Our era has witnessed tremendous technique advances and mechanically epigenetic improvement in plant epigenetics, mainly including histone post-translational modifications (PTMs) and DNA methylation, which have been characterized as playing vital roles in development processes and plant response to environmental factors. Recently, chemical modifications on RNAs like 5-methylcytosine (m⁵C) and N6-methyladenosine (m⁶A) have been revealed as a new layer of epigenetic marks to regulate gene translation efficiency in model plant Arabidopsis thaliana and with later discovery of horticultural species like tomato (Solanum lycopersicum) and poplar (Populus trichocarpa). In model plants, these epigenetic modifications on DNA, RNA, and histone tails largely trigger innumerable studies on how epigenetic mechanisms are involved in gene regulation and biological functions. As an emerging research field in horticultural plants, epigenetic modifications have bloomed in fruit development and ripening, grafting, and bud dormancy. In this Review, we have demonstrated recent advances of high-throughput sequencing methods, summarized epigenetic enzymatic systems to install, remove and recognize epigenetic marks, discussed essential roles of epigenetic regulation, and proposed how innovative computation techniques like machine learning and deep learning are set to understanding epigenetic regulation mechanisms in horticultural plants. We also raise future perspectives on how epigenetic modifications act as new additions for understanding their roles in gene expression that is required for development and environmental adaptation in horticultural plants.

我们这个时代见证了植物表观遗传学的巨大技术进步和机械表观遗传学改进，主要包括组蛋白翻译后修饰 (PTM) 和 DNA 甲基化，它们在发育过程和植物对环境因素的反应中起着至关重要的作用。最近，对 5-甲基胞嘧啶 (m ⁵ C) 和N6-甲基腺苷(m ⁶ A)等 RNA 的化学修饰已被揭示为新的表观遗传标记层，可调节模式植物拟南芥中的基因翻译效率，并且后来发现了园艺番茄（Solanum lycopersicum）和杨树（Populus trichocarpa）等物种）。在模型植物中，这些对 DNA、RNA 和组蛋白尾部的表观遗传修饰在很大程度上引发了对表观遗传机制如何参与基因调控和生物学功能的无数研究。作为园艺植物的新兴研究领域，表观遗传修饰在果实发育和成熟、嫁接、芽休眠等方面已经开花结果。在这篇综述中，我们展示了高通量测序方法的最新进展，总结了用于安装、去除和识别表观遗传标记的表观遗传酶系统，讨论了表观遗传调控的重要作用，并提出了如何设置机器学习和深度学习等创新计算技术。了解园艺植物的表观遗传调控机制。