Patterns of Population Epigenomic Diversity

Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.

• Publication year

  2013

• Venue

  Nature

• Publication date

  2013-03-06

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/nature11968PMID 23467092PMCID 3798000
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• An efficient multi-locus mixed model approach for genome-wide association studies in structured populations

  2012cited by this paper
• Widespread dynamic DNA methylation in response to biotic stress

  2012cited by this paper
• Linking photoreceptor excitation to changes in plant architecture.

  2012cited by this paper
• 'Leveling' the playing field for analyses of single-base resolution DNA methylomes.

  2012cited by this paper
• Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

  2012cited by this paper
• Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA.

  2012cited by this paper
• Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

  2011cited by this paper
• Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

  2011cited by this paper
• Whole-genome sequencing of multiple Arabidopsis thaliana populations

  2011cited by this paper
• Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

  2011cited by this paper
• The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

  2010cited by this paper
• Conservation and divergence of methylation patterning in plants and animals

  2010cited by this paper
• Variance component model to account for sample structure in genome-wide association studies

  2010cited by this paper
• Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines

  2010cited by this paper
• Establishing, maintaining and modifying DNA methylation patterns in plants and animals

  2010cited by this paper
• Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

  2010cited by this paper
• Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

  2010cited by this paper
• A Role for RNAi in the Selective Correction of DNA Methylation Defects

  2009cited by this paper
• A transposon-induced epigenetic change leads to sex determination in melon

  2009cited by this paper
• Selective epigenetic control of retrotransposition in Arabidopsis

  2009cited by this paper
• Human DNA methylomes at base resolution show widespread epigenomic differences

  2009cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009cited by this paper
• Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

  2009cited by this paper
• Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

  2009cited by this paper
• University of Groningen Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

  2009cited by this paper
• Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.

  2009cited by this paper
• Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes.

  2009cited by this paper
• Epigenome dynamics: a quantitative genetics perspective

  2008cited by this paper
• Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana

  2008cited by this paper
• Genetical Genomics: Spotlight on QTL Hotspots

  2008cited by this paper
• Sequencing of natural strains of Arabidopsis thaliana with short reads.

  2008cited by this paper
• Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

  2008cited by this paper
• VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization.

  2007cited by this paper
• VIM 1 , a methylcytosine-binding protein required for centromeric heterochromatinization

  2007cited by this paper
• Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription

  2007cited by this paper
• Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

  2007cited by this paper
• A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline

  2006cited by this paper
• A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening

  2006cited by this paper
• A gene expression map of Arabidopsis thaliana development

  2005cited by this paper
• A population-epigenetic model to infer site-specific methylation rates from double-stranded DNA methylation patterns.

  2005cited by this paper
• One-Way Control of FWA Imprinting in Arabidopsis Endosperm by DNA Methylation

  2004cited by this paper
• Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase.

  2003cited by this paper
• A direct approach to false discovery rates

  2002cited by this paper
• An epigenetic mutation responsible for natural variation in floral symmetry

  1999cited by this paper
• Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis.

  1995cited by this paper

• Intragenic methylation repatterning is associated with alternative splicing and unique epigenetic phenotypes

  2026cites this paper
• Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species

  2025cites this paper
• Planting Genomes in the Wild: Arabidopsis From Genetics History to the Ecology and Evolutionary Genomics Era.

  2025cites this paper
• Genome-wide DNA methylation analysis of Medicago sativa L. treated with plasma and plasma-activated water

  2025cites this paper
• Naturally Occurring Epialleles and Their Roles in Response to Climate Change in Birch

  2025influential citation
• A maternal transcriptome bias in early Arabidopsis embryogenesis.

