The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.

中文翻译：

---

基于水稻模型理解表观基因组学。

本文的目的是全面概述近年来水稻表观基因组学的研究，包括 DNA 甲基化、组蛋白修饰、非编码 RNA 和三维基因组学。讨论了水稻未来研究的挑战和前景。水稻作为表观基因组研究的模型植物，在目前对植物表观遗传学的理解方面取得了很大进展。水稻表观基因组分析和三维染色质结构研究的最新结果揭示了水稻植物发育和适应环境变化过程中基因调控的特定特征和意义。水稻染色质调节功能的结果揭示了植物表观基因组信息的建立、识别和重置机制。几个与重要农艺性状相关的水稻表观等位基因的克隆突出了表观基因组变异在水稻植物生长、适应性和产量中的重要性。在这篇综述中，我们总结和分析了水稻表观基因组学的最新进展，并讨论了该领域未来研究的挑战和方向。