Sugarcane (Saccharum spp.) is a vital sugar and bioenergy crop with an exceptionally complex polyploid genome (10–12 sets of chromosomes). This complexity resulted from nobilization—a historical breeding process involving interspecific hybridization and repeated backcrossing1. However, the extreme ploidy has long impeded efforts to elucidate the genetic basis of its considerable sucrose-storing capacity. Here we present a fully phased genome assembly of the foundational cultivar POJ2878, achieved using a Pore-C-based assembly algorithm. This assembly resolved 118 chromosomes, revealing extensive subgenome recombination and non-homologous chromosomal rearrangements. Using identity-by-descent and allele-specific expression profiling, we identified breeder-favoured haplotypes, including a SUS2 haplotype with enhanced sucrose content. Resequencing of 981 Saccharum accessions traced POJ2878’s pervasive contribution to modern cultivars and identified key domestication and improvement sweeps. Genes under selection include CBL1 for cold tolerance, TIP1 for cell size regulation and TB1 for tillering control. A genome-wide association study tailored for polyploid genomes resolved loci associated with parenchyma cell size and sucrose storage capacity, including the functionally validated sucrose transporter Saccharum hybrid SUT2. These findings clarify the genetic architecture underlying sugarcane’s biomass productivity and sugar yield, offering a genomic foundation for accelerating improvement in sugarcane and other polyploid crops critical for global food and bioenergy security.