  2025cites this paper
• Testing the potential of zebularine to induce heritable changes in crop growth and development

  2025cites this paper
• ASET: an end-to-end pipeline for quantification and visualization of allele specific expression

  2025cites this paper
• Heritable Epigenetic Changes in Plant Stress Responses: Implications for Crop Resilience

  2025cites this paper
• Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations

  2025cites this paper
• DDM1 Controls Heritable Natural Epigenetic Variation in Arabidopsis

  2025influential citation
• DNA methylation shows footprints of altitude selection in the clonal plant species Fragaria vesca

  2025cites this paper
• Natural variation in FLOWERING LOCUS C and FLOWERING LOCUS M underlies the weak temperature sensitivity of the Arabidopsis accession Ellershausen

  2025cites this paper
• Genomic advancements in goat breeding: enhancing productivity, disease resistance, and sustainability in India’s rural economy

  2025cites this paper
• Harnessing neo-domestication of wild pigmented rice for enhanced nutrition and sustainable agriculture

  2025cites this paper
• ASET: An end-to-end pipeline for quantification and visualization of allele specific expression

  2025cites this paper
• Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits

  2024influential citation
• Genome-wide DNA methylation and their transgenerational pattern differ in Arabidopsis thaliana populations originated along the elevation of West Himalaya

  2024cites this paper
• Climate‐related naturally occurring epimutation and their roles in plant adaptation in A. thaliana

  2024influential citation
• Dynamic DNA methylation modification in catechins and terpenoids biosynthesis during tea plant (Camellia sinensis) leaf development

  2024cites this paper
• Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms

  2024cites this paper
• Epigenetic inheritance mediates phenotypic diversity in natural populations

  2024cites this paper
• Potent pollen gene regulation by DNA glycosylases in maize

  2024cites this paper
• Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects

  2024cites this paper
• Dynamic evolution of the heterochromatin sensing histone demethylase IBM1

  2024cites this paper
• Dual-trait genomic analysis in highly stratified Arabidopsis thaliana populations using genome-wide association summary statistics

  2024cites this paper
• Population epigenetics: DNA methylation in the plant omics era.

  2024cites this paper
• The Role of Plant DNA Methylation in Development, Stress Response, and Crop Breeding

  2024cites this paper
• Epiallelic variation of non-coding RNA genes and their phenotypic consequences

  2024cites this paper
• Molecular basis and evolutionary drivers of endosperm-based hybridization barriers

  2024cites this paper
• High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar

  2024cites this paper
• Epigenetic gene regulation in plants and its potential applications in crop improvement

  2024cites this paper
• A novel high-dimensional model for identifying regional DNA methylation QTLs

  2024cites this paper
• Population genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality

  2024cites this paper
• Survival Rate and Chronic Diseases of TCGA Cancer and KoGES Normal Samples by Clustering for DNA Methylation

  2024cites this paper
• Transgenerational epigenetic inheritance during plant evolution and breeding.

  2024cites this paper
• Time's up: Epigenetic clocks in plants.

  2024cites this paper
• Improved inference of population histories by integrating genomic and epigenomic data

  2024influential citation
• One Hundred Years of Progress and Pitfalls: Maximising Heterosis through Increasing Multi-Locus Nuclear Heterozygosity

  2024cites this paper
• DNA Methylation of the Autonomous Pathway Is Associated with Flowering Time Variations in Arabidopsis thaliana

  2024cites this paper
• DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis

  2023cites this paper
• Study of vacuole glycerate transporter NPF8.4 reveals a new role of photorespiration in C/N balance

  2023cites this paper
• Concepts, mechanisms and implications of long-term epigenetic inheritance.

  2023cites this paper
• An evolutionary epigenetic clock in plants

  2023cites this paper
• The genetic basis of epigenetic variation and its consequences for adaptation.

  2023cites this paper
• Transgenerational epigenetic control of constitutive heterochromatin, transposons, and centromeres.

  2023cites this paper
• Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice.

  2023cites this paper
• Epigenetic Changes Occurring in Plant Inbreeding

  2023cites this paper
• Genomic variations combined with epigenetic modifications rewire open chromatin in rice.

