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 worldwide. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome. Now, an international team of researchers has generated a polyploid reference genome for R570, a typical modern sugarcane cultivar.
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Saccharum officinarum. Image credit: Ton Rulkens / CC BY-SA 2.0 Deed.
Sugarcane domestication began approximately 10,000 years ago with the first ‘sweet’ cultivars (Saccharum officinarum) derived from Saccharum robustum.
Modern day cultivars, however, are all derived from a few interspecific hybridizations performed by breeders a century ago between the ‘sweet’ Saccharum officinarum and the ‘wild’ Saccharum spontaneum.
Sugarcane 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.
The complexity of hybrid sugarcane genomes and pedigrees is exemplified by the development of the R570 cultivar, which was generated by breeders on Reunion Island in 1980.
“Sugarcane’s genome is so complex both because it is large and because it contains more copies of chromosomes than a typical plant, a feature called polyploidy,” said Dr. Jeremy Schmutz, a researcher at the HudsonAlpha Institute for Biotechnology, and his colleagues.
“Sugarcane has about 10 billion base pairs, the building blocks of DNA; for comparison, the human genome has about 3 billion.”
“Many sections of sugarcane’s DNA are identical both within and across different chromosomes. That makes it a challenge to correctly reassemble all the small segments of DNA while reconstructing the full genetic blueprint.”
“We solved the puzzle by combining multiple genetic sequencing techniques, including a newly developed method known as PacBio HiFi sequencing that can accurately determine the sequence of longer sections of DNA.”
“This was the most complicated genome sequence we’ve yet completed,” Dr. Schmutz added.
“It shows how far we’ve come. This is the kind of thing that 10 years ago people thought was impossible. We’re able to accomplish goals now that we just didn’t think were possible to do in plant genomics.”
“The breakthrough addresses the critical challenge of stagnating sugar yields by tapping into the previously inaccessible genetic information in the sugarcane genome,” said CSIRO researcher Dr. Karen Aitken.
“This is a major step forward for sugarcane research and will improve our understanding of complex traits like yield and adaption to diverse environmental conditions as well as disease resistance.”
“We are working to understand how specific genes in plants relate to the quality of the biomass we get downstream, which we can then turn into biofuels and bioproducts,” said Dr. Blake Simmons, a researcher at the Joint BioEnergy Institute.
“With a better understanding of sugarcane genetics, we can better understand and control the plant genotypes needed to produce the sugars and bagasse-derived intermediates we need for sustainable sugarcane conversion technologies at a scale relevant to the bioeconomy.”
The results appear in the journal Nature.
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A.L. Healey et al. The complex polyploid genome architecture of sugarcane. Nature, published online March 27, 2024; doi: 10.1038/s41586-024-07231-4
