Sugarcane’s genome is finally mapped and ready for new breeding era

Modern hybrid sugarcane, one of the most harvested crops on the planet, has finally had its genome mapped out by a team of dedicated scientists.

This breakthrough marks a significant milestone in the field of plant genomics, as sugarcane was the last major crop without a complete and highly accurate genome due to its complex genetic blueprint.

Unraveling the sugarcane genome complexity

The research, conducted at the U.S. Department of Energy Joint Genome Institute (JGI), was led by Jeremy Schmutz. He is the Plant Program lead at the JGI and faculty investigator at the HudsonAlpha Institute for Biotechnology.

“This was the most complicated genome sequence we’ve yet completed. It shows how far we’ve come,” Schmutz explained. “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.”

Sugarcane’s genome is incredibly complex, with about 10 billion base pairs (the building blocks of DNA) compared to the human genome’s 3 billion.

The complexity arises from sugarcane’s polyploidy, meaning it contains more copies of chromosomes than a typical plant.

Many sections of sugarcane’s DNA are identical both within and across different chromosomes, making it a challenge to correctly reassemble all the small segments of DNA while reconstructing the full genetic blueprint.

Innovative gene sequencing techniques

To solve this puzzle, researchers combined 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 innovative approach allowed them to successfully map out sugarcane’s genetic code and verify the specific location that provides resistance to the impactful brown rust disease, which can devastate sugar crops if left unchecked.

“When we sequenced the genome, we were able to fill a gap in the genetic sequence around brown rust disease. There are hundreds of thousands of genes in the sugarcane genome, but it’s only two genes, working together, that protect the plant from this pathogen,” said Adam Healey, first author of the paper and a researcher at HudsonAlpha.

“Across plants, there are only a handful of instances that we know of where protection works in a similar way. Better understanding of how this disease resistance works in sugarcane could help protect other crops facing similar pathogens down the road,” Healey explained.

Unlocking the potential for improved sugarcane varieties

The study focused on a cultivar of sugarcane known as R570, which has been used for decades around the world as the model to understand sugarcane genetics.

Like all modern sugarcane cultivars, R570 is a hybrid made by crossing the domesticated species of sugarcane (which excelled in sugar production) and a wild species (which carried the genes for disease resistance).

“Knowing R570’s complete genetic picture will let researchers trace which genes descended from which parent, enabling breeders to more easily identify the genes that control the traits of interest for improved production,” said Angélique D’Hont, last author of the paper and a sugarcane researcher at the French Agricultural Research Center for International Development (CIRAD).

Sugarcane genome implications for agriculture and bioenergy

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 also an important feedstock for producing biofuels, particularly ethanol, and other bioproducts.

The residues that remain after the pressing of sugarcane, referred to as bagasse, can be broken down and converted into biofuels and bioproducts.

“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 Blake Simmons, Chief Science and Technology Officer for the Joint BioEnergy Institute, a DOE Bioenergy Research Center led by Berkeley Lab.

“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,” Simmons concluded.

What the future holds for this sweet success story

In summary, the successful mapping of sugarcane’s complex genome marks a significant milestone in plant genomics and opens up exciting possibilities for the future.

By combining innovative sequencing techniques, researchers have unlocked the genetic secrets of this important crop. This has, in turn, cleared the path for breeding improved varieties that can enhance sugar production, increase disease resistance, and contribute to sustainable bioenergy solutions.

As scientists continue to explore the intricacies of sugarcane’s genetic blueprint, they will undoubtedly uncover new insights that will shape the future of agriculture and bioenergy, ultimately leading to a more sustainable and prosperous world.

The full study is published in the journal Nature, and the genome is available through the JGI’s plant portal, Phytozome

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