Sugarcane’s complicated genetics have made it the last major crop without a complete and highly accurate genome, even though it is one of the most harvested crops on the planet.
An international team of researchers, including several from the Community Science Program at the Joint Genome Institute (JGI) and the Joint BioEnergy Institute (JBEI), have recently published the complete genome in the journal Nature. The genome is available through the JGI’s plant portal, Phytozome.
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. 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. Researchers 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.
Having a complete “reference genome” makes it easier to study sugarcane, enabling researchers to compare its genes and pathways with those in other well-studied crops such as sorghum or other biofuel crops of interest, like switchgrass and miscanthus. By comparing this reference to other crops, it becomes easier to understand how each gene influences a trait of interest, such as which genes are highly expressed during sugar production, or which genes are important for disease resistance. This study found that the genes responsible for resistance to brown rust, a fungal pathogen that previously caused millions of dollars of damage to sugarcane crops, are found in only one location in the genome.
Improving future varieties of sugarcane has potential applications in both agriculture and bioenergy. Enhancing how sugarcane produces sugar could increase the yield farmers get from their crops, providing more sugar from the same amount of growing space. Sugarcane is an important feedstock, or starting material, for producing biofuels, particularly ethanol, and other bioproducts. The residues that remain after the pressing of sugarcane, referred to as bagasse, are an important type of agricultural residue that can also be broken down and converted into biofuels and bioproducts.
