Brazilian scientists sequence “most complete” commercial sugarcane genome

05 Dec 2019 --- The most complete genome sequence of commercial sugarcane has been assembled by an international group of researchers led by Brazilian scientists, who mapped 373,869 genes, or 99.1 percent of the total genome. This is the result of almost 20 years of research supported by São Paulo Research Foundation (FAPESP) in Brazil. This latest progress is positioned to open up an array of possibilities, ranging from applications in biotechnology to genetic improvement and gene editing.

“It took us a long time, but we were very persistent. We were surprised to find so many genes. We had to develop new ways to identify and analyze the sequences to be able to capture the differences,” Glaucia Mendes Souza, Professor at the University of São Paulo’s Chemistry Institute and the study’s lead author tells FoodIngredientsFirst.

Sequencing the genome is a remarkable scientific endeavor, requiring substantial computing power to assemble the DNA fragments while keeping homologous chromosomes separate. In comparison with the human genome, sugarcane has more than 100 chromosomes, while humans have 46. Sugarcane also has 300,000 genes, with humans just at 23,000. While humans have two copies of each gene, sugar cane has more than ten copies, Souza explains. 

Sugarcane has evolved many different copies of each gene with almost identical sequences, but different promoters. Promoters are the gene regions that can tell when, where and how much each gene will be expressed.

This research can help improve sugarcane's disease resistance and increase its biomass yield for fuel or sugar production. “The human genome took ten years to sequence. With the sugarcane, we also took ten actually, if you consider that the first decade was a survey,” she recalls.

During the first ten years, the researchers sequenced a large number of expressed sequence tags, (EST) which were instrumental in assessing how complex the genome was. At this point in time, long-read sequencing technology was not available. However, as sequencing technologies became more accurate and cheaper, the researchers began testing alternatives and strategies. 

“That was the second decade. It was only in the last five years of the 20-year run that we actually had what we needed to develop the assembly,” Souza says. This research also presents the first time all the genes of the sugarcane plant, or the vast majority, have been seen. In previous projects by various research groups, the sequences had to be collapsed for lack of a proper assembly tool, providing only an approximation, she explains.

Future prospects
Having completed this genome sequencing project, the researchers are now aiming to alter carbon pathways to produce new compounds and bioproducts from sugar, lignin, fiber and other plant metabolites. “We can expect that the knowledge of the genome will allow us to route metabolic pathways to make more sugar, different molecules and more bioenergy. This has a direct impact on the food industry,” Souza explains. 

“Sugarcane is the largest world’s tonnage crop, the average yields are 80 tons per hectare. We calculate the theoretical potential yield to be 381 tons per hectare. There is a lot of potential to grow,” she adds. 

Sugarcane has great potential as a carbon capture machine, given it is grown in over 100 countries. It could be expanded to produce food, feed, energy while mitigating greenhouse gas (GHG) emissions in many regions of the globe.

Researchers in the field of gene sequencing and editing have been particularly busy. Recent research conducted by the University of Cambridge’s Sainsbury Laboratory (SLCU), UK, has shown that rider retrotransposons’ or “jumping genes,” native regeneration attributes have the potential to vary fruit and vegetable traits. 

At UK-based John Innes Centre (JIC), researchers developed an open-source reproducible Agrobacterium-mediated transformation system for the spring wheat cultivar “Fielder” (Triticum aestivum L.). These steps in this scientific field present numerous opportunities for breakthroughs in crop yield improvements. 

By Anni Schleicher