ArticleScience China. Life sciences2023
Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity.
Article in Science China. Life sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Genome-wide association studies in horticultural crops: decoding genetic diversity for precision breeding.Horticulture research · 2026Article
- Stem microanatomical phenomic uncovers a potential role for ZmLSM2 in regulating maize stem bending strength.Journal of integrative plant biology · 2026Article
- Metagenomic analysis of wolfberry branch substrates under tomato cultivation without additional nitrogen fertilization.BMC plant biology · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Unveiling Plant Metabolic Diversity: Integrating Metabolomics with Multi-Omics Approaches for Crop Improvement.Plants (Basel, Switzerland) · 2026Review
- Domestication of Tartary Buckwheat Shaped a Regulatory Module for Seedling Salt Tolerance by Targeting the Magnesium Transporter Gene FtMGT2.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Tomato and its relatives are breaking the genomics barriers.Journal of experimental botany · 2025Review
- Genome assembly and DNA methylation variation in an epimutant population of hybrid poplar clone NL895.Plant physiology · 2025Article
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- Epigenetics in the modern era of crop improvements.Science China. Life sciences · 2025Review
- Review
- Potato steroidal glycoalkaloids: properties, biosynthesis, regulation and genetic manipulation.Molecular horticulture · 2024Review
- Metabolic and Transcriptional Analysis Reveals Flavonoid Involvement in the Drought Stress Response of Mulberry Leaves.International journal of molecular sciences · 2024Article
- Genetic and epigenetic signatures for improved breeding of cultivated blueberry.Horticulture research · 2024Article
- Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication.BMC plant biology · 2024Article
- Gene identification, expression analysis, and molecular docking of SAT and OASTL in the metabolic pathway of selenium in Cardamine hupingshanensis.Plant cell reports · 2024Article
- Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement.Genome biology · 2024Article
- The conservation of allelic DNA methylation and its relationship with imprinting in maize.Journal of experimental botany · 2024Article
- Proteomic and metabolomic insights into the impact of topping treatment on cigar tobacco.Frontiers in plant science · 2024Article
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13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is an important epigenetic marker, yet its diversity and consequences in tomato breeding at the population level are largely unknown. We performed whole-genome bisulfite sequencing (WGBS), RNA sequencing, and metabolic profiling on a population comprising wild tomatoes, landraces, and cultivars. A total of 8,375 differentially methylated regions (DMRs) were identified, with methylation levels progressively decreasing from domestication to improvement. We found that over 20% of DMRs overlapped with selective sweeps. Moreover, more than 80% of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms (SNPs), and DMRs had strong linkages with adjacent SNPs. We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs. We detected 971 and 711 large-effect loci via SNP and DMR markers, respectively. Combined with multi-omics, we identified 13 candidate genes and updated the polyphenol biosynthetic pathway. Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity. Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.
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