ArticleThe Plant cell2023
Asymmetric variation in DNA methylation during domestication and de-domestication of rice.
Article in The Plant cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Genetic Analysis of Genomic and Methylomic Variation and Identification of Multi-Trait Mutants in Rice Carried on Chang'e-5.Plants (Basel, Switzerland) · 2026Article
- Genomic analyses of weedy rice reveal historical connections between European and northwestern Chinese rice.Plant communications · 2026Article
- Integrated Comparative Genomics and Population Genomics Reveal the Genomic and Epigenomic Basis of Barley (Plants (Basel, Switzerland) · 2026Article
- Stem microanatomical phenomic uncovers a potential role for ZmLSM2 in regulating maize stem bending strength.Journal of integrative plant biology · 2026Article
- DNA Methylation Dynamics in Plant Abiotic Stress Response: Mechanisms, Memory, and Breeding Applications.Genes · 2026Review
- Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution.iScience · 2026Review
- Nanopore sequencing and multiomics reveal predictable non-coding RNA activation in DNA methylation deficient Arabidopsis thaliana.Communications biology · 2025Article
- DNA methylation dynamics: patterns, regulation, and function.Current opinion in plant biology · 2025Review
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- "Two scoops, please!": Twin cryo-EM structures of an Arabidopsis thaliana DNA methyltransferase.The Plant cell · 2025Article
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- Lactuca super-pangenome provides insights into lettuce genome evolution and domestication.Nature communications · 2025Article
- DNA Methylation ofBiology · 2025Article
- Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.International journal of molecular sciences · 2025Review
- Article
- Epigenetic odyssey to decrypt the hidden code for sustainable brassica production: enhancing yield, stress resilience and nutritional quality.Frontiers in plant science · 2025Review
- Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean.Genome biology · 2024Article
- Transgenerational epigenetic inheritance during plant evolution and breeding.Trends in plant science · 2024Review
- Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants.Molecular biology and evolution · 2024Article
- Insights into heterosis from histone modifications in the flag leaf of inter-subspecific hybrid rice.BMC plant biology · 2024Article
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12 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Hundreds of plant species have been domesticated to feed human civilization, while some crops have undergone de-domestication into agricultural weeds, threatening global food security. To understand the genetic and epigenetic basis of crop domestication and de-domestication, we generated DNA methylomes from 95 accessions of wild rice (Oryza rufipogon L.), cultivated rice (Oryza sativa L.) and weedy rice (O. sativa f. spontanea). We detected a significant decrease in DNA methylation over the course of rice domestication but observed an unexpected increase in DNA methylation through de-domestication. Notably, DNA methylation changes occurred in distinct genomic regions for these 2 opposite stages. Variation in DNA methylation altered the expression of nearby and distal genes through affecting chromatin accessibility, histone modifications, transcription factor binding, and the formation of chromatin loops, which may contribute to morphological changes during domestication and de-domestication of rice. These insights into population epigenomics underlying rice domestication and de-domestication provide resources and tools for epigenetic breeding and sustainable agriculture.
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