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.

The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid ‘Yuluxiang’ pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm. Using the constructed pangenome, we identified 21224 gene PAVs (Presence-absence variation) and 1158812 SNPs (Single Nucleotide Polymorphism) in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, PAV-based analysis provides additional insights into the pear population structure. In addition, some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in ‘Xuehuali’ which is vital for pear quality. PsbMGH3.1 may play a role in the IAA pathway, contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene. This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.