Graph pan-genome facilitates crop genetic improvement

<p indent="0mm">With breakthroughs in sequencing technology and genome assembly methods, the graph pan-genome has gradually become a core tool for analyzing crop genetic diversity and structural variations. The singularity of traditional linear reference genomes limits their ability to represent the extensive variations within species. In contrast, the graph pan-genome incorporates sequences from multiple genotypes into a single graph structure that captures both conserved regions and genetic variants. This paradigm enables a more comprehensive analysis of agronomic trait architecture, domestication and adaptation processes, and the genomic basis of heterosis. This article systematically reviews the application progress of the graph pan-genome in crop genetic improvement, including the exploration of the genetic basis of important traits, the analysis of domestication and adaptive evolution imprints, the investigation of genomic mechanisms underlying heterosis, and innovations in genomics-assisted breeding technologies. It delves into the technical challenges and performance evaluation bottlenecks in identifying structural variations in complex crop genomes, such as polyploids and genomes with high repeat sequences, and proposes future strategies, such as algorithm optimization, multi-omics integration, and the utilization of wild germplasm resources to advance precision breeding and innovation in germplasm resources.