Recent advances in the genomics of sugarcane (Saccharum)

Sugarcane (Saccharum spp.) is a globally important C₄ crop that contributes substantially to sugar production and renewable bioenergy systems. Modern sugarcane cultivars were derived from interspecific hybridization between high-sucrose S. officinarum and stress-resilient wild S. spontaneum, followed by extensive backcrossing and selection. Such breeding trajectory has generated an extremely complex polyploid genome marked by high ploidy, pervasive aneuploidy, mosaic subgenome composition, and a reticulate evolution history. For decades, this complexity has resulted in persistent taxonomic ambiguities, constrained genomic analyses, complicated genetic dissection of agronomic traits, and limited breeding efficiency. The rapid development of third-generation long-read sequencing, haplotype-resolved assembly, and polyploid-aware computational approaches has fundamentally revolutionized sugarcane research. This review synthesizes recent progress in Saccharum taxonomy, polyploid genome architecture and evolution, high-quality genomic resource development, germplasm exploration, and genome-informed breeding strategies. We propose an integrated framework connecting taxonomic refinement, genome biology, and breeding applications. Critical challenges are elaborated, including the taxonomy-genomics disconnect, diploid-centric analytical bias, insufficient haplotype resolution, the lack of polyploid-aware genetic models, and underutilization of wild germplasm. Finally, we outline future priorities toward predictive and design-oriented sugarcane improvement by addressing unresolved core questions. This review provides a comprehensive and forward-looking perspective for accelerating genetic improvement in sugarcane and other highly complex polyploid crops.