中国农业科学2025，Vol.58Issue(11)：2045-2061,17.DOI:10.3864/j.issn.0578-1752.2025.11.001
作物泛基因组研究进展与展望
Research Progress and Prospects on Crop Pan-Genomics
摘要
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.关键词
分子育种/泛基因组/结构变异/新质生产力/遗传多样性Key words
molecular breeding/pangenome/structural variations/new productivity/genetic diversity引用本文复制引用
王晖,丁保朋,李彧贤,任泉如,周海,赵均良,胡海飞..作物泛基因组研究进展与展望[J].中国农业科学,2025,58(11):2045-2061,17.基金项目
国家自然科学基金青年基金(32400512 和 32102364)、广东省自然科学基金(2024A1515011981)、广东省农业科学院青年骨干人才计划(R2023YJ-QC001)、山西省高等学校青年学术带头人(2024Q031)、广东省水稻科学技术重点实验室(2023B1212060042) （32400512 和 32102364）
