Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

ARC Centre of Excellence for Plant Success in Nature and Agriculture University of Queensland Brisbane Queensland Australia

Arizona Genomics Institute University of Arizona Tucson AZ USA

CIRAD UMR AGAP Institut Montpellier France

Corteva Agriscience Johnston IA USA

CSIRO Agriculture and Food Queensland Bioscience Precinct St Lucia Queensland Australia

CSIRO Agriculture and Food Urrbrae South Australia Australia

Department of Energy Joint Genome Institute Lawrence Berkeley National Laboratory Berkeley CA USA

ERCANE Sainte Clotilde La Réunion France

Genome Sequencing Center HudsonAlpha Institute for Biotechnology Huntsville AL USA

Institute of Experimental Botany of the Czech Academy of Sciences Centre of Plant Structural and Functional Genomics Olomouc Czech Republic

Joint BioEnergy Institute Lawrence Berkeley National Laboratory Emeryville CA USA

Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Queensland Australia

Sugar Research Australia Te Kowai Queensland Australia

UMR AGAP Institut Univ Montpellier CIRAD INRAE Institut Agro Montpellier France

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