【摘要】 苹果（Malus domestica）是全球种植最广泛的温带落叶果树之一。因其为多年生乔木、遗传背景复杂，传统育种方法效率低、遗传改良周期长。近年来，苹果组学研究取得了显著进展，逐步实现从单一参考基因组到图形泛基因组的跃升，系统揭示了苹果属演化轨迹及重要性状形成机制，推动了复杂结构变异与功能区域的深度解析；表观组、代谢组与蛋白质组等多维数据的协同应用，支撑了果实品质、矮化和抗逆等性状的精准定位。在此基础上，分子标记开发、基因组选择与育种芯片加快了优异种质的早期筛选；CRISPR/Cas等基因编辑技术，则推动了功能验证与定向改良进程。本研究系统梳理了苹果组学研究的最新进展，重点聚焦于参考基因组升级、多组学数据集成、复杂性状解析及其在分子设计育种中的实践路径。同时，分析了当前在数据整合、功能识别、表型测量与基因编辑体系等方面存在的关键挑战，并展望了分子设计育种体系突破方向，为苹果种质创新与现代育种提供理论支撑与技术框架。更多还原

【Abstract】 Apple(Malus domestica) is one of the most widely cultivated temperate deciduous fruit trees worldwide. However, as a perennial woody plant with a highly heterozygous and complex genetic background, traditional breeding approaches are constrained by low efficiency and long breeding cycles. In recent years, significant progress has been made in apple omics research, with a gradual transition from a single reference genome to a graph-based pan-genome. This has systematically revealed the evolutionary trajectory of the Malus genus and the genetic basis of important traits, while facilitating in-depth analysis of structural variations and functional genomic regions. The integrative application of epigenomics, metabolomics, and proteomics has further enhanced the precise dissection of key traits such as fruit quality, dwarfing, and stress resistance. On this basis, the development of molecular markers, genomic selection strategies, and trait-specific breeding chips has accelerated early-stage identification of elite germplasm. Meanwhile, gene-editing technologies such as CRISPR/Cas have greatly advanced functional validation and targeted trait improvement. This review provides a comprehensive summary of recent progress in apple multi-omics research, with a focus on reference genome upgrading, integration of multi-omics data, dissection of complex trait, and their application in molecular design breeding. Moreover, it analyzes current technical bottlenecks,such as data integration, functional identification, phenotypic measurement, genome editing system, and looks forward to the breakthrough directions of molecular design breeding systems, providing a theoretical basis and technical framework for apple germplasm innovation and modern breeding.更多还原