A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions

He, Li; Wu, Wenwu; Zinta, Gaurav; Yang, Lan; Liu, Renyi; Zhang, Huiming; Zheng, Zhimin; Huang, Huan; Zhang, Qingzhu; Zhu, Jian‐Kang

doi:10.1038/s41467-018-02839-3

Cited by 90 publications

(81 citation statements)

References 61 publications

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“…As evidence accumulates regarding the mechanisms underlying epigenetic inheritance (Yu, Wang, & Moazed, 2018) and the adaptive benefits of epialleles (He et al, 2018), DNA methylation has the potential to be worked into a framework of adaptive divergence (Greenspoon & Spencer, 2018;Vogt, 2017Vogt, , 2018 and ultimately into the ecological speciation model (Feder et al, 2012). It is possible that the interplay of subtle nuclear divergence and DNA methylation could mediate local adaptation via hypermethylation of locally deleterious genes, although longitudinal common garden or translocation experiments are required to explore this (Dubin et al, 2015;Vilgalys, Rogers, Jolly, Mukherjee, & Tung, 2019).…”

Section: Dna Methylation Improves Detection Of Population Structurementioning

confidence: 99%

“…Moreover, an aspect of molecular variation that is undetected by standard genetic sequencing involves direct modifications to the structure of DNA. Epigenetic modifications like DNA methylation are influenced by environmental conditions and affect gene expression, and thus could be indicative of early divergence due to local adaptation (Greenspoon & Spencer, ; He et al, ; Vogt, ).…”

Section: Introductionmentioning

confidence: 99%

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Genome‐scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx

2019

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Determining the molecular signatures of adaptive differentiation is a fundamental component of evolutionary biology. A key challenge is to identify such signatures in wild organisms, particularly between populations of highly mobile species that undergo substantial gene flow. The Canada lynx (Lynx canadensis) is one species where mainland populations appear largely undifferentiated at traditional genetic markers, despite inhabiting diverse environments and displaying phenotypic variation. Here, we used high‐throughput sequencing to investigate both neutral genetic structure and epigenetic differentiation across the distributional range of Canada lynx. Newfoundland lynx were identified as the most differentiated population at neutral genetic markers, with demographic modelling suggesting that divergence from the mainland occurred at the end of the last glaciation (20–33 KYA). In contrast, epigenetic structure revealed hidden levels of differentiation across the range coincident with environmental determinants including winter conditions, particularly in the peripheral Newfoundland and Alaskan populations. Several biological pathways related to morphology were differentially methylated between populations, suggesting that epigenetic modifications might explain morphological differences seen between geographically peripheral populations. Our results indicate that epigenetic modifications, specifically DNA methylation, are powerful markers to investigate population differentiation in wild and non‐model systems.

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Section: Dna Methylation Improves Detection Of Population Structurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome‐scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx

2019

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“…The pattern of DNA methylation can affect ecologically important phenotypes and plasticity (Herrera & Bazaga, 2013; Nicotra et al., 2015; Zhang et al., 2013) and may play a significant role in adaptation to various habitat conditions (Foust et al., 2016; Richards et al., 2012; Schulz et al., 2014). For example, a naturally occurring epiallele named “NMR19‐4” has been discovered in Arabidopsis accessions , and its DNA methylation status is inheritable and independent of genetic variation (He et al., 2018). This epiallele controls leaf senescence and associates with local climates.…”

Section: Introductionmentioning

confidence: 99%

Genetic and epigenetic changes during the invasion of a cosmopolitan species (Phragmites australis)

Liu

Cuiping

Liu

et al. 2018

Ecology and Evolution

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While many introduced invasive species can increase genetic diversity through multiple introductions and/or hybridization to colonize successfully in new environments, others with low genetic diversity have to persist by alternative mechanisms such as epigenetic variation. Given that Phragmites australis is a cosmopolitan reed growing in a wide range of habitats and its invasion history, especially in North America, has been relatively well studied, it provides an ideal system for studying the role and relationship of genetic and epigenetic variation in biological invasions. We used amplified fragment length polymorphism (AFLP) and methylation‐sensitive (MS) AFLP methods to evaluate genetic and epigenetic diversity and structure in groups of the common reed across its range in the world. Evidence from analysis of molecular variance (AMOVA) based on AFLP and MS‐AFLP data supported the previous conclusion that the invasive introduced populations of P. australis in North America were from European and Mediterranean regions. In the Gulf Coast region, the introduced group harbored a high level of genetic variation relative to originating group from its native location, and it showed epigenetic diversity equal to that of the native group, if not higher, while the introduced group held lower genetic diversity than the native. In the Great Lakes region, the native group displayed very low genetic and epigenetic variation, and the introduced one showed slightly lower genetic and epigenetic diversity than the original one. Unexpectedly, AMOVA and principal component analysis did not demonstrate any epigenetic convergence between native and introduced groups before genetic convergence. Our results suggested that intertwined changes in genetic and epigenetic variation were involved in the invasion success in North America. Although our study did not provide strong evidence proving the importance of epigenetic variation prior to genetic, it implied the similar role of stable epigenetic diversity to genetic diversity in the adaptation of P. australis to local environment.

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“…To date, the major advances in the field of epigenomics have rarely shown a direct relationship with downstream phenotypes [16,17]. In addition, changes in chromatin state are often found to be confounded with genetic variation present between samples.…”

Section: Introductionmentioning

confidence: 99%

Extending the genotype inBrachypodiumby including DNA methylation reveals a joint contribution with genetics on adaptive traits

Eichten

Srivastava

Reddiex

et al. 2019

Preprint

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Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modelling revealed large genetic differences between families and a minor contribution of epigenomic variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation towards heritable phenotypic variation relative to genetic differences.Recently, there has been great excitement investigating the role of possible epigenomic sources of variation, in the form of stable DNA or histone modifications, which may act alongside, or independently, of traditional genetic variation. A range of population-level studies have reported substantial diversity between different genetic backgrounds [4][5][6][7][8][9]. In certain cases, measures of DNA methylation were combined with genetic variation identifying genetic factors that can influence chromatin between populations and geographical locations [6,[10][11][12]. Results often highlight the covariation of genetic variation with chromatin state, transposable element (TE) methylation, and differential cytosine methylation among accessions. Nonetheless, a small portion of geneticallyindependent methylation variation, often in the CG context and in promoter regions, may contribute to phenotypic variance [6,[13][14][15].

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A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions

Cited by 90 publications

References 61 publications

Genome‐scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx

Genome‐scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx

Genetic and epigenetic changes during the invasion of a cosmopolitan species (Phragmites australis)

Extending the genotype inBrachypodiumby including DNA methylation reveals a joint contribution with genetics on adaptive traits

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