ArticlePlant physiology2021
An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment.
Article in Plant physiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 28 citations in OpenAlex.
- Flooding stress resilience and crop improvement.Plant cell reports · 2026Review
- Epigenetic control of seed development and dormancy in cereals.Plant signaling & behavior · 2025Review
- Loss of function of chromatin remodeler OsCLSY4 leads to RdDM-mediated mis-expression of endosperm-specific genes affecting grain qualities.PLoS genetics · 2025Article
- Understanding anaerobic germination in direct-seeded rice: a genomic mapping approach.BMC plant biology · 2024Article
- Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler.Nature communications · 2024Article
- Natural polymorphisms in ZMET2 encoding a DNA methyltransferase modulate the number of husk layers in maize.Plant physiology · 2024Article
- Genetic factors underlying anaerobic germination in rice: Genome-wide association study and transcriptomic analysis.The plant genome · 2024Article
- DNA methylation: an emerging paradigm of gene regulation under drought stress in plants.Molecular biology reports · 2024Review
- To live or let die? Epigenetic adaptations to climate change-a review.Environmental epigenetics · 2024Review
- A bird's-eye view: exploration of the flavin-containing monooxygenase superfamily in common wheat.Frontiers in plant science · 2024Article
- Moving targets: Mechanisms regulating siRNA production and DNA methylation during plant development.Current opinion in plant biology · 2023Review
- The Impact of Carbohydrate Management on Coleoptile Elongation in Anaerobically Germinating Seeds of Rice (Plants (Basel, Switzerland) · 2023Article
- Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province.Scientific reports · 2022Article
- Flavonoids Modulate the Accumulation of Toxins FromFrontiers in plant science · 2021Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex traits, we quantified percentage anaerobic germination (AG) in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice genotypes and performed genome-wide association studies (GWAS) using 693,502 single nucleotide polymorphisms. This was followed by post-GWAS analysis with a generalized SNP-to-gene set analysis, meta-analysis, and network analysis. We determined that percentage AG is intermediate-to-high among indica subpopulations, and AG is a polygenic trait associated with transcription factors linked to ethylene responses or genes involved in metabolic processes that are known to be associated with AG. Our post-GWAS analysis identified several genes involved in a wide variety of metabolic processes. We subsequently performed functional analysis focused on the small RNA and methylation pathways. We selected CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation (RdDm) pathway, for further analyses under AG and found several lines of evidence that CLSY1 influences AG. We propose that the RdDm pathway plays a role in rice responses to water status during germination and seedling establishment developmental stages.
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