【摘要】 全球人口的持续增长和气候变化给粮食供给带来了严峻挑战，粮食安全问题因此愈发突出。为了满足不断增长的人口对粮食的需求，提升作物产量并增强其对环境的适应性已成为农业领域的重要目标。在此背景下，基因组学被视为加速作物育种进程的重要手段。通过深入挖掘和利用作物优异功能基因信息，不仅能有效提高作物产量，还能增强其抗逆性和适应性，为保障全球粮食安全和实现农业可持续发展提供有力支撑。然而，传统的单一参考基因组往往无法全面反映作物在驯化和改良过程中所累积的所有基因组变异，导致研究者对功能基因及其调控网络的认识存在局限。随着高通量测序技术的不断发展，基因组学研究开始迈入泛基因组学时代。通过整合多个高质量基因组，构建涵盖物种基因序列全集的泛基因组，能精准地鉴定包括单核苷酸多态性（SNPs）及结构变异（SVs）在内的多种遗传变异，全面地捕获物种在不同品种、亚种及野生亲缘种中广泛存在的遗传多样性，为系统挖掘优异功能基因提供更完善的分析框架。通过结合多组学数据（如转录组、蛋白质组、表观组等），泛基因组研究能在更精细的水平上挖掘优异功能基因，进而为分子育种提供更具针对性和准确性的基因靶标。同时，借助CRISPR-Cas9等基因编辑技术，可进一步对重要基因位点进行定向改造，剔除影响作物生长的不利性状或强化其对环境胁迫的抗性，从而为培育兼具高产、优质和抗逆特性的新一代作物品种奠定坚实基础。本文阐述了目前泛基因组的主要构建方法及展现形式的研究进展，并系统地梳理了作物泛基因组的发展及其在育种改良中的应用，深入探讨了泛基因组在未来作物育种中面临的挑战，对如何更好地应用泛基因组进行作物遗传改良进行了讨论，为未来精准分子育种改良提供了新的思路和策略。更多还原

【Abstract】 The global population continues to rise and climate change imposes severe challenges on food supply, the issue of food security has become increasingly prominent. To meet the growing demand for food, enhancing crop yield and improving environmental adaptability have become critical goals in agriculture. Under this situation, genomics is regarded as an essential method for accelerating crop breeding, as it enables the in-depth exploration and utilization of superior functional genes to not only boost crop productivity but also strengthen stress tolerance and adaptability, thereby providing robust support for ensuring global food security and achieving sustainable agricultural development. Nonetheless, the traditional single-reference genome often fails to capture the entire spectrum of genomic variations accumulated during crop domestication and improvement, which constrains our understanding of functional genes and their regulatory networks. With the continual advancement of high-throughput sequencing technologies, genomics research has now entered the pangenomics era. By integrating multiple high-quality genomes into a comprehensive catalog of genomic content, researchers can precisely identify a variety of genetic variations, including single nucleotide polymorphisms(SNPs) and structural variations(SVs), thereby capturing the extensive genetic diversity present across different cultivars, subspecies, and wild relatives. Pangenomics framework greatly facilitates the exploration of superior functional genes. Moreover, by combining pangenomic data with other multi-omics datasets(e.g., transcriptomics, proteomics, and epigenomics), researchers can accurately identify superior functional genes, enabling the provision of more targeted and accurate genetic loci for molecular breeding. With emerging gene-editing tools such as CRISPR-Cas9, researchers can further modify essential genetic loci in a directed manner to remove undesirable traits or reinforce resistance to environmental stressors. This will lay a foundation for cultivating the next generation of crops that exhibit higher yield, improved quality, and enhanced resilience. This review summarizes recent developments in major pangenome construction methods and formats, and systematically reviews the progress made in crop pangenomes as well as their applications in crop breeding improvement. It also discusses the challenges pangenomics faces in future crop breeding, offering insights into leveraging pangenome resources for crop genetic improvement, and ultimately provides new perspectives and strategies for future molecular breeding.更多还原