ArticleGenome biology2017
Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers.
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120 citing papers in PubMed, 272 citations in OpenAlex.
- An Intronic Structural Variant in GhEBS1 Drives Cotton Fruit Size Divergence by Modulating Chromatin Accessibility and Gene Expression.Plant biotechnology journal · 2026Article
- Precision Editing of Cis-Regulatory Elements Drives Crops Quantitative Traits Genetic Improvement: From Functional Dissection to Intelligent Design.Rice (New York, N.Y.) · 2026Review
- Convergence and divergence of DNA methylation and gene expression patterns in neopolyploid Arabidopsis kamchatica.Nature communications · 2026Article
- Copper-sensitive OsSPL9 TF regulates expression of indica rice domestication-associated miRNAs and phenotypes.Communications biology · 2026Article
- Response of DNA methylation and gene expression to light treatments in Norway spruce [Picea abies (L.) Karst.].BMC genomics · 2026Article
- Plant Genetic Engineering: Technological Pathways, Application Scenarios, and Future Directions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Transcriptomic and DNA methylation insights into polyploidy-enhanced heat tolerance in rice (Oryza sativa L.).Plant physiology · 2026Article
- Differential methylation analysis of floral buds between two morphs unravels the contributions of key genes to flowering time in heterodichogamousHorticulture research · 2026Article
- Structural Variation and 3D Genome-Driven DNA/RNA Methylation Divergence Contributing to Cotton Fiber Domestication.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Comparative single-cell transcriptomic map reveals divergence in leaves between two cotton species at cell type resolution.Journal of advanced research · 2026Article
- Genomic and epigenomic coordination maintains subgenome transcriptional balance in allotetraploidHorticulture research · 2026Article
- Review
- Intra species dissection of phytophthora capsici resistance in black pepper.Journal of advanced research · 2025Article
- Epigenetic insights into the domestication of tetraploid peanut.Plant physiology · 2025Article
- Empowering plant epigenetics to breed resilience of crops: From nucleolar dominance to transgenerational epigenetic inheritance.The plant genome · 2025Review
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- A modulatory role of CG methylation on gene expression in soybean implicates its potential utility in breeding.Plant biotechnology journal · 2025Article
- GhCOL2 Positively Regulates Flowering by Activating the Transcription of GhHD3A in Upland Cotton (Gossypium hirsutum L.).Biochemical genetics · 2025Article
- Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish.Genomics, proteomics & bioinformatics · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
60 more citing papers are in PubMed but not listed here.
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4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPolyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produce meiotically stable epialleles, which are transmissible through selection and breeding. However, the relationship between DNA methylation and polyploid plant domestication remains elusive.
resultsWe report comprehensive epigenomic and functional analyses, including ~12 million differentially methylated cytosines in domesticated allotetraploid cottons and their tetraploid and diploid relatives. Methylated genes evolve faster than unmethylated genes; DNA methylation changes between homoeologous loci are associated with homoeolog-expression bias in the allotetraploids. Significantly, methylation changes induced in the interspecific hybrids are largely maintained in the allotetraploids. Among 519 differentially methylated genes identified between wild and cultivated cottons, some contribute to domestication traits, including flowering time and seed dormancy. CONSTANS (CO) and CO-LIKE (COL) genes regulate photoperiodicity in Arabidopsis. COL2 is an epiallele in allotetraploid cottons. COL2A is hypermethylated and silenced, while COL2D is repressed in wild cottons but highly expressed due to methylation loss in all domesticated cottons tested. Inhibiting DNA methylation activates COL2 expression, and repressing COL2 in cultivated cotton delays flowering.
conclusionsWe uncover epigenomic signatures of domestication traits during cotton evolution. Demethylation of COL2 increases its expression, inducing photoperiodic flowering, which could have contributed to the suitability of cotton for cultivation worldwide. These resources should facilitate epigenetic engineering, breeding, and improvement of polyploid crops.
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