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.

甘蔗是世界上产量最大的作物，它影响了全球历史、贸易和地缘政治，目前占全球食糖产量的 80% ¹。虽然传统的甘蔗育种方法已有效地培育出适应新环境和病原体的品种，但糖产量的提高最近已趋于稳定²。产量增长的停止可能是由于育种群体内的遗传多样性有限、育种周期长以及基因组的复杂性造成的，后者阻碍了育种者利用最近全基因组测序的爆炸式增长，而全基因组测序已经使许多其他作物受益。因此，现代甘蔗杂交种是最后剩下的没有参考质量基因组的主要作物。在这里，我们通过为 R570 生成多倍体参考基因组，向推进甘蔗生物技术迈出了重要一步，R570 是一种典型的现代品种，源自驯化物种 ( Saccharum officinarum ) 和野生物种 ( Saccharum spontaneum ) 之间的种间杂交。与 R570 现有的单一单倍型（“单倍体”）表示形式相比，我们的 87 亿个碱基组装体包含跨该多倍体基因组中约 12 个染色体拷贝的独特 DNA 序列的完整表示。利用这种高度连续的基因组组装，我们填补了 R570 物理遗传图谱中先前未大小的空白，以描述单拷贝Bru1褐锈病抗性基因座背后可能的因果基因。这种多倍体基因组组装以及生物技术的基因组结构和分子靶标的细粒度描述将有助于加速分子和转基因育种以及甘蔗对未来环境条件的适应。