  2023cites this paper
• Natural methylation epialleles correlate with gene expression in maize

  2023cites this paper
• A tool for rapid, automated characterization of population epigenomics in plants

  2023cites this paper
• Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations.

  2023cites this paper
• Moving targets: Mechanisms regulating siRNA production and DNA methylation during plant development.

  2023cites this paper
• The conservation of allelic DNA methylation and its relationship with imprinting in maize

  2023cites this paper
• Patterns of Genetic And Epigenetic Diversity Across A Range Expansion in The White-Footed Mouse (Peromyscus Leucopus)

  2023cites this paper
• Stochasticity in gene body methylation.

  2023cites this paper
• Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits

  2023cites this paper
• Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs.

  2023cites this paper
• On the causes of gene-body methylation variation in Arabidopsis thaliana

  2023cites this paper
• The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato

  2023cites this paper
• Epigenome‐wide methylation haplotype association analysis identified HLA‐DRB1, HLA‐DRB5 and HLA‐DQB1 as risk factors for rheumatoid arthritis

  2023influential citation
• Epigenetic Regulation in Heterosis and Environmental Stress: The Challenge of Producing Hybrid Epigenomes to Face Climate Change

  2023cites this paper
• Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns

  2023cites this paper
• Molecular mechanisms of transgenerational epigenetic inheritance

  2022cites this paper
• A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana

  2022cites this paper
• The pan-genome and local adaptation of Arabidopsis thaliana

  2022cites this paper
• MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant WGBS data

  2022cites this paper
• Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms—An Insightful Perspective on Ecoepigenetics

  2022cites this paper
• (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions.

  2022cites this paper
• Hybridization alters maternal and paternal genome contributions to early plant embryogenesis.

  2022cites this paper
• MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data

  2022cites this paper
• Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations

  2022cites this paper
• Population Specific Methylome Remodeling in High and Low Elevation Populations of Indian West Himalayan Arabidopsis thaliana in Response to Elevated CO2

  2022cites this paper
• Phenotypic plasticity as a facilitator of microbial evolution

  2022cites this paper
• Exploring epigenetic variation for breeding climate resilient apple crops.

  2022cites this paper
• Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation

  2022cites this paper
• Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3

  2022cites this paper
• Genome‐wide methylation in the panmictic European eel (Anguilla anguilla)

  2022cites this paper
• Understanding of the various aspects of gene regulatory networks related to crop improvement.

  2022cites this paper
• Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions

  2022cites this paper
• Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense

  2022cites this paper
• Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions

  2022cites this paper
• Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

  2022cites this paper
• Integrated network analyses identify MYB4R1 neofunctionalization in the UV-B adaptation of Tartary buckwheat

  2022cites this paper
• Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana

  2022cites this paper
• Molecular properties of epimutation hotspots

  2022cites this paper
• Mitostasis is the Central Biological Hub Underlying the Response of Plants to Cadmium Stress

  2022cites this paper
• Epigenome guided crop improvement: current progress and future opportunities

  2022cites this paper
• Epigenetic inheritance mediates phenotypic diversity in natural 1 populations 2 3

  2021cites this paper
• Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’

  2021cites this paper
• Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements

  2021cites this paper
• Epigenome plasticity in plants

  2021cites this paper
• The complete mitochondrial genome of Arabidopsis thaliana (Brassicaceae) isolated in Korea

  2021influential citation
• CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation

  2021cites this paper
• Genome-wide analysis of genomic imprinting in the endosperm and allelic variation in flax.

  2021cites this paper
• Epimutations and mutations, nurturing phenotypic diversity

  2021cites this paper
• Epimutations define a fast-ticking molecular clock in plants.

  2021cites this paper
• Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

  2021cites this paper
• Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress

  2021cites this paper
• Multi-omics analyses on Kandelia obovata reveal its response to transplanting and genetic differentiation among populations

  2021cites this paper