From sugarcane to polyploid crops: Graph pangenomes usher in a new era of complex-genome breeding

From sugarcane to polyploid crops: Graph pangenomes usher in a new era of complexgenome breedingPolyploidy is a major driver of plant evolution and a defining feature of many domesticated crops.Comparative cytogenetic and phylogenomic surveys indicate that roughly one-third of extant vascular plant species are polyploids, and recurrent polyploidization has contributed to the domestication and improvement of wheat, cotton, potato, sugarcane, and numerous other staples.However, the multiple, often heterogeneous chromosome complements in polyploids make their genomes substantially more difficult to analyze than those of diploids, hindering efforts to resolve homoeologous chromosomes, quantify gene dosage, and map agronomic traits.Sugarcane represents an extreme case: modern Saccharum hybrids originated from interspecific crosses between Saccharum officinarum and Saccharum spontaneum, followed by extensive and uneven polyploidization and aneuploidy, yielding one of the most structurally complex genomes among major crops (Healey et al., 2024).Conventional linear reference genomes, which perform well in diploids, collapse haplotype diversity, obscure structural and dosage variation, and are poorly suited to such mixed-ploidy architectures.This limitation has contributed to the lag in both basic genomics and breeding applications in highly polyploid crops.