The eukaryotic genome has a hierarchical three-dimensional (3D) organization with functional implications for DNA replication, DNA repair, and transcriptional regulation. Over the past decade, scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation capturing technologies such as Hi-C, ChIA-PET, and HiChIP. Here, we systematically review current understanding of chromatin organization in plants at multiple scales. We also discuss the emerging opinions and concepts in 3D genome research, focusing on state-of-the-art 3D genome techniques, RNA–chromatin interactions, liquid–liquid phase separation, and dynamic chromatin alterations. We propose the application of single-cell/single-molecule multi-omics, multiway (DNA–DNA, DNA–RNA, and RNA–RNA interactions) chromatin conformation capturing methods, and proximity ligation-independent 3D genome-mapping technologies to explore chromatin organization structure and function in plants. Such methods could reveal the spatial interactions between trait-related SNPs and their target genes at various spatiotemporal resolutions, and elucidate the molecular mechanisms of the interactions among DNA elements, RNA molecules, and protein factors during the formation of key traits in plants.

真核基因组具有分级的三维（3D）组织，对DNA复制，DNA修复和转录调控具有功能意义。在过去的十年中，科学家们努力使用高通量染色质构象捕获技术（例如Hi-C，ChIA-PET和HiChIP）阐明植物基因组结构的空间特征和功能。在这里，我们系统地复习了当前对多种规模植物中染色质组织的了解。我们还将讨论3D基因组研究中出现的新观点和新概念，重点是最新的3D基因组技术，RNA-染色质相互作用，液相-液相分离和动态染色质改变。我们建议应用单细胞/单分子多组学，多途径（DNA–DNA，DNA–RNA，和RNA–RNA相互作用）染色质构象捕获方法，以及与邻近连接无关的3D基因组映射技术，以探索植物中染色质的组织结构和功能。这样的方法可以揭示各种时空分辨率下性状相关SNP与靶基因之间的空间相互作用，并阐明植物关键性状形成过程中DNA元素，RNA分子和蛋白质因子之间相互作用的分子机制。