ArticleThe Plant cell2013
Epigenetic and genetic influences on DNA methylation variation in maize populations.
Article in The Plant cell, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
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Who cites it
133 citing papers in PubMed.
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Methylome differences among barley inbreds and their association with genomic, transcriptomic, and phenotypic variation.Journal of experimental botany · 2026Article
- Genotype-dependent DNA methylation patterns are negatively associated with allelic variation rather than heat-induced gene expression in two contrasting potato genotypes.The Plant journal : for cell and molecular biology · 2026Article
- Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.Genome biology and evolution · 2025Article
- Beyond the Standard GWAS-A Guide for Plant Biologists.Plant & cell physiology · 2025Review
- Testing the potential of zebularine to induce heritable changes in crop growth and development.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.Cell research · 2024Article
- Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms.Molecular biology and evolution · 2024Review
- Genetic variability of aquaporin expression in maize: From eQTLs to a MITE insertion regulating PIP2;5 expression.Plant physiology · 2024Article
- Natural polymorphisms in ZMET2 encoding a DNA methyltransferase modulate the number of husk layers in maize.Plant physiology · 2024Article
- Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations.Genome biology and evolution · 2024Article
- Cisplatin exposure alters tRNA-derived small RNAs but does not affect epimutations in C. elegans.BMC biology · 2023Article
- Insights into the Evolution of Ohnologous Sequences and Their Epigenetic Marks Post-WGD in Malus Domestica.Genome biology and evolution · 2023Article
- Epigenetic Regulation of Subgenomic Gene Expression in AllotetraploidPlants (Basel, Switzerland) · 2023Article
- A complete telomere-to-telomere assembly of the maize genome.Nature genetics · 2023Article
- Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding.Plants (Basel, Switzerland) · 2023Review
- Beyond transcription factors: more regulatory layers affecting soybean gene expression under abiotic stress.Genetics and molecular biology · 2023Article
- LncRNA evolution and DNA methylation variation participate in photosynthesis pathways of distinct lineages ofForestry research · 2023Article
73 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, genetic changes such as transposon insertions can also lead to changes in DNA methylation. Genome-wide profiles of DNA methylation for 20 maize (Zea mays) inbred lines were used to discover differentially methylated regions (DMRs). The methylation level for each of these DMRs was also assayed in 31 additional maize or teosinte genotypes, resulting in the discovery of 1966 common DMRs and 1754 rare DMRs. Analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable. A local association scan found that nearly half of the DMRs with common variation are significantly associated with single nucleotide polymorphisms found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the variation in DNA methylation. Analysis of gene expression in the same samples used for DNA methylation profiling identified over 300 genes with expression patterns that are significantly associated with DNA methylation variation. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic changes that are often stably inherited and can influence the expression of nearby genes.
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