ArticleGenome biology2024
Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- The Landscape of Long Non-Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The Dual Role of Lignin in Fruit Trees: Unraveling Regulatory Networks from Stress Resilience to Quality Control.Plants (Basel, Switzerland) · 2026Review
- Phased T2T genome of a tetraploid grapevine reveals segmental allopolyploid origin and allele-specific alternative splicing during fruit development.Plant physiology · 2026Article
- Dynamic chromatin regulatory programs of sucrose and citric acid metabolism during fruit ripening in Citrus.The Plant cell · 2026Article
- Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution.iScience · 2026Review
- Cis-regulatory elements in CAMTA-mediated stress signalling: mechanisms and prospects for CRISPR-based crop improvement.Frontiers in plant science · 2026Review
- Nanopore sequencing and multiomics reveal predictable non-coding RNA activation in DNA methylation deficient Arabidopsis thaliana.Communications biology · 2025Article
- Integrated genomic and DNA methylome analyses reveal epigenetic regulation of stevia glycoside biosynthesis inHorticulture research · 2025Article
- Genomic insights into deleterious mutations and their impact on agronomic traits during pear domestication.Horticulture research · 2025Article
- An Antagonism Between Ethylene Signaling and DNA Methylation Orchestrates the Progression of Leaf Senescence in Non-heading Chinese Cabbage.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- Haplotype-resolved, gap-free genome assemblies provide insights into the divergence between Asian and European pears.Nature genetics · 2025Article
- Regulatory effects of gibberellin and cytokinin on citrus peel cell wall metabolism.BMC plant biology · 2025Article
- Gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH zinc finger protein as a key regulator of stone cell formation in pear fruit.Plant communications · 2025Article
- DNA Methylation Is Crucial for 1-Methylcyclopropene Delaying Postharvest Ripening and Senescence of Tomato Fruit.International journal of molecular sciences · 2024Article
- Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change.Plant communications · 2024Review
- Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement.Genome biology · 2024Article
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Authors and funding
12 authors.
Funding
Abstract
backgroundDNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown.
resultsHere, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening.
conclusionsOur study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.
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