Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sug

The complex polyploid genome architecture of sugarcane

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2024-04-04 16:00:11

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.

Sugarcane domestication began approximately 10,000 years ago with the first ‘sweet’ cultivars (Saccharum officinarum) derived from Saccharum robustum3. Modern day cultivars, however, are all derived from a few interspecific hybridizations performed by breeders a century ago between ‘sweet’ octoploid S. officinarum and the ‘wild’ polyploid Saccharum spontaneum. Sugarcane interspecific hybridization has provided major breakthroughs in disease resistance and adaptation to otherwise stressful environmental conditions. However, early generation hybrids also had much lower sugar yield, owing to the large wild genomic contribution. To re-establish high sugar yield, breeders backcrossed hybrids to S. officinarum4. This process was accelerated by the unreduced (‘2n’) transmission of S. officinarum chromosomes in the first two generations so backcrossed (BC1) cultivars contained 11% more domesticated sequence than would be expected by typical (n + n) inheritance patterns.

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