The evolutionary consequences of interactions between the epigenome, the genome and the environment

The evolutionary consequences of interactions between the epigenome, the genome and the environment

Additive and partially dominant effects from genomic variation contribute to rice heterosis

Transposable elements are prevalent vectors of transgenerational epigenetic inheritance in nature

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