ArticleCell research2024
Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
Article in Cell research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Translating functional molecular knowledge into crop-breeding success.Nature reviews. Genetics · 2026Review
- Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance.Nature plants · 2026Article
- Harnessing polyploidy for climate-resilient crops: Lessons from the evolutionary model, allotetraploid cotton.Proceedings of the National Academy of Sciences of the United States of America · 2026Review
- Application of deep learning in crop research: From genomics to phenomics.The plant genome · 2026Review
- Sex and gender differences in responses to antianemic therapies: biological mechanisms and clinical implications.Naunyn-Schmiedeberg's archives of pharmacology · 2026Review
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- DNA Methylation Dynamics in Plant Abiotic Stress Response: Mechanisms, Memory, and Breeding Applications.Genes · 2026Review
- Emerging opportunities for DNA methylation biomarkers in cattle improvement.The Journal of reproduction and development · 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
- Epigenetic Regulation of Salt Stress Responses in Rice: Mechanisms and Prospects for Enhancing Tolerance.Epigenomes · 2025Review
- DNA methylation changes in Medicago sativa under salt-alkaline stress and the function of 5-azacytidine in enhancing stress tolerance.BMC plant biology · 2025Article
- Towards smart agriculture: AI-driven prediction of key genes for revolutionizing crop breeding.Planta · 2025Review
- Genome assembly and DNA methylation variation in an epimutant population of hybrid poplar clone NL895.Plant physiology · 2025Article
- The Association Between DNA Methylation and Three-Dimensional Genome During Whole Genome Doubling inPlants (Basel, Switzerland) · 2025Article
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- Transposon Dynamics Drive Genome Evolution and Regulate Genetic Mechanisms of Agronomic Traits in Cotton.Plants (Basel, Switzerland) · 2025Article
- Identifying potential drug targets for tourette syndrome: a Mendelian randomization study based on druggable genes.Italian journal of pediatrics · 2025Article
- Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.Genome biology and evolution · 2025Article
- A cost-effective method for combining the power of genetic and epigenetic selection in animal production.Environmental epigenetics · 2025Article
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Authors and funding
30 authors.
Funding
Abstract
DNA methylation plays multiple regulatory roles in crop development. However, the relationships of methylation polymorphisms with genetic polymorphisms, gene expression, and phenotypic variation in natural crop populations remain largely unknown. Here, we surveyed high-quality methylomes, transcriptomes, and genomes obtained from the 20-days-post-anthesis (DPA) cotton fibers of 207 accessions and extended the classical framework of population genetics to epigenetics. Over 287 million single methylation polymorphisms (SMPs) were identified, 100 times more than the number of single nucleotide polymorphisms (SNPs). These SMPs were significantly enriched in intragenic regions while depleted in transposable elements. Association analysis further identified a total of 5,426,782 cis-methylation quantitative trait loci (cis-meQTLs), 5078 cis-expression quantitative trait methylation (cis-eQTMs), and 9157 expression quantitative trait loci (eQTLs). Notably, 36.39% of cis-eQTM genes were not associated with genetic variation, indicating that a large number of SMPs associated with gene expression variation are independent of SNPs. In addition, out of the 1715 epigenetic loci associated with yield and fiber quality traits, only 36 (2.10%) were shared with genome-wide association study (GWAS) loci. The construction of multi-omics regulatory networks revealed 43 cis-eQTM genes potentially involved in fiber development, which cannot be identified by GWAS alone. Among these genes, the role of one encoding CBL-interacting protein kinase 10 in fiber length regulation was successfully validated through gene editing. Taken together, our findings prove that DNA methylation data can serve as an additional resource for breeding purposes and can offer opportunities to enhance and expedite the crop improvement process.
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