A Complex Confection Decoded: Sugarcane Reference Genome

Sugarcane was the last major crop without a reference quality genome and now crop researchers can work toward advancing sugarcane biotechnology.

The Science

Considered the world’s most harvested crop by tonnage, sugarcane accounts for 80% of global sugar production. A reference genome for the sugarcane cultivar R570 has been published in Nature by an international consortium. With the genetic code of sugarcane, researchers were able to map the location of genes that provide resistance to the brown rust disease that can devastate a crop.

The Impact

In providing a reference sugarcane genome, the JGI provides foundational genetic information that crop breeders can use to improve sugarcane varieties and advance a sustainable bioeconomy. Researchers and farmers could improve future sugarcane varieties so that they can adapt to future environmental conditions. Additionally, insights from the genome could help scale sustainable sugarcane conversion technologies for biofuels and other bioproducts. Finally, understanding how brown rust disease resistance works in sugarcane could help protect other crops facing similar pathogens.

Summary

Many plants, sugarcane included, are polyploid and have multiple copies of chromosomes. Sugarcane accounts for 80% of sugar production worldwide, but has one of the most complex genetic blueprints. Assembling a genome has been compared to putting together a puzzle without necessarily knowing the final image. In contrast, assembling the sugarcane genome was more challenging and took more than a decade because there were pieces from multiple boxes, including some duplicates, to sort through in order to form a single cohesive image.

An approximately nine billion base (Gigabase or Gb) reference genome for the sugarcane cultivar R570 has been generated and reported in the journal Nature. The work led by researchers at Australia’s national science agency CSIRO, the French Agricultural Research Centre for International Development (CIRAD), and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), with assistance from partners at the HudsonAlpha Institute for Biotechnology and the Arizona Genomics Institute.

The work was partly enabled by the JGI’s Community Science Program; in 2018, a monoploid reference sequence of sugarcane was published as a step forward in this effort. Sequencing and assembling the genome required a custom pipeline and techniques. High quality primary assembly not only includes a full representation of the diversity present in R570 but shows the genomic effects of breeding practices that transformed sugarcane into production factories for sugar and biomass. Additionally, the team was able to identify a major locus (Bru1) that durable resistance to brown rust disease caused by the fungus, Puccinia melanocephala. This plant pathogen used to cause sugarcane crop losses of up to 50% of the expected yields.

The reference genome of R570 is available on the JGI plant data portal, Phytozome.