ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Genetics, Epigenetics and Chromosome Biology
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1707950
This article is part of the Research TopicRegulatory Layers Shaping Plant Adaptation: Epigenetics, Non-Coding RNAs and BeyondView all articles
Genome-wide DNA methylation dynamics at 'heading' stage of panicle and flag leaf in contrasting rice cultivars under field-drought condition
Provisionally accepted
- 1University of Delhi Department of Plant Molecular Biology, New Delhi, India
- 2National Institute of Plant Genome Research, New Delhi, India
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Drought stress induces widespread genome-wide alterations in DNA methylation of rice. This study explores the variations in the methylome patterns in the panicle and flag leaf tissue of IR64 (drought-sensitive) and N22 (drought-tolerant) rice cultivars under field-drought conditions during the 'heading' stage of panicle development. The DNA methylation dynamics in adult tissue (flowering stage) was found to be clearly distinct from that of the seedling stage. Further, the contrasting rice genotypes also exhibited cultivar-specific and drought-induced dynamism in the methylation signatures. Notably, the two cultivars demonstrate inherent distinctions in sequence preferences of hyper-and hypo-methylation even prior to experiencing drought stress, and these preferences persist under the influence of the stress. Approximately 90% of the drought-induced differentially methylated region (DMR) are cultivar-specific, and about 70% of the cultivar differences (cultivar-DMR) under stress are unique compared to control condition. There is higher prevalence of hyper-methylated DMR that co-localized with differentially expressed genes in panicle. DMR of CHH sequence exhibit stronger negative correlation with expression compared to CpG and CHG sequence. Examination of differentially expressed genes with DMR highlights their functional relevance under drought stress, especially with DMR found in gene bodies and promoter regions. Notably, in panicle, methylation divergence of the two cultivars influences flowering regulation genes. Additionally, the findings also suggest a regulatory role for DNA methylation in drought induced response of miRNA genes, particularly in the panicle of N22 cultivars.
Keywords: Methylation, bisulphite sequencing, Oryza sativa, rice, drought, N22, IR64, stress
Received: 19 Sep 2025; Accepted: 20 Oct 2025.
Copyright: © 2025 Jajo, Kansal, Mathur and Raghuvanshi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Saurabh Raghuvanshi, saurabh@genomeindia.org
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