Pan-genomics of polyploid crops: from complexity to breeding

Improving crop productivity is essential to ensure global food security in the context of climate change and an increasing global population. Over the past few decades, sequencing has significantly expanded our ability to explore complex genomes. However, the inherent genomic complexity of many plant species, characterized by large genome sizes, high repetitiveness and polyploidy, continues to pose significant challenges for genome assembly and the accurate detection of genetic variation. In particular, structural variations, which are key drivers of trait diversity and genome evolution, are often underrepresented in analyses based on a single linear reference genome due to reference bias. To overcome these constraints, the concept of the pan-genome has emerged. By capturing both core and variable sequences/genes across individuals of a species or genus, pan-genomes offer a more comprehensive representation of genomic diversity. This approach has been successfully implemented in many major crops, including complex polyploids like wheat, peanut, cotton, oat and mustard, and is increasingly contributing to ecological and evolutionary research. This review provides an overview of the development of pan-genome approaches and their application in understanding plant genome complexity, with a focus on trait discovery and modern breeding strategies. It also addresses current challenges and outlines future directions for leveraging pan-genomic resources in crop improvement and biodiversity conservation. In addition, the emerging need for polyploid-aware pan-genome frameworks that explicitly resolve subgenomes, homoeolog dosage, and homoeologous exchange is emphasized to enable breeder-ready applications